The Experts below are selected from a list of 60 Experts worldwide ranked by ideXlab platform
Patrick J. Hrdlicka - One of the best experts on this subject based on the ideXlab platform.
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c2 pyrene functionalized triazole linked DNA universal DNA RNA Hybridization probes
Journal of Organic Chemistry, 2012Co-Authors: Sujay P. Sau, Patrick J. HrdlickaAbstract:Development of universal Hybridization probes, that is, oligonucleotides displaying identical affinity toward matched and mismatched DNA/RNA targets, has been a longstanding goal due to potential applications as degenerate PCR primers and microarray probes. The classic approach toward this end has been the use of “universal bases” that either are based on hydrogen-bonding purine derivatives or aromatic base analogues without hydrogen-bonding capabilities. However, development of probes that result in truly universal Hybridization without compromising duplex thermostability has proven challenging. Here we have used the “click reaction” to synthesize four C2′-pyrene-functionalized triazole-linked 2′-deoxyuridine phosphoramidites. We demonstrate that oligodeoxyribonucleotides modified with the corresponding monomers display (a) minimally decreased thermal affinity toward DNA/RNA complements relative to reference strands, (b) highly robust universal Hybridization characteristics (average differences in therma...
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C2'-pyrene-functionalized triazole-linked DNA: universal DNA/RNA Hybridization probes.
The Journal of organic chemistry, 2011Co-Authors: Sujay P. Sau, Patrick J. HrdlickaAbstract:Development of universal Hybridization probes, that is, oligonucleotides displaying identical affinity toward matched and mismatched DNA/RNA targets, has been a longstanding goal due to potential applications as degenerate PCR primers and microarray probes. The classic approach toward this end has been the use of “universal bases” that either are based on hydrogen-bonding purine derivatives or aromatic base analogues without hydrogen-bonding capabilities. However, development of probes that result in truly universal Hybridization without compromising duplex thermostability has proven challenging. Here we have used the “click reaction” to synthesize four C2′-pyrene-functionalized triazole-linked 2′-deoxyuridine phosphoramidites. We demonstrate that oligodeoxyribonucleotides modified with the corresponding monomers display (a) minimally decreased thermal affinity toward DNA/RNA complements relative to reference strands, (b) highly robust universal Hybridization characteristics (average differences in therma...
Sujay P. Sau - One of the best experts on this subject based on the ideXlab platform.
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c2 pyrene functionalized triazole linked DNA universal DNA RNA Hybridization probes
Journal of Organic Chemistry, 2012Co-Authors: Sujay P. Sau, Patrick J. HrdlickaAbstract:Development of universal Hybridization probes, that is, oligonucleotides displaying identical affinity toward matched and mismatched DNA/RNA targets, has been a longstanding goal due to potential applications as degenerate PCR primers and microarray probes. The classic approach toward this end has been the use of “universal bases” that either are based on hydrogen-bonding purine derivatives or aromatic base analogues without hydrogen-bonding capabilities. However, development of probes that result in truly universal Hybridization without compromising duplex thermostability has proven challenging. Here we have used the “click reaction” to synthesize four C2′-pyrene-functionalized triazole-linked 2′-deoxyuridine phosphoramidites. We demonstrate that oligodeoxyribonucleotides modified with the corresponding monomers display (a) minimally decreased thermal affinity toward DNA/RNA complements relative to reference strands, (b) highly robust universal Hybridization characteristics (average differences in therma...
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C2'-pyrene-functionalized triazole-linked DNA: universal DNA/RNA Hybridization probes.
The Journal of organic chemistry, 2011Co-Authors: Sujay P. Sau, Patrick J. HrdlickaAbstract:Development of universal Hybridization probes, that is, oligonucleotides displaying identical affinity toward matched and mismatched DNA/RNA targets, has been a longstanding goal due to potential applications as degenerate PCR primers and microarray probes. The classic approach toward this end has been the use of “universal bases” that either are based on hydrogen-bonding purine derivatives or aromatic base analogues without hydrogen-bonding capabilities. However, development of probes that result in truly universal Hybridization without compromising duplex thermostability has proven challenging. Here we have used the “click reaction” to synthesize four C2′-pyrene-functionalized triazole-linked 2′-deoxyuridine phosphoramidites. We demonstrate that oligodeoxyribonucleotides modified with the corresponding monomers display (a) minimally decreased thermal affinity toward DNA/RNA complements relative to reference strands, (b) highly robust universal Hybridization characteristics (average differences in therma...
Frederick P. Schwarz - One of the best experts on this subject based on the ideXlab platform.
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thermodynamic dependence of DNA DNA and DNA RNA Hybridization reactions on temperature and ionic strength
Biophysical Chemistry, 2007Co-Authors: Brian E. Lang, Frederick P. SchwarzAbstract:The thermodynamics of 5'-ATGCTGATGC-3' binding to its complementary DNA and RNA strands was determined in sodium phosphate buffer under varying conditions of temperature and salt concentration from isothermal titration calorimetry (ITC). The Gibbs free energy change, DeltaG degrees of the DNA Hybridization reactions increased by about 6 kJ mol(-1) from 20 degrees C to 37 degrees C and exhibited heat capacity changes of -1.42 +/- 0.09 kJ mol(-1) K(-1) for DNA/DNA and -0.87 +/- 0.05 kJ mol(-1) K(-1) for DNA/RNA. Values of DeltaG degrees decreased non-linearly by 3.5 kJ mol(-1) at 25 degrees C and 6.0 kJ mol(-1) at 37 degrees C with increase in the log of the sodium chloride concentration from 0.10 M to 1.0 M. A near-linear relationship was observed, however, between DeltaG degrees and the activity coefficient of the water component of the salt solutions. The thermodynamic parameters of the Hybridization reaction along with the heat capacity changes were combined with thermodynamic contributions from the stacking to unstacking transitions of the single-stranded oligonucleotides from differential scanning calorimetry (DSC) measurements, resulting in good agreement with extrapolation of the free energy changes to 37 degrees C from the melting transition at 56 degrees C.
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Thermodynamic dependence of DNA/DNA and DNA/RNA Hybridization reactions on temperature and ionic strength
Biophysical Chemistry, 2007Co-Authors: Brian E. Lang, Frederick P. SchwarzAbstract:The thermodynamics of 5'-ATGCTGATGC-3' binding to its complementary DNA and RNA strands was determined in sodium phosphate buffer under varying conditions of temperature and salt concentration from isothermal titration calorimetry (ITC). The Gibbs free energy change, DeltaG degrees of the DNA Hybridization reactions increased by about 6 kJ mol(-1) from 20 degrees C to 37 degrees C and exhibited heat capacity changes of -1.42 +/- 0.09 kJ mol(-1) K(-1) for DNA/DNA and -0.87 +/- 0.05 kJ mol(-1) K(-1) for DNA/RNA. Values of DeltaG degrees decreased non-linearly by 3.5 kJ mol(-1) at 25 degrees C and 6.0 kJ mol(-1) at 37 degrees C with increase in the log of the sodium chloride concentration from 0.10 M to 1.0 M. A near-linear relationship was observed, however, between DeltaG degrees and the activity coefficient of the water component of the salt solutions. The thermodynamic parameters of the Hybridization reaction along with the heat capacity changes were combined with thermodynamic contributions from the stacking to unstacking transitions of the single-stranded oligonucleotides from differential scanning calorimetry (DSC) measurements, resulting in good agreement with extrapolation of the free energy changes to 37 degrees C from the melting transition at 56 degrees C.
Brian E. Lang - One of the best experts on this subject based on the ideXlab platform.
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thermodynamic dependence of DNA DNA and DNA RNA Hybridization reactions on temperature and ionic strength
Biophysical Chemistry, 2007Co-Authors: Brian E. Lang, Frederick P. SchwarzAbstract:The thermodynamics of 5'-ATGCTGATGC-3' binding to its complementary DNA and RNA strands was determined in sodium phosphate buffer under varying conditions of temperature and salt concentration from isothermal titration calorimetry (ITC). The Gibbs free energy change, DeltaG degrees of the DNA Hybridization reactions increased by about 6 kJ mol(-1) from 20 degrees C to 37 degrees C and exhibited heat capacity changes of -1.42 +/- 0.09 kJ mol(-1) K(-1) for DNA/DNA and -0.87 +/- 0.05 kJ mol(-1) K(-1) for DNA/RNA. Values of DeltaG degrees decreased non-linearly by 3.5 kJ mol(-1) at 25 degrees C and 6.0 kJ mol(-1) at 37 degrees C with increase in the log of the sodium chloride concentration from 0.10 M to 1.0 M. A near-linear relationship was observed, however, between DeltaG degrees and the activity coefficient of the water component of the salt solutions. The thermodynamic parameters of the Hybridization reaction along with the heat capacity changes were combined with thermodynamic contributions from the stacking to unstacking transitions of the single-stranded oligonucleotides from differential scanning calorimetry (DSC) measurements, resulting in good agreement with extrapolation of the free energy changes to 37 degrees C from the melting transition at 56 degrees C.
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Thermodynamic dependence of DNA/DNA and DNA/RNA Hybridization reactions on temperature and ionic strength
Biophysical Chemistry, 2007Co-Authors: Brian E. Lang, Frederick P. SchwarzAbstract:The thermodynamics of 5'-ATGCTGATGC-3' binding to its complementary DNA and RNA strands was determined in sodium phosphate buffer under varying conditions of temperature and salt concentration from isothermal titration calorimetry (ITC). The Gibbs free energy change, DeltaG degrees of the DNA Hybridization reactions increased by about 6 kJ mol(-1) from 20 degrees C to 37 degrees C and exhibited heat capacity changes of -1.42 +/- 0.09 kJ mol(-1) K(-1) for DNA/DNA and -0.87 +/- 0.05 kJ mol(-1) K(-1) for DNA/RNA. Values of DeltaG degrees decreased non-linearly by 3.5 kJ mol(-1) at 25 degrees C and 6.0 kJ mol(-1) at 37 degrees C with increase in the log of the sodium chloride concentration from 0.10 M to 1.0 M. A near-linear relationship was observed, however, between DeltaG degrees and the activity coefficient of the water component of the salt solutions. The thermodynamic parameters of the Hybridization reaction along with the heat capacity changes were combined with thermodynamic contributions from the stacking to unstacking transitions of the single-stranded oligonucleotides from differential scanning calorimetry (DSC) measurements, resulting in good agreement with extrapolation of the free energy changes to 37 degrees C from the melting transition at 56 degrees C.
Krishna N. Ganesh - One of the best experts on this subject based on the ideXlab platform.
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cis cyclopentyl pna cppna as constrained chiral pna analogues stereochemical dependence of DNA RNA Hybridization
Chemical Communications, 2004Co-Authors: Thimmaiah Govindaraju, Vaijayanti A. Kumar, Krishna N. GaneshAbstract:DNA/RNA Hybridization studies of PNA-T oligomers with cis-(1S,2R/1R,2S)-cyclopentyl units in the backbone show stereochemistry dependent binding with RNA/DNA discrimination.
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cis-Cyclopentyl PNA (cpPNA) as constrained chiral PNA analogues: stereochemical dependence of DNA/RNA Hybridization
Chemical communications (Cambridge England), 2004Co-Authors: Thimmaiah Govindaraju, Vaijayanti A. Kumar, Krishna N. GaneshAbstract:DNA/RNA Hybridization studies of PNA-T oligomers with cis-(1S,2R/1R,2S)-cyclopentyl units in the backbone show stereochemistry dependent binding with RNA/DNA discrimination.
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expanding the repertoire of pyrrolidyl pna analogues for DNA RNA Hybridization selectivity aminoethylpyrrolidinone pna aepone pna
Chemical Communications, 2003Co-Authors: Nagendra K. Sharma, Krishna N. GaneshAbstract:New PNA analogues derived from aminoethylpyrrolidin-5-one backbone show stabilization of aepone-PNA:DNA hybrids and destabilization of the corresponding RNA hybrids compared to unmodified PNA.
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Expanding the repertoire of pyrrolidyl PNA analogues for DNA/RNA Hybridization selectivity: aminoethylpyrrolidinone PNA (aepone-PNA).
Chemical communications (Cambridge England), 2003Co-Authors: Nagendra K. Sharma, Krishna N. GaneshAbstract:New PNA analogues derived from aminoethylpyrrolidin-5-one backbone show stabilization of aepone-PNA:DNA hybrids and destabilization of the corresponding RNA hybrids compared to unmodified PNA.