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Optimization of Molecular Beacon-Based Multicomponent Probes for Analysis of Nucleic Acids
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
Quantum Chemical Studies for the Engineering of Metal Organic Materials
Title
Quantum Chemical Studies for the Engineering of Metal Organic Materials.
Creator
Rivera Jacquez, Hector, Masunov, Artem, Balaeff, Alexander, Harper, James, Heider, Emily, Zou, Shengli, Kaden, William, University of Central Florida
Abstract / Description
Metal Organic Materials (MOM) are composed of transition metal ions as connectors and organic ligands as linkers. MOMs have been found to have high porosity, catalytic, and optical properties. Here we study the gas adsorption, color change, and non-linear optical properties of MOMs. These properties can be predicted using theoretical methods, and the results may provide experimentalists with guidance for rational design and engineering of novel MOMs. The theory levels used include semi...
Show moreMetal Organic Materials (MOM) are composed of transition metal ions as connectors and organic ligands as linkers. MOMs have been found to have high porosity, catalytic, and optical properties. Here we study the gas adsorption, color change, and non-linear optical properties of MOMs. These properties can be predicted using theoretical methods, and the results may provide experimentalists with guidance for rational design and engineering of novel MOMs. The theory levels used include semi-empirical quantum mechanical calculations with the PM7 Hamiltonian and, Density Functional Theory (DFT) to predict the geometry and electronic structure of the ground state, and Time Dependent DFT (TD-DFT) to predict the excited states and the optical properties.The molecular absorption capacity of aldoxime coordinated Zn(II) based MOMs (previously measured experimentally) is predicted by using PM7 Theory level. The 3D structures were optimized with and without host molecules inside the pores. The absorption capacity of these crystals was predicted to be 8H2 or 3N2 per unit cell. When going beyond this limit, the structural integrity of the bulk material becomes fractured and microcrystals are observed both experimentally and theoretically.The linear absorption properties of Co(II) based complexes are known to change color when the coordination number is altered. In order to understand the mechanism of this color change TD-DFT methods are employed. The chromic behavior of the Co(II) based complexes studied was confirmed to be due to a chain in coordination number that resulted in lower metal to ligand distances. These distances destabilize the occupied metal d orbitals, and as a consequence of this, the metal to ligand transition energy is lowered enough to allow the crystals to absorb light at longer wavelengths.Covalent organic frameworks (COFs) present an extension of MOM principles to the main group elements. The synthesis of ordered COFs is possible by using predesigned structures andcarefully selecting the building blocks and their conditions for assembly. The crystals formed by these systems often possess non-linear optical (NLO) properties. Second Harmonic Generation (SHG) is one of the most used optical processes. Currently, there is a great demand for materials with NLO optical properties to be used for optoelectronic, imaging, sensing, among other applications. DFT calculations can predict the second order hyperpolarizability ?2 and tensor components necessary to estimate NLO. These calculations for the ?2 were done with the use of the Berry's finite field approach. An efficient material with high ?2 was designed and the resulting material was predicted to be nearly fivefold higher than the urea standard.Two-photon absorption (2PA) is another NLO effect. Unlike SHG, it is not limited to acentric material and can be used development of in vivo bio-imaging agents for the brain. Pt(II) complexes with porphyrin derivatives are theoretically studied for that purpose. The mechanism of 2PA enhancement was identified. For the most efficient porphyrin, the large 2PA cross-section was found to be caused by a HOMO-LUMO+2 transition. This transition is strongly coupled to 1PA allowed Q-band HOMO-LUMO states by large transition dipoles. Alkyl carboxyl substituents delocalize the LUMO+2 orbital due to their strong ?-acceptor effect, enhancing transition dipoles and lowering the 2PA transition to the desirable wavelengths range.The mechanism 2PA cross-section enhancement of aminoxime and aldoxime ligands upon metal addition of is studied with TD-DFT methods. This mechanism of enhancement is found to be caused by the polarization of the ligand orbitals by the metal cation. After polarization an increase in ligand to ligand transition dipole moment. This enhancement of dipole moment is related to the increase in 2PA cross-sections.
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Date Issued
2015
Identifier
CFE0005990, ucf:50777
Format
Document (PDF)
PURL
http://purl.flvc.org/ucf/fd/CFE0005990