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(1 - 5 of 5)
- Title
- Split Aptameric Turn-On Fluorescence Sensor for Detection of Sequence Specific Nucleic Acid.
- Creator
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Kikuchi, Nanami, Kolpashchikov, Dmitry, Zhai, Lei, Chumbimuni Torres, Karin, Chen, Gang, Teter, Kenneth, University of Central Florida
- Abstract / Description
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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.
Show less - Date Issued
- 2018
- Identifier
- CFE0007031, ucf:51976
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0007031
- Title
- APTAMERIC SENSORS: IN VITRO SELECTION OF DNA THAT BINDS BROMOCRESOL PURPLE.
- Creator
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Miller, Derek B, Kolpshchikov, Dmitry, University of Central Florida
- Abstract / Description
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Aptamers being used as sensors is an emerging field that has capabilities of being tomorrow's diagnostic tools. As aptameric sensors have become more popular, their visualization systems have been limited. The majority of today's aptameric sensors require expensive machinery such as a fluorometer in order to visualize results. We propose a system that will cut the need for instrumentation and be detected via the naked eye. With the selection of an aptamer to bind the pH indicating dye...
Show moreAptamers being used as sensors is an emerging field that has capabilities of being tomorrow's diagnostic tools. As aptameric sensors have become more popular, their visualization systems have been limited. The majority of today's aptameric sensors require expensive machinery such as a fluorometer in order to visualize results. We propose a system that will cut the need for instrumentation and be detected via the naked eye. With the selection of an aptamer to bind the pH indicating dye bromocresol purple (BCP) this may be achieved. When rendered active, the binding towards BCP will facilitate a color change from yellow to purple or vice versa. Previous studies have shown albumin contains the ability to facilitate this role and we now intend to use a DNA aptamer to achieve this as well. The BCP aptamer has the potential to serve as a signaling domain to any already selected aptamer thus making it a universal tool for both research and diagnostic measures. We have found that an alternative structure-switching systematic evolution of ligands by exponential enrichment (SELEX) method which left the dye unaltered was not sufficient for selecting an aptamer. We believe that a classical SELEX will enable us to select an aptamer that may be used to accomplish this role as a universal visual detector.
Show less - Date Issued
- 2016
- Identifier
- CFH2000112, ucf:45951
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFH2000112
- Title
- ALPHA-SYNUCLEIN: INSIGHT INTO THE HALLMARK OF PARKINSON'S DISEASE AS A TARGET FOR QUANTITATIVE MOLECULAR DIAGNOSTICS AND THERAPEUTICS.
- Creator
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Evangelista, Baggio A, Kim, Yoon-Seong, University of Central Florida
- Abstract / Description
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Parkinson's disease (PD) is the second-most common neurodegenerative disease after Alzheimer's disease. With 500,000 individuals currently living with Parkinson's and nearly 60,000 new cases diagnosed each year, this disease causes significant financial burden on the healthcare system - amassing to annual expenditures totaling 200 billion dollars; predicted to increase through 2050. The disease phenotype is characterized by a combination of a resting tremor, bradykinesia, muscular rigidity,...
Show moreParkinson's disease (PD) is the second-most common neurodegenerative disease after Alzheimer's disease. With 500,000 individuals currently living with Parkinson's and nearly 60,000 new cases diagnosed each year, this disease causes significant financial burden on the healthcare system - amassing to annual expenditures totaling 200 billion dollars; predicted to increase through 2050. The disease phenotype is characterized by a combination of a resting tremor, bradykinesia, muscular rigidity, and depression due to dopaminergic neuronal death in the midbrain. The cause of the neurotoxicity has been largely discussed, with strong evidence suggesting that the protein, alpha-Synuclein, is a key factor. Under native conditions, alpha-Synuclein can be found localized at synaptic terminals where it is hypothesized to be involved in vesicle trafficking and recycling. However, its biochemical profile reveals a hydrophobic region that, once subjected to insult, initiates an aggregation cascade. Oligomeric species-products of the aggregation cascade-demonstrate marked neurotoxicity in dopaminergic neurons and illustrate migratory potential to neighboring healthy neurons, thereby contributing to progressive neurodegeneration. The current golden standard for PD diagnostics is a highly qualitative system involving a process-by-elimination with accuracy that is contingent upon physician experience. This, and a lack of standardized clinical testing procedures, lends to a 25% misdiagnosis rate. Even under circumstances of an accurate PD diagnosis, the only treatment options are pharmacologics that have a wide range of adverse side effects and ultimately contribute to systemic metabolic dysfunction. Thus, the research presented in this thesis seeks to overcome these current challenges by providing (1) a quantitative diagnostic platform and (2) a biomolecular therapeutic, towards oligomeric alpha-Synuclein. Aim 1: serves as a proof-of-concept for the use of catalytic nucleic acid moieties, deoxyribozymes and aptamers, to quantify alpha-Synuclein in a novel manner and explore the ability to detect oligomeric cytotoxic species. The cost-effective nature of these sensors allows for continued optimization. Aim 2: serves to establish a potential therapy that can abrogate alpha-synuclein oligomerization and toxicity through use of a modified Protein Disulfide Isomerase (PDI) peptide when introduced to live cells treated to simulate pre-parkinsonian pathology.
Show less - Date Issued
- 2017
- Identifier
- CFH2000188, ucf:46024
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFH2000188
- Title
- IN VITRO SELECTION OF DNA APTAMERS AGAINST PROSTATE CANCER PEPTIDE BIOMARKERS.
- Creator
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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.
Show less - Date Issued
- 2014
- Identifier
- CFH0004671, ucf:45294
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFH0004671
- Title
- Development of in vitro point of care diagnostics (IVPCD) based on Aptamers integrated Biosensors.(&)nbsp;.
- Creator
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Saraf, Nileshi, Seal, Sudipta, Fang, Jiyu, Florczyk, Stephen, Dong, Yajie, Self, William, University of Central Florida
- Abstract / Description
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The global market for the medical diagnostic industry is worth 25 billion dollars in the United States and is expected to grow exponentially each year. Presently available methods for biodetection, such as immunoassays, chemiluminescence and fluorescent based assays are expensive, time consuming and require skilled labor with high-end instruments. Therefore, development of novel, passive colorimetric sensors and diagnostic technologies for detection and surveillance is of utmost importance...
Show moreThe global market for the medical diagnostic industry is worth 25 billion dollars in the United States and is expected to grow exponentially each year. Presently available methods for biodetection, such as immunoassays, chemiluminescence and fluorescent based assays are expensive, time consuming and require skilled labor with high-end instruments. Therefore, development of novel, passive colorimetric sensors and diagnostic technologies for detection and surveillance is of utmost importance especially in resource constrained communities. The present work focusses on developing novel and advanced in vitro biodiagnostic tools based on aptamer integrated biosensors for an early detection of specific viral proteins or small biomolecules used as potential markers for deadly diseases. Aptamers are short single stranded deoxyribonucleic acid (DNA) which are designed to bind to a specific target biomolecule. These are readily synthesized in laboratory and offers several advantages over antibodies/enzymes such as stable in harsh environment, easily functionalized for immobilization, reproducibility etc. These undergo conformational changes upon target binding and produces physical or chemical changes in the system which are measured as colorimetric or electrochemical signals. Here, we have explored the aptamer-analyte interaction on different platforms such as microfluidic channel, paper based substrate as well as organic electrochemical transistor to develop multiple compact, robust and self-contained diagnostic tools. These testing tools exhibit high sensitivity (detection limit in picomolar) and selectivity against the target molecule, require no sophisticated instruments or skilled labor to implement and execute, leading a way to cheaper and more consumer driver health care. These innovative platforms provide flexibility to incorporate additional or alternative targets by simply designing aptamers to bind to the specific biomolecule.
Show less - Date Issued
- 2018
- Identifier
- CFE0007766, ucf:52388
- Format
- Document (PDF)
- PURL
- http://purl.flvc.org/ucf/fd/CFE0007766
