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Title: LITERATURE REVIEW ON THE USE OF NUCLEIC ACID-BASED LOGIC GATES FOR THE DETECTION OF HUMAN DISEASES.
Creator: Blanco Martinez, Enrique J, Kolpashchikov, Dmitry, University of Central Florida
Abstract / Description: Conventional methods for diagnosis of human disease are, at times, limited in different regards including time requirement, either experimental or data processing, sensitivity, and selectivity. It is then that a Point of Care Criteria, which considers the true utility and usefulness of the device, is employed to propose new diagnostic devices capable of overcoming the aforementioned shortcomings of conventional tools. Nucleic acid, characterized for its predictable base-pairing nature, is...
Show moreConventional methods for diagnosis of human disease are, at times, limited in different regards including time requirement, either experimental or data processing, sensitivity, and selectivity. It is then that a Point of Care Criteria, which considers the true utility and usefulness of the device, is employed to propose new diagnostic devices capable of overcoming the aforementioned shortcomings of conventional tools. Nucleic acid, characterized for its predictable base-pairing nature, is considered to be a highly-selective, yet greatly modifiable device. Its behavior is then described through Boolean Logic, where "true" or "false" outputs are mathematically described as "1" and "0", respectively. This mathematical approach is then referred to as Logic Gates, where outputs can be predicted based on satisfied environmental conditions. The mechanisms, capable of exhibiting Logic Gate behavior, are described.
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Date Issued: 2017
Identifier: CFH2000256, ucf:46006
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFH2000256

Title: IN VITRO SELECTION OF DNA APTAMERS AGAINST PROSTATE CANCER PEPTIDE BIOMARKERS.
Creator: Kuguoglu, Elif, Kolpashchikov, Dmitry, University of Central Florida
Abstract / Description: This project is aimed toward finding DNA aptamers against prostate cancer peptide antigens. DNA aptamers can function to find and indicate the presence of certain molecules in a specimen. These aptamers will be obtained through the process of evolutionary selection, a specific process called SELEX which stands for Systemic Evolution of Ligands by Experimental Enrichment. By conducting several rounds of SELEX, a DNA aptamer will be selected to bind to a known peptide antigen. A biotinylated...
Show moreThis project is aimed toward finding DNA aptamers against prostate cancer peptide antigens. DNA aptamers can function to find and indicate the presence of certain molecules in a specimen. These aptamers will be obtained through the process of evolutionary selection, a specific process called SELEX which stands for Systemic Evolution of Ligands by Experimental Enrichment. By conducting several rounds of SELEX, a DNA aptamer will be selected to bind to a known peptide antigen. A biotinylated column will be utilized to stabilize a random library of DNA aptamers, and those peptides that bind to certain aptamers will cause a conformational change leading to the elution of those specific DNA aptamers. This SELEX process will be conducted again on the eluted aptamers to further select for strong binding DNA aptamers. The DNA aptamers that are obtained can further on be sequenced or used for prostate cancer research studies. Another possible usage of aptamers is to diagnose and determine the stage of various different cancer types. Our prediction is that this research will produce a DNA aptamer that will bind to a specific prostate cancer peptide antigen.
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Date Issued: 2014
Identifier: CFH0004671, ucf:45294
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFH0004671

Title: USING ANTENNA TILE-ASSISTED SUBSTRATE DELIVERY TO IMPROVE THE DETECTION LIMITS OF DEOXYRIBOZYME BIOSENSORS.
Creator: Cox, Amanda, Kolpashchikov, Dmitry, University of Central Florida
Abstract / Description: One common limitation of enzymatic reactions is the diffusion of a substrate to the enzyme active site and/or the release of the reaction products. These reactions are known as diffusion-controlled. Overcoming this limitation may enable faster catalytic rates, which in the case of catalytic biosensors can potentially lower limits of detection of specific analyte. Here we created an artificial system to enable deoxyribozyme (Dz) 10-23 based biosensor to overcome its diffusion limit. The sensor...
Show moreOne common limitation of enzymatic reactions is the diffusion of a substrate to the enzyme active site and/or the release of the reaction products. These reactions are known as diffusion-controlled. Overcoming this limitation may enable faster catalytic rates, which in the case of catalytic biosensors can potentially lower limits of detection of specific analyte. Here we created an artificial system to enable deoxyribozyme (Dz) 10-23 based biosensor to overcome its diffusion limit. The sensor consists of the two probe strands, which bind to the analyzed nucleic acid by Watson-Crick base pairs and, upon binding re-form the catalytic core of Dz 10-23. The activated Dz 10-23 cleaves the fluorophore and quencher-labeled DNA-RNA substrate which separates the fluorophore from the quencher thus producing high fluorescent signal. This system uses a Dz 10-23 biosensor strand associated to a DNA antenna tile, which captures the fluorogenic substrate and channels it to the reaction center where the Dz 10-23 cleaves the substrate. DNA antenna tile captures fluorogenic substrate and delivers it to the activated Dz 10-23 core. This allows for lower levels of analyte to be detected without compromising the specificity of the biosensor. The results of this experiment demonstrated that using DNA antenna, we can create a synthetic environment around the Dz 10-23 biosensor to increase its efficiency and allow for lower levels of analyte to be detected without using amplification techniques like PCR.
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Date Issued: 2015
Identifier: CFH0004887, ucf:45432
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFH0004887

Title: A TRIPARTILE BIOSENSOR FOR REAL-TIME SNPS DETECTION IN DNA HAIRPIN MOTIF.
Creator: Nguyen, Camha, Kolpashchikov, Dmitry, University of Central Florida
Abstract / Description: The hybridization between two complementary strands of nucleic acid is the basis for a number of applications in DNA and RNA analysis, including in vivo RNA monitoring, microarrays, SNPs detection, and so on. The short oligonucleotide probes form Watson/Crick base pairs (A-T and G-C) with the analyzed nucleic acid. Molecular beacon (MB) probe is one of the most advantageous tools for nucleic acid analysis in real-time. A traditional MB probe consists of a DNA strand folded in hairpin motif...
Show moreThe hybridization between two complementary strands of nucleic acid is the basis for a number of applications in DNA and RNA analysis, including in vivo RNA monitoring, microarrays, SNPs detection, and so on. The short oligonucleotide probes form Watson/Crick base pairs (A-T and G-C) with the analyzed nucleic acid. Molecular beacon (MB) probe is one of the most advantageous tools for nucleic acid analysis in real-time. A traditional MB probe consists of a DNA strand folded in hairpin motif with a fluorophore attached to the 5'end and a quencher attached to the 3' end. The loop segment is complementary to the analytes. Upon hybridization to a complementary single-stranded nucleic acid, MB probe switches to the elongated conformation, which separates the fluorophore from the quencher, resulting in high fluorescence signal. However, DNA or RNA folded in hairpin motifs are difficult to analyze by a conventional MB probes. Inefficient formation of the duplex between the secondary analyte and the MB probe results in low or undetectable fluorescent signal. In this project, we developed a tripartite probe consisting of one MB probe and two adaptor strands to genotype single nucleotide polymorphism (SNPs) in DNA hairpin motifs in real-time fluorescent assays. Each adaptor strand contains a fragment complementary to the analyte and a fragment complementary to an MB probe. One adaptor strand hybridizes to the analyte and unwinds its secondary structure, and the other strand forms stable complex only with the fully complementary analyte sequence. The tri-component probe promises to simplify nucleic acid analysis at ambient temperatures in such application as in vivo RNA monitoring and isothermal detection of specific DNA/RNA targets.
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Date Issued: 2011
Identifier: CFH0003768, ucf:44722
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFH0003768

Title: The Owl Sensor: a smart nanostructure for single nucleotide variation analysis.
Creator: Karadeema, Rebekah, Kolpashchikov, Dmitry, Chumbimuni Torres, Karin, Harper, James, University of Central Florida
Abstract / Description: Analysis of single nucleotide variations (SNVs) in DNA and RNA sequences is extensively used in healthcare for detection of genetic mutations and analysis of drug resistant pathogens. Here we developed a nucleic acid sensor able to differentiate between a fully matched analyte and one with a SNV in a wide temperature range of 5(&)deg;C-32(&)deg;C. The sensor, dubbed here the 'Owl Sensor' due to the complex's resemblance to owl eyes, utilizes recent developments in DNA nanotechnology and...
Show moreAnalysis of single nucleotide variations (SNVs) in DNA and RNA sequences is extensively used in healthcare for detection of genetic mutations and analysis of drug resistant pathogens. Here we developed a nucleic acid sensor able to differentiate between a fully matched analyte and one with a SNV in a wide temperature range of 5(&)deg;C-32(&)deg;C. The sensor, dubbed here the 'Owl Sensor' due to the complex's resemblance to owl eyes, utilizes recent developments in DNA nanotechnology and synthetic biology to self-assemble a fluorescent DNA nanostructure called a Double Crossover, or DX Tile, capable of differentiating SNVs in a large temperature range, including ambient temperature. In the presence of fully matched nucleic acid analytes, a stable complex is formed with high fluorescent signal; however in the presence of a single base variation in the analyte, unfavourable helicity results in little-to-no observed complex formation. The novelty of the approach is that selectivity of analyte recognition is, at least in part, determined by the structural rigidity of the entire nanostructure rather than by the stability of analyte-probe hybrid, as is the case for conventional hybridization probes. The rigid nanostructure collapses if a minor imperfection, e.g. if a single-base mispairing, is present. Owl Sensor differentiates fully matched analyte from mismatched in a wide temperature range, with mismatched analyte producing only the background fluorescence, selectivity that is hard to achieve by conventional hybridization probes. Owl Sensor therefore promises to add to the toolbox for diagnosis of genetic disorders and infectious diseases at ambient temperatures.
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Date Issued: 2016
Identifier: CFE0006691, ucf:51916
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0006691

Title: Strategies for Enhanced Genetic Analysis of Trace DNA from Touch DNA Evidence and Household Dust.
Creator: Farash, Katherine, Ballantyne, John, Kolpashchikov, Dmitry, Bridge, Candice, University of Central Florida
Abstract / Description: In forensic casework it is often necessary to obtain genetic profiles from crime scene samples that contain increasingly smaller amounts of genetic material, called Low Template DNA (LTDNA). Two examples of LTDNA sources are touch DNA evidence and dust bunnies. Touch DNA refers to DNA that is left behind through casual contact of a donor with an object or another person. Touch DNA can be used to prove a suspect was present at a crime scene. Dust bunnies, or dust conglomerates, typically...
Show moreIn forensic casework it is often necessary to obtain genetic profiles from crime scene samples that contain increasingly smaller amounts of genetic material, called Low Template DNA (LTDNA). Two examples of LTDNA sources are touch DNA evidence and dust bunnies. Touch DNA refers to DNA that is left behind through casual contact of a donor with an object or another person. Touch DNA can be used to prove a suspect was present at a crime scene. Dust bunnies, or dust conglomerates, typically contain trapped shed skin cells of anyone in the vicinity along with fibers, dirt, hair, and other trace materials. Dust specimens are a potential source of forensic evidence that has been widely underutilized in the forensic community. This is unfortunate because a dust bunny could not only be used to associate a person or crime scene (-) through trace materials such as fibers (-) but also to positively identify (-) through a DNA profile. For example, if a dust specimen is found on a piece of evidence suspected of being moved from its original location, for instance as a body that is too heavy to carry and therefore collects dust while being dragged, then it could be used to link a suspect to a crime scene.Standard methods for obtaining and analyzing touch DNA have been established, but the techniques are not ideal. First, by nature, the 'blind-swabbing' technique, which involves cotton swabs or adhesive tape being applied to an area of interest, can artificially create mixtures of biological material that was originally spatially separated. Second, because the amount of DNA present is typically very low, standard analysis methods may not be sensitive enough to produce probative profiles. In the case of mixtures, the minor component's DNA may go undetected. Dust specimens contain degraded genetic material that has been accumulating for an unknown amount of time. Additionally, dust is usually a conglomeration of genetic material from multiple donors so a mixed profile, if any, is likely to be recovered if standard analysis methods are used.In order to overcome these obstacles presented by LTDNA, a micro-manipulation and combined cell lysis/direct PCR amplification technique has been developed that is sensitive enough to obtain full or probative STR profiles from single or clumped bio-particles collected from touch DNA and dust evidence. Sources of touch DNA evidence such as worn clothing items, touched objects, and skin/skin mixtures are easily sampled using an adhesive material on a microscope slide. Dust specimens can be dispersed onto an adhesive material as well. Targeted bio-particles are then (")picked(") with a water-soluble adhesive on a tungsten needle and deposited into a micro-volume STR amplification mix. Individual selection and analysis of isolated bio-particles reduces the chance of mixed profile recovery. To aid in the release of genetic material present in the bio-particles, a lysis mix containing a thermostable proteinase is then added to the sample. Samples are then analyzed using standard capillary electrophoresis (CE) methods.In addition to identifying the donor source of these LTDNA sources, it would be beneficial to a criminal investigation to identify the tissue source of the biological material as well. While it is widely speculated that the material originates from shed skin cells, there is little confirmatory evidence proving this assertion. Knowledge of the nature of the evidence could be vital to prevent its misinterpretation during the investigation and prosecution of a crime. Here tissue specific mRNA biomarkers have been evaluated for their use in tissue source determination using a highly sensitive High Resolution Melt (HRM) temperature assay that detects the selectively amplified targets based on their melt temperatures.Using the enhanced genetic analysis technique described above, DNA profile recovery has been markedly enhanced in sources of Touch DNA evidence and dust specimens compared to standard methods. Additionally, the molecular-based characterization method could potentially provide a better understanding of the meaningfulness of the recovered DNA profiles. This optimized strategy provides a method for recovering highly probative data from biological material in low template samples in an efficient and cost effect manner.
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Date Issued: 2015
Identifier: CFE0006033, ucf:50979
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0006033

Title: A Binary Approach for Selective Recognition of Nucleic Acids and Proteins.
Creator: Cornett, Evan, Kolpashchikov, Dmitry, Self, William, Ye, Jingdong, University of Central Florida
Abstract / Description: The design of probes for the selective recognition of biopolymers (nucleic acids and proteins) is a fundamental task for studying, diagnosing, and treating diseases. Traditional methods utilize a single component (small molecule or oligonucleotide) that binds directly to the target biopolymer. However, many biopolymers are unable to be targeted with this approach. The overarching goal of this dissertation is to explore a new, binary approach for designing probes. The binary approach requires...
Show moreThe design of probes for the selective recognition of biopolymers (nucleic acids and proteins) is a fundamental task for studying, diagnosing, and treating diseases. Traditional methods utilize a single component (small molecule or oligonucleotide) that binds directly to the target biopolymer. However, many biopolymers are unable to be targeted with this approach. The overarching goal of this dissertation is to explore a new, binary approach for designing probes. The binary approach requires two components that cooperatively bind to the target, triggering a recognition event. The requisite binding of two-components allows the probes to have excellent selectivity and modularity.The binary approach was applied to design a new sensor, called operating cooperatively (OC) sensor, for recognition of nucleic acids, including selectively differentiating between single nucleotide polymorphisms (SNPs). An OC sensor contains two oligonucleotide probe strands, called O and C, each with two domains. The first domain contains a target recognition sequence, whereas the second domain is complementary to a molecular beacon (MB) probe. Binding of both probe strands to the fully matched analyte generates a full MB probe recognition site, allowing a MB to bind and report the presence of the target analyte. Importantly, we show that the OC sensor selectively discriminates between single nucleotide polymorphisms (SNPs) in DNA and RNA targets at room temperature, including those with stable secondary structures. Furthermore, the combinatorial use of OC sensors to create a DNA logic gate capable of analyzing DNA sequences of Mycobacterium tuberculosis is described.The binary approach was also applied to design covalent inhibitors for HIV-1 reverse transcriptase (RT). In this application, two separate pre-reactive groups were attached to a natural RT ligand, deoxythymidine triphosphate (dTTP). Upon binding of both dTTP analogs in the RT active site, the pre-reactive groups are brought into the proper proximity and react with each other forming an intermediate that subsequently reacts with an amino acid side chain from the RT. This leads to covalent modification of RT, and inhibition of its DNA polymerase activity. This concept was tested in vitro using dTTP analogs containing pre-reactive groups derived from ?-lactamase inhibitors clavulanic acid (CA) and sulbactam (SB). Importantly, our in vitro assays show that CA based inhibitors are more potent than zidovudine (AZT), a representative of the dominant class of RT inhibitors currently used in anti-HIV therapy. Furthermore, molecular dynamics simulations predict that complexes of RT with these analogs are stable, and point to possible reaction mechanisms. The inhibitors described in this work may serve as the basis for the development of the first covalent inhibitors for RT. Moreover, the pre-reactive groups used in this study can be used to design covalent inhibitors for other targets by attaching them to different ligands. Overall, the work presented herein establishes the binary approach as a straightforward way to develop new probes to selectively recognize nucleic acids and proteins.
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Date Issued: 2015
Identifier: CFE0006031, ucf:51010
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0006031

Title: The Estimation of Germ Line De Novo Mutation Rates of Extended Sets of Y-STR Haplotypes to Aid in the Differentiation of Male Biological Relatives in Criminal Investigations.
Creator: Masker, Nicole, Ballantyne, John, Kolpashchikov, Dmitry, Koculi, Eda, University of Central Florida
Abstract / Description: An important forensic application for Y-chromosome short tandem repeats (Y-STRs) is the identification of male DNA. Since the Y-chromosome is non-recombining and most Y-STRs have slippage mutation rates on the order of 1x10-3 or lower, Y-STR commercial multiplex systems do not yet allow personal individualization. This is problematic in criminal investigations where the persons of interest include males of the same paternal line. In order to obtain discrimination among paternal male relatives...
Show moreAn important forensic application for Y-chromosome short tandem repeats (Y-STRs) is the identification of male DNA. Since the Y-chromosome is non-recombining and most Y-STRs have slippage mutation rates on the order of 1x10-3 or lower, Y-STR commercial multiplex systems do not yet allow personal individualization. This is problematic in criminal investigations where the persons of interest include males of the same paternal line. In order to obtain discrimination among paternal male relatives, it would be necessary to use a larger number of Y-STRs or a selection of Y-loci with higher slippage mutations with the hope of encountering a germline meiotic mutation. In this study, Y-STR loci from three multiplexes were examined: an ultra-high discrimination multiplex of 14 non-core loci; Promega's PowerPlex(&)#174; Y23; and a rapidly mutating 13-locus panel (mutation rates above 1x10-2). Taking the three multiplexes together provides a unique 40-locus Y-STR panel (the (")Masker Set(")), a powerful tool to separate closely related males. The loci were examined for discriminative slippage mutations in pairs of paternally related South Brazilian males: 99 grandfather-grandson, 103 uncle-nephew, and 140 brothers. The goal of this study was to analyze the (")Masker Set(") loci by: describing the characteristics and frequency of germ-line mutations; noting differences in mutation rates between and within loci; determining repeat gain and loss rates; and identifying the most informative loci to differentiate male relatives. Using the (")Masker Set("), pairs of male relatives were distinguished by at least one mutation 53% of the time for grandfather-grandson, 62% for uncle-nephew, and 54% for brothers. The most discriminating Y-STR loci were: DYF387S1, DYF404S1, DYS526B, DYS389II, DYS449, DYS547, DYF399S1, DYS458, DYS576, DYF403S1A, DYS508, DYS612, DYS403S1B, DYS518, and DYS627.
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Date Issued: 2016
Identifier: CFE0006837, ucf:51784
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0006837

Title: Development of Micro Volume DNA and RNA Profiling Assays to Identify the Donor and Tissue Source of Origin of Trace Forensic Biological Evidence.
Creator: Morgan, Brittany, Ballantyne, John, Kolpashchikov, Dmitry, Ye, Jingdong, University of Central Florida
Abstract / Description: In forensic casework analysis it is necessary to obtain genetic profiles from increasingly smaller amounts of biological material left behind by perpetrators of crime. The ability to obtain profiles from trace biological evidence is demonstrated with so-called 'touch DNA evidence' which is perceived to be the result of DNA obtained from shed skin cells transferred from donor to an object or person during physical contact. However, the current method of recovery of trace DNA involves cotton...
Show moreIn forensic casework analysis it is necessary to obtain genetic profiles from increasingly smaller amounts of biological material left behind by perpetrators of crime. The ability to obtain profiles from trace biological evidence is demonstrated with so-called 'touch DNA evidence' which is perceived to be the result of DNA obtained from shed skin cells transferred from donor to an object or person during physical contact. However, the current method of recovery of trace DNA involves cotton swabs or adhesive tape to sample an area of interest. This (")blind-swabbing(") approach may result in the recovery of biological material from different individuals resulting in admixed DNA profiles which are often difficult to interpret. Profiles recovered from these samples are reported to be from shed skin cells with no biological basis for that determination. A specialized approach for the isolation of single or few cells from 'touch DNA evidence' is necessary to improve the analysis and interpretation of recovered profiles. Here we describe the development of optimized and robust micro volume PCR reactions (1-5 uL) to improve the sensitivity and efficiency of 'touch DNA' analysis. These methods will permit not only the recovery of the genetic profile of the donor of the biological material, but permit an identification of the tissue source of origin using mRNA profiling. Results showed that the 3.5 uL amplification volume, a fraction of the standard 25 uL amplification volume, was the most ideal volume for the DNA assay, as it had very minimal evaporation with a 50% profile recovery rate at a single cell equivalent input (~5 pg) with reducing amplification volume alone. Findings for RNA showed that by reducing both amplification steps, reverse transcriptase PCR (20 uL) and body fluid multiplex PCR (25 uL), to 5 uL, ideal results were obtained with an increase in sensitivity and detection of six different body fluids down to 50 pg. Once optimized at the trace level, the assays were applied to the collection of single and few cells. DNA findings showed that about 40% of a full profile could be recovered from a single buccal cell, with nearly 80% of a full profile recovered from only two cells. RNA findings from collected skin particles of (")touched(") surfaces showed accurate skin detection down to 25 particles and detection in one clump of particles. The profiles recovered were of high quality and similar results were able to be replicated through subsequent experiments. More studies are currently underway to optimize these developed assays to increase profile recovery at the single cell level. Methods of doing so include comparing different locations on touched surfaces for highest bio-particle recovery and the development of physical characteristics of bio-particles that would provide the most ideal results.
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Date Issued: 2013
Identifier: CFE0005385, ucf:50468
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0005385

Title: A Complete Approach to Predict Biodistribution of Nanomaterials Within Animal Species from In-vitro Data.
Creator: Price, Edward, Gesquiere, Andre, Huo, Qun, Kolpashchikov, Dmitry, Rex, Matthew, Ebert, Steven, University of Central Florida
Abstract / Description: Smart drug-design for antibody and nanomaterial-based therapies allows for optimization of drug efficacy and more efficient early-stage pre-clinical trials. The ideal drug must display maximum efficacy at target tissue sites, but to track and predict distribution to these sites, one must have a mechanistic understanding of the kinetics involved with the individual cells of the tissue itself. This process can be tracked through biological simulations coupled with in-vitro approaches, which...
Show moreSmart drug-design for antibody and nanomaterial-based therapies allows for optimization of drug efficacy and more efficient early-stage pre-clinical trials. The ideal drug must display maximum efficacy at target tissue sites, but to track and predict distribution to these sites, one must have a mechanistic understanding of the kinetics involved with the individual cells of the tissue itself. This process can be tracked through biological simulations coupled with in-vitro approaches, which result in a rapid and efficient in-depth understanding of drug transport within tissue vasculature and cellular environment. As a result, it becomes possible to predict drug biodistribution within live animal tissue cells without the need for animal studies. Herein, we use in-vitro assays to translate transport kinetics to whole-body animal simulations to predict drug distribution from vasculature into individual tissue cells for the first time. Our approach is based on rate constants obtained from an in-vitro assay that accounts for cell-induced degradation, which are translated to a complete animal simulation to predict nanomedicine biodistribution at the single cell level. This approach delivers predictions for therapies of varying size and type for multiple species of animals solely from in-vitro data. Thus, we expect this work to assist in refining, reducing, and replacing animal testing, while at the same time, giving scientists a new perspective during early stages of drug development.
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Date Issued: 2019
Identifier: CFE0007900, ucf:52747
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0007900

Title: Polyelectrolyte complexes based on poly(acrylic acid): mechanics and applications.
Creator: Lu, Xiaoyan, Zhai, Lei, Zou, Shengli, Chumbimuni Torres, Karin, Kolpashchikov, Dmitry, Dong, Yajie, University of Central Florida
Abstract / Description: Poly(acrylic acid) (PAA) is a weak polyelectrolyte presenting negative charge at basic conditionwhen the carboxylic group loses a proton. These carboxylate group can interact with polycationsand metal ions to form stable polyelectrolyte complexes (PECs), leading to tunable propertiesand multifunctional nanoscale structures through chemical reactions. This research focuses onnanofiber and nanoparticle fabricated by PAA-based PECs. We demonstrated the effect of ferricion concentration on the...
Show morePoly(acrylic acid) (PAA) is a weak polyelectrolyte presenting negative charge at basic conditionwhen the carboxylic group loses a proton. These carboxylate group can interact with polycationsand metal ions to form stable polyelectrolyte complexes (PECs), leading to tunable propertiesand multifunctional nanoscale structures through chemical reactions. This research focuses onnanofiber and nanoparticle fabricated by PAA-based PECs. We demonstrated the effect of ferricion concentration on the mechanical properties of PAA-based single naonofiber by using dark fieldmicroscopy imaging and persistence length analysis. The application of PAA-based nanofibermats loaded with MnO2 for supercapacitors was also explored. As a free-standing and flexiblesupercapacitor electrode, the nanofiber mat exhibited outstanding properties including high specificcapacitance, excellent reversible redox reactions, and fast charge/discharge ability. Since PAA is abiocompatible polymer, PAA-based PEC was applied as a drug-carrier in a drug delivery system.In this project, core-shell nanoparticles were fabricated with chitosan as the core and PAA as theshell to incorporate with the drug gemcitabine. Several parameters were investigated to obtainthe optimal nanoparticle size. The as-prepared drug delivery system shows prolonged releasingprofile.
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Date Issued: 2018
Identifier: CFE0007045, ucf:52004
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0007045

Title: A Universal Electrochemical Biosensor for the Detection of Nucleic Acids based on a Four-Way Junction Structure.
Creator: Mills, Dawn, Chumbimuni Torres, Karin, Kolpashchikov, Dmitry, Campiglia, Andres, Dupras, Tosha, Tetard, Laurene, University of Central Florida
Abstract / Description: Electrochemical hybridization sensors have been explored extensively for analysis of specific nucleic acids. However, commercialization of the platform is hindered by the need for attachment of separate oligonucleotide probes complementary to a RNA or DNA target to an electrode's surface. This dissertation demonstrates that a single probe can be used to analyze several nucleic acid targets of different lengths with high selectivity, low cost and can be regenerated in 30 seconds by a simple...
Show moreElectrochemical hybridization sensors have been explored extensively for analysis of specific nucleic acids. However, commercialization of the platform is hindered by the need for attachment of separate oligonucleotide probes complementary to a RNA or DNA target to an electrode's surface. This dissertation demonstrates that a single probe can be used to analyze several nucleic acid targets of different lengths with high selectivity, low cost and can be regenerated in 30 seconds by a simple water rinse. The universal electrochemical four-way junction (4J)-forming (UE4J) sensor consists of a universal DNA stem-loop (USL) probe attached to the electrode's surface and two adaptor strands (m and f) which hybridize to the USL probe and the analyte to form a 4J structure. The UE4J sensor enables a high selectivity by recognition of a single base substitution, even at room temperature. The sensor was monitored with voltammetry and electrochemical impedance spectroscopy using different redox labeling strategies and optimized using synthetic nucleic acid sequences. After the sensor was optimized and fully characterized, it was modified for the detection of the Zika virus. The UE4J sensor presented here opens a venue for a re-useable universal platform that can be adopted at low cost for the analysis of potentially any DNA or RNA targets.
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Date Issued: 2017
Identifier: CFE0007290, ucf:52146
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0007290

Title: A deoxyribozyme sensor and isothermal amplification for human sex determination.
Creator: Smith, Alexandra, Kolpashchikov, Dmitry, Campiglia, Andres, Harper, James, Beazley, Melanie, Tetard, Laurene, University of Central Florida
Abstract / Description: Ribozymes are known to catalyze biochemical reactions and behave like enzymes. They are naturally occurring and have very diverse functions within a cell. After investigating ribozymes that next step was to find if DNA can exhibit the same characteristics since RNA and DNA only differ by a ribose 2'-hydroxyl group. This evolution in curiosity gave rise to artificial DNA enzymes that can catalyze certain reactions and have been created by in vitro selection methods. Due to the ability to...
Show moreRibozymes are known to catalyze biochemical reactions and behave like enzymes. They are naturally occurring and have very diverse functions within a cell. After investigating ribozymes that next step was to find if DNA can exhibit the same characteristics since RNA and DNA only differ by a ribose 2'-hydroxyl group. This evolution in curiosity gave rise to artificial DNA enzymes that can catalyze certain reactions and have been created by in vitro selection methods. Due to the ability to manipulate and control DNA hybridization, the deoxyribozyme is advantageous to the field of molecular diagnostics. Other hybridization probes like Taqman for PCR (polymerase chain reaction) or a molecular beacon are more conventional methods for molecular diagnostics, but deoxyribozyme-based nucleic acid sensors are overall more sensitive due to their catalytic enhancement of a signal and more selective due to structural design. When the deoxyribozyme is split into two probes, it is very efficient in identifying a minute difference in sequence compared to the monolith structure. This binary deoxyribozyme sensor (BiDz) has two probes, each containing an analyte binding arm, substrate binding arm, and half of the catalytic core. The monolith structure, known as a catalytic molecular beacon (CMB), contains a hairpin that contains the analyte binding arm in the loop and the substrate binding arms in the stem. The catalytic core is fully intact but deemed inactive due to the substrate binding arms being complimentary to an inhibitory sequence forming the stem. Once the sensor binds the analyte, catalytic core is formed/activated and cleaves a substrate containing a fluorophore and quencher. When the substrate is cleaved a fluorescent signal is given off denoting the detection of the target DNA. Deoxyribozyme sensors can be applied to the field of human sex determination by detecting the Amelogenin gene. Found on both sex chromosomes, the Amelogenin gene is the most common marker used for sex determination because it exhibits dimorphism in length and sequence. Sex identification from ancient skeletal remains is crucial to understanding the social structure of our history. When conventional methods, such as metric analysis, are not an option due to the fragmented or prepubescent remains, molecular diagnostics are needed. Amplification of DNA is required to be able to detect the target sequence in human samples. Isothermal loop-mediated amplification (LAMP) is a fast and simple technique that provides ample amounts of amplicon. It is advantageous over PCR because it amplifies at one temperature and no thermal cycler is needed. Two different sensors have been designed to detect the X and Y specific sequences with high selectivity. From a direct comparison between the CMB and BiDZ, the binary structure has shown to be simpler and less expensive to design, and highly selective toward single base substitutions (SNS). While both sensors contain detection limits in the picomolar range, which is consistent with data published by other research groups, the CMB sensors failed to function at higher temperatures (55oC). BiDz sensors are shown to be superior to the CMB design, particularly when selectivity based analysis is desired. For human sex determination, the binary sensor detected sex specific sequences with great selectivity. The sensor then detected LAMP amplified DNA from male and female teeth after 30 minutes of amplification. Combining a binary deoxyribozyme sensor and isothermal amplification can provide a new and valuable method for human sex determination.
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Date Issued: 2017
Identifier: CFE0007133, ucf:52306
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0007133

Title: Split Aptameric Turn-On Fluorescence Sensor for Detection of Sequence Specific Nucleic Acid.
Creator: Kikuchi, Nanami, Kolpashchikov, Dmitry, Zhai, Lei, Chumbimuni Torres, Karin, Chen, Gang, Teter, Kenneth, University of Central Florida
Abstract / Description: Nucleic acid amplification tests (NAATs) enable sensitive detection of low density infections that microscopy and rapid diagnostic test are not capable of detecting. They enable quantitative and qualitative nucleic acid detection, genotype analysis, and single nucleotide polymorphism (SNP) detection. Current state of the art molecular probes used with NAATs includes molecular beacon (MB), Taqman and its variations. This work presents novel molecular probe designed from Spinach and Dapoxyl...
Show moreNucleic acid amplification tests (NAATs) enable sensitive detection of low density infections that microscopy and rapid diagnostic test are not capable of detecting. They enable quantitative and qualitative nucleic acid detection, genotype analysis, and single nucleotide polymorphism (SNP) detection. Current state of the art molecular probes used with NAATs includes molecular beacon (MB), Taqman and its variations. This work presents novel molecular probe designed from Spinach and Dapoxyl aptamers. The aptamers are split into two parts (split aptamer), allowing greater sensitivity and selectivity towards fully complementary nucleic acid analyte. The major advantage of split aptamer probe over state-of-the-art fluorescent probes is its high selectivity: in the presence of a single base mismatched analyte, it produces only background fluorescence, even at room temperature. SSA is a promising tool for label-free analysis of nucleic acids at ambient temperatures.Split spinach aptamer (SSA) probes and split dapoxyl aptamer (SDA) for fluorescent analysis of nucleic acids were designed and tested. In both split aptamer design, two RNA or RNA/DNA or DNA strands hybridized to a specific nucleic acid analyte and formed a binding site for fluorescent dye, which was accompanied by up to 270-fold and 69-fold increase in fluorescence. SSAr consisted entirely of ribonucleotides which potentially be expressed in live cells and used for imaging of specific mRNAs. For in vitro RNA/DNA analysis, SDA consisting of entirely DNA are preferable due to greater chemical stability, lower synthetic cost and reduced ability to form intramolecular structures. Additionally, we designed two DNA strands that function as an adapter for SSA and demonstrated how a single universal spinach aptamer (USSA) probe can be used to detect multiple (potentially any) nucleic acid sequences. USSA can be used for cost-efficient and highly selective analysis of even folded DNA and RNA analytes, as well as for the readout of outputs of DNA logic circuits.
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Date Issued: 2018
Identifier: CFE0007031, ucf:51976
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0007031

Title: Self-assembly of Amyloid Aggregates Simulated with Molecular Dynamics.
Creator: Berhanu, Workalemahu, Masunov, Artem, Kolpashchikov, Dmitry, Ye, Jingdong, Zou, Shengli, Schulte, Alfons, University of Central Florida
Abstract / Description: ABSTRACTAmyloids are highly ordered cross-? sheet aggregates that are associated with many diseases such as Alzheimer's, type II diabetes and prion diseases. Recently a progress has been made in structure elucidation, environmental effects and thermodynamic properties of amyloid aggregates. However, detailed understanding of how mutation, packing polymorphism and small organic molecules influence amyloid structure and dynamics is still lacking. Atomistic modeling of these phenomena with...
Show moreABSTRACTAmyloids are highly ordered cross-? sheet aggregates that are associated with many diseases such as Alzheimer's, type II diabetes and prion diseases. Recently a progress has been made in structure elucidation, environmental effects and thermodynamic properties of amyloid aggregates. However, detailed understanding of how mutation, packing polymorphism and small organic molecules influence amyloid structure and dynamics is still lacking. Atomistic modeling of these phenomena with molecular dynamics (MD) simulations holds a great promise to bridge this gap. This Thesis describes the results of MD simulations, which provide insight into the effects of mutation, packing polymorphism and molecular inhibitors on amyloid peptides aggregation. Chapter 1 discusses the structure of amyloid peptides, diseases associated with amyloid aggregation, mechanism of aggregation and strategies to treat amyloid diseases. Chapter 2 describes the basic principles of molecular dynamic simulation and methods of trajectory analysis used in the Thesis. Chapter 3 presents the results of the study of several all-atom molecular dynamics simulations with explicit solvent, starting from the crystalline fragments of two to ten monomers each. Three different hexapeptides and their analogs produced with single glycine replacement were investigated to study the structural stability, aggregation behavior and thermodynamics of the amyloid oligomers. Chapter 4 presents multiple molecular dynamics (MD) simulation of a pair polymorphic form of five short segments of amyloid peptide. Chapter 5 describes MD study of single-layer oligomers of the full-length insulin with a goal to identify the structural elements that are important for insulin amyloid stability, and to suggest single glycine mutants that may improve formulation. Chapter 6 presents the investigation of the mechanism of the interaction of polyphenols molecules with the protofibrils formed by an amyloidogenic hexapeptide fragment (VQIVYK) of Tau peptide by molecular dynamics simulations in explicit solvent. We analyzed the trajectories of the large (7(&)#215;4) aggregate with and without the polyphenols.Our MD simulations for both the short and full length amyloids revealed adding strands enhances the internal stability of wildtype aggregates. The degree of structural similarity between the oligomers in simulation and the fibril models constructed based on experimental data may explain why adding oligomers shortens the experimentally observed nucleation lag phase of amyloid aggregation. The MM-PBSA free energy calculation revealed nonpolar components of the free energy is more favorable while electrostatic solvation is unfavorable for the sheet to sheet interaction. This explains the acceleration of aggregation by adding nonpolar co-solvents (methanol, tri?uoroethanol, and hexa?uoroisopropanol). Free energy decomposition shows residues situated at the interface were found to make favorable contribution to the peptide -peptide association.The results from the simulations might provide both the valuable insight for amyloid aggregation as well as assist in inhibitor design efforts. First, the simulation of the single glycine mutants at the steric zipper of the short segments of various pathological peptides indicates the intersheet steric zipper is important for amyloid stability. Mutation of the side chains at the dry steric zipper disrupts the sheet to sheet packing, making the aggregation unstable. Thus, designing new peptidomimetic inhibitors able to prevent the fibril formation based on the steric zipper motif of the oligomers, similar to the ones examined in this study may become a viable therapeutic strategy. The various steric zipper microcrystal structures of short amyloid segments could be used as a template to design aggregation inhibitor that can block growth of the aggregates. Modification of the steric zipper structure (structure based design) with a single amino acid changes, shuffling the sequences, N- methylation of peptide amide bonds to suppress hydrogen bonding ability of NH groups or replacement with D amino acid sequence that interact with the parent steric zipper could be used in computational search for the new inhibitors. Second, the polyphenols were found to interact with performed oligomer through hydrogen bonding and induce conformational change creating an altered aggregate. The conformational change disrupts the intermolecular amyloid contact remodeling the amyloid aggregate. The recently reported microcrystal structure of short segments of amyloid peptides with small organic molecules could serve as a pharamcophore for virtual screening of aggregation inhibitor using combined docking and MD simulation with possible enhancement of lead enrichment. Finally, our MD simulation of short segments of amyloids with steric zipper polymorphism showed the stability depends on both sequence and packing arrangements. The hydrophilic polar GNNQQNY and NNQNTF with interface containing large polar and/or aromatic side chains (Q/N) are more stable than steric zipper interfaces made of small or hydrophobic residues (SSTNVG, VQIVYK, and MVGGVV). The larger sheet to sheet interface of the dry steric zipper through polar Q/N rich side chains was found to holds the sheets together better than non Q/N rich short amyloid segments. The packing polymorphism could influence the structure based design of aggregation inhibitor and a combination of different aggregation inhibitors might be required to bind to various morphologic forms of the amyloid peptides.
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Date Issued: 2011
Identifier: CFE0004088, ucf:49131
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0004088

Title: Optimization of Molecular Beacon-Based Multicomponent Probes for Analysis of Nucleic Acids.
Creator: Stancescu, Maria, Kolpashchikov, Dmitry, Clausen, Christian, Koculi, Eda, Balaeff, Alexander, Shuler, Michael, University of Central Florida
Abstract / Description: Detection of single nucleotide substitutions (SNS) in DNA and RNA has a growing importance in biology and medicine. One traditional approach for recognition of SNS takes advantage of hybridization probes that bind target nucleic acids followed by measuring ?Tm, the difference in melting temperatures of matched and mismatched hybrids. The approach enables SNS differentiation at elevated temperatures (usually 40-65oC) often only in a narrow range of (
Show moreDetection of single nucleotide substitutions (SNS) in DNA and RNA has a growing importance in biology and medicine. One traditional approach for recognition of SNS takes advantage of hybridization probes that bind target nucleic acids followed by measuring ?Tm, the difference in melting temperatures of matched and mismatched hybrids. The approach enables SNS differentiation at elevated temperatures (usually 40-65oC) often only in a narrow range of (<)10oC and requires high-resolution melting devices. Here we demonstrate that a specially designed DNA probe (X sensor) can broaden ?Tm from ~10oC to ~16oC and distinguish SNS in the interval of ~5-40oC. Therefore, there is no need for heating or measuring Tm for accurate SNS differentiation. Our data indicate that this wide differentiation range is in part due to the non-equilibrium hybridization conditions. Further we explored the idea that it is possible to improve the performance of an X sensor operable in close to equilibrium conditions by shifting its operability to non-equilibrium conditions. One way to achieve this is to introduce as many as possible structured ligands in analyte's dissociated state. Here we show that by introducing the maximum possible conformational constraints in X probe it is possible to shift its operation to non-equilibrium conditions and to improve its selectivity at temperatures (<)15oC. Thus, this work points towards a new strategy for the design of highly selective hybridization sensors which operate in non-equilibrium conditions at close to room temperature. The X sensors could be utilized in qPCR, microarrays, as well as RNA analysis in living cells and for ambient temperature point-of-care diagnostics. In the last part of this work, X sensors were used in real time detection of PCR products. The sensors were optimized to operate in PCR buffer with optimal Mg2+ concentration. They were able to detect the target amplicon together with nonspecific products. The results presented here suggest that X sensors might be adopted for real time PCR format.
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Date Issued: 2015
Identifier: CFE0006009, ucf:51006
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0006009

Title: Electrical, Optical and Chemical Properties of Organic Photo Sensitve Materials.
Creator: Shi, Zheng, Liao, Yi, Kolpashchikov, Dmitry, Ye, Jingdong, Zou, Shengli, Su, Ming, University of Central Florida
Abstract / Description: Light as a (")green(") source of energy has become increasingly attractive throughout the past century and has shown versatility for the application of activating chemical reactions. Compared with traditional energy sources, it provides a more direct, selective and controllable method. My PhD study was focused on the study of photochemistry of organic materials in two different systems. The first system is regarding reversible photoacids which generate protons on irradiation. With the aim of...
Show moreLight as a (")green(") source of energy has become increasingly attractive throughout the past century and has shown versatility for the application of activating chemical reactions. Compared with traditional energy sources, it provides a more direct, selective and controllable method. My PhD study was focused on the study of photochemistry of organic materials in two different systems. The first system is regarding reversible photoacids which generate protons on irradiation. With the aim of systematically studying these novel types of long lived photoacids, a series of photoacids was designed, synthesized and whose chemical mechanism was thoroughly investigated. This type of photoacid changes from a weak acid to a strong acid with a pH change of several units, which achieves nearly complete proton dissociation upon visible light irradiation. The whole process is reversible and the half-life of the proton-dissociation state is long enough to be used in many applications. Besides fundamental studies, different applications based on this type of photoacids were also completed. An esterification reaction was catalyzed and the volume of a pH-sensitive polymer was altered due to the large amount of photo generated protons from this photoacid. A reversible electrical conductivity change of polyaniline (PANI) was also achieved by doping with this reversible photoacid. In order to induce a large conductivity increase, an irreversible photoacid generator (PAG) was embedded in a novel PANI/PAG/PVA novel composition. In this system, Poly (vinyl alcohol) (PVA) forms a hydrogen-bonding network to facilitate proton transfer between the PAG and PANI. A final electrical conductivity of 10-1 S cm-1 was successfully achieved after irradiation. The second system in which I explored photochemistry of organic molecules concerns Photo-retro-Diels-Alder (PrDA) reactions and a variety of Diels-Alder (DA) adducts were designed for these studies. UV light was used to trigger the retro-Diels-Alder reactions. Quantum yield of each DA adducts was investigated. This revealed that the photo-reactivity of this process depends on the electron-donating ability of the diene and the electron-withdrawing ability of the dienophile component. Mechanistic studies of this PrDA reaction reveal that a charge-separated intermediate is generated from a singlet excited state. This was applied to an unsaturated cyclic ?-diketones (DKs), which underwent PrDA reactions and generated anthracene derivatives and carbon monoxide (CO), which itself plays profound and important roles in biological systems. These unsaturated cyclic ?-diketones (DKs) encapsulated in micelles are effective CO-releasing molecules (CORMs) and are capable of carrying and releasing CO in cellular systems. This novel type of organic CORMs has potentially low toxicity and generates fluorescence, which provides a useful tool for the study of the biological functions of CO.
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Date Issued: 2013
Identifier: CFE0005114, ucf:50748
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0005114

Title: Development of Molecular Diagnostic Tools for Mycobacterium Species.
Creator: Bengtson, Hillary, Kolpashchikov, Dmitry, Rohde, Kyle, Self, William, Jewett, Travis, Masternak, Michal, University of Central Florida
Abstract / Description: This dissertation focuses on the development of diagnostic tools for mycobacteria using hybridization based technologies including binary deoxyribozyme (BiDz) sensors and microarrays. The genus Mycobacterium, is a diverse group of bacteria containing 150+ species including M. tuberculosis (M.tb) and non-tuberculous mycobacteria (NTM) which exhibit a range of pathogenicity, drug susceptibility and growth characteristics. M. tuberculosis (M.tb) is the causative agent of tuberculosis (TB) and...
Show moreThis dissertation focuses on the development of diagnostic tools for mycobacteria using hybridization based technologies including binary deoxyribozyme (BiDz) sensors and microarrays. The genus Mycobacterium, is a diverse group of bacteria containing 150+ species including M. tuberculosis (M.tb) and non-tuberculous mycobacteria (NTM) which exhibit a range of pathogenicity, drug susceptibility and growth characteristics. M. tuberculosis (M.tb) is the causative agent of tuberculosis (TB) and the leading cause of infectious disease related deaths worldwide. The control of TB is limited by the lack of sensitive and specific diagnostic tools available at the point of care (POC). The studies presented here illustrate the advances in our technology for the detection and differentiation of M.tb and NTM. The use of BiDz sensors enables the selective recognition of DNA/RNA analytes containing single nucleotide polymorphisms associated with species-specific identification, drug susceptibility testing (DST) and strain typing. First, we developed a platform for the detection of M.tb and drug susceptibility using multiplex PCR and BiDz sensors. However, this method relies on the use of expensive instrumentation which is often not available in high TB burden countries. Therefore, additional studies focused on the development of tools for the detection of isothermal amplification products and the direct detection of rRNA. Based on these findings, we also developed an NTM species typing tool using BiDz sensors for species identification in ~1 hour. Despite the advantages of BiDz sensor technology, their use is limited to the detection of a few selected mutations. To address this limitation, we developed a 15-loci multiplex PCR followed by analysis with a custom microarray for high-throughput identification of SNPs. The work presented in this dissertation has the potential to enable the rapid, specific and sensitive identification of mycobacterial species necessary to reduce the diagnostic delay, ensure initiation of effective therapy, and prevent further transmission.
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Date Issued: 2017
Identifier: CFE0006856, ucf:51735
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0006856

Title: Two-Component Covalent Inhibitors (TCCI) of the Human Immunodeficiency Virus Reverse Transcriptase (HIV-RT).
Creator: Ledezma, Carlos, Kolpashchikov, Dmitry, Yestrebsky, Cherie, Hernandez, Florencio, Zhai, Lei, Tatulian, Suren, University of Central Florida
Abstract / Description: The traditional design of nucleoside reverse transcriptase inhibitors (NRTI's) involves the synthesis of chain-terminated nucleoside analogs. HIV-RT has relatively low fidelity which facilitates mutations that confer resistance towards NRTI's, also, drug promiscuity from NRTI's result in various side-effects that lead to poor patient adherence to treatment. We designed and tested two-component covalent inhibitors against HIV-RT. Our inhibitor design results in higher specificity due to its...
Show moreThe traditional design of nucleoside reverse transcriptase inhibitors (NRTI's) involves the synthesis of chain-terminated nucleoside analogs. HIV-RT has relatively low fidelity which facilitates mutations that confer resistance towards NRTI's, also, drug promiscuity from NRTI's result in various side-effects that lead to poor patient adherence to treatment. We designed and tested two-component covalent inhibitors against HIV-RT. Our inhibitor design results in higher specificity due to its binary approach, which has previously been used in biosensing applications, where both components are necessary for therapeutic effect, and lower chances for mutagenesis because of its inhibitory action. The TCCI approach results in up to 93% inhibition of HIV-RT Furthermore, our inhibitor design is highly modular and can be adjusted towards the therapeutic targeting of other biopolymers.
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Date Issued: 2017
Identifier: CFE0006893, ucf:51712
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0006893

Title: Novel optical properties of metal nanostructures based on surface plasmons.
Creator: Wang, Haining, Zou, Shengli, Liao, Yi, Kolpashchikov, Dmitry, Gesquiere, Andre, Su, Ming, University of Central Florida
Abstract / Description: Surface plasmons have been attracted extensive interests in recent decades due to the novel properties in nanometer sized dimensions. My work focused on the novel optical properties of metal nanostructures based on surface plasmons using theoretical simulation methods. In the first part, we investigated metal nanofilms and nanorods and demonstrated that extremely low scattering efficiency, high absorption efficiency and propagation with long distance could be obtained by different metal...
Show moreSurface plasmons have been attracted extensive interests in recent decades due to the novel properties in nanometer sized dimensions. My work focused on the novel optical properties of metal nanostructures based on surface plasmons using theoretical simulation methods. In the first part, we investigated metal nanofilms and nanorods and demonstrated that extremely low scattering efficiency, high absorption efficiency and propagation with long distance could be obtained by different metal nanostructures. With a perforated silver film, we demonstrated that an extremely low scattering cross section with an efficiency of less than 1% can be achieved at tunable wavelengths with tunable widths. The resonance wavelength, width, and intensity are influenced by the shape, size and arrangement pattern of the holes, as well as the distance separating the holes along the polarization direction. The extremely low scattering could be used to obtain high absorption efficiency of a two-layer silver nanofilm. Using the discrete dipole approximation method, we achieved enhanced absorption efficiencies, which are close to 100%, at tunable wavelengths in a two-layer silver thin film. The film is composed of a 100 nm thick perforated layer facing the incident light and a 100 nm thick solid layer. Resonance wavelengths are determined by the distances between perforated holes in the first layer as well as the separation between two layers. The resonance wavelengths shift to red with increasing separation distance between two layers or the periodic distance of the hole arrays. Geometries of conical frustum shaped holes in the first layer are critical for the improved absorption efficiencies. When the hole bottom diameter equals the periodic distance and the upper diameter is about one-third of the bottom diameter, close to unit absorption efficiency can be obtained. We examined the electromagnetic wave propagation along a hollow silver nanorod with subwavelength dimensions. The calculations show that light may propagate along the hollow nanorod with growing intensities. The influences of the shape, dimension, and length of the rod on the resonance wavelength and the enhanced local electric field, |E|2, along the rod were investigated. In the second part, a generalized electrodynamics model is proposed to describe the enhancement and quenching of fluorescence signal of a dye molecule placed near a metal nanoparticle (NP). Both the size of the Au NPs and quantum yield of the dye molecule are crucial in determining the emission intensity of the molecule. Changing the size of the metal NP will alter the ratio of the scattering and absorption efficiencies of the metal NP and consequently result in different enhancement or quenching effect to the dye molecule. A dye molecule with a reduced quantum yield indicates that the non-radiative channel is dominant in the decay of the excited dye molecules and the amplification of the radiative decay rate will be easier. In general, the emission intensity will be quenched when the size of metal NP is small and the quantum yield of dye molecule is about unity. A significant enhancement factor will be obtained when the quantum yield of the molecule is small and the particle size is large. When the quantum yield of the dye molecule is less than 10-5, the model is simplified to the surface enhanced Raman scattering equation.
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Date Issued: 2013
Identifier: CFE0004769, ucf:49786
Format: Document (PDF)
PURL: http://purl.flvc.org/ucf/fd/CFE0004769

DNA (5)	+ -
Biosensors (2)	+ -
Deoxyribozyme (2)	+ -
Mycobacterium tuberculosis (2)	+ -
RNA (2)	+ -

nanostructure (2)	+ -
nucleic acids (2)	+ -
4-way junction (1)	+ -
Amyloid fibril (1)	+ -
Beta sheet inhibitor (1)	+ -
Binary Aptamer (1)	+ -
Biological (1)	+ -
Body Fluid (1)	+ -
Chemo Hydrothermally Treated (1)	+ -
Chitin (1)	+ -
Chitosan (1)	+ -
Clumps (1)	+ -
Copper-Chitosan (1)	+ -
Covalent Inhibition (1)	+ -
Covalent Inhibitors (1)	+ -
DNA aptamers (1)	+ -
DNA nanotechnology (1)	+ -
DNA tri-component probe (1)	+ -
Diffusion Limitation (1)	+ -
Donor (1)	+ -
Drug delivery (1)	+ -
Dust (1)	+ -
Dz 10-23 (1)	+ -
Energy storage (1)	+ -
Evidence (1)	+ -

ETD Collection (19)	+ -
Honors Collection (4)	+ -

Kolpashchikov, Dmitry (23)	+ -
University of Central Florida (23)	+ -
Ye, Jingdong (7)	+ -
Chumbimuni Torres, Karin (5)	+ -
Zou, Shengli (5)	+ -

Zhai, Lei (4)	+ -
Ballantyne, John (3)	+ -
Harper, James (3)	+ -
Koculi, Eda (3)	+ -
Self, William (3)	+ -
Campiglia, Andres (2)	+ -
Gesquiere, Andre (2)	+ -
Liao, Yi (2)	+ -
Santra, Swadeshmukul (2)	+ -
Su, Ming (2)	+ -
Tetard, Laurene (2)	+ -
Balaeff, Alexander (1)	+ -
Basumallick, Srijita (1)	+ -
Beazley, Melanie (1)	+ -
Bengtson, Hillary (1)	+ -
Berhanu, Workalemahu (1)	+ -
Blanco Martinez, Enrique J (1)	+ -
Bridge, Candice (1)	+ -
Chen, Gang (1)	+ -
Clausen, Christian (1)	+ -
Cornett, Evan (1)	+ -
Cox, Amanda (1)	+ -
Dong, Yajie (1)	+ -
Dupras, Tosha (1)	+ -
Ebert, Steven (1)	+ -

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