The Experts below are selected from a list of 252 Experts worldwide ranked by ideXlab platform
Francis Dsouza - One of the best experts on this subject based on the ideXlab platform.
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binding electrochemical activation and cleavage of dna by cobalt ii tetrakis n methylpyridyl porphyrin and its β pyrrole brominated derivative
Bioconjugate Chemistry, 2006Co-Authors: Shivaraj Yellappa, Jaldappagari Seetharamappa, Lisa M Rogers, Raghu Chitta, Ram P Singhal, Francis DsouzaAbstract:The binding of nucleic acids by water-soluble cobalt(II) tetrakis-N-methylpyridyl porphyrin, (TMPyP)Co, and its highly electron-deficient derivative cobalt(II) tetrakis-N-methyl pyridyl-β-octabromoporphyrin, (Br8TMPyP)Co, was investigated by UV−visible absorption, circular dichroism (CD), and electrochemical and gel electrophoresis methods. The changes of the absorption spectra during the titration of these complexes with Polynucleotides revealed a shift in the absorption maxima and a hypochromicity of the porphyrin Soret bands. The intrinsic binding constants were found to be in the range of 105−106 M-1. These values were higher for the more electron-deficient (Br8TMPyP)Co. Induced CD bands were noticed in the Soret region of the complexes due to the interaction of these complexes with different Polynucleotides, and an analysis of the CD spectra supported a mainly external mode of binding. Electrochemical studies revealed the cleavage of Polynucleotides by (TMPyP)Co and (Br8TMPyP)Co in the presence of ox...
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binding electrochemical activation and cleavage of dna by cobalt ii tetrakis n methylpyridyl porphyrin and its β pyrrole brominated derivative
Bioconjugate Chemistry, 2006Co-Authors: Shivaraj Yellappa, Jaldappagari Seetharamappa, Lisa M Rogers, Raghu Chitta, Ram P Singhal, Francis DsouzaAbstract:The binding of nucleic acids by water-soluble cobalt(II) tetrakis-N-methylpyridyl porphyrin, (TMPyP)Co, and its highly electron-deficient derivative cobalt(II) tetrakis-N-methyl pyridyl-beta-octabromoporphyrin, (Br(8)TMPyP)Co, was investigated by UV-visible absorption, circular dichroism (CD), and electrochemical and gel electrophoresis methods. The changes of the absorption spectra during the titration of these complexes with Polynucleotides revealed a shift in the absorption maxima and a hypochromicity of the porphyrin Soret bands. The intrinsic binding constants were found to be in the range of 10(5)-10(6) M(-1). These values were higher for the more electron-deficient (Br(8)TMPyP)Co. Induced CD bands were noticed in the Soret region of the complexes due to the interaction of these complexes with different Polynucleotides, and an analysis of the CD spectra supported a mainly external mode of binding. Electrochemical studies revealed the cleavage of Polynucleotides by (TMPyP)Co and (Br(8)TMPyP)Co in the presence of oxygen preferentially at the A-T base pair region. Gel electrophoresis experiments further supported the cleavage of nucleic acids. The results indicate that the beta-pyrrole brominated porphyrin, (Br(8)TMPyP)Co, binds strongly and cleaves nucleic acids efficiently as compared with (TMPyP)Co. This electrolytic procedure offers a unique tool in biotechnology for cleaving double-stranded DNA with specificity at the A-T regions.
Shivaraj Yellappa - One of the best experts on this subject based on the ideXlab platform.
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binding electrochemical activation and cleavage of dna by cobalt ii tetrakis n methylpyridyl porphyrin and its β pyrrole brominated derivative
Bioconjugate Chemistry, 2006Co-Authors: Shivaraj Yellappa, Jaldappagari Seetharamappa, Lisa M Rogers, Raghu Chitta, Ram P Singhal, Francis DsouzaAbstract:The binding of nucleic acids by water-soluble cobalt(II) tetrakis-N-methylpyridyl porphyrin, (TMPyP)Co, and its highly electron-deficient derivative cobalt(II) tetrakis-N-methyl pyridyl-β-octabromoporphyrin, (Br8TMPyP)Co, was investigated by UV−visible absorption, circular dichroism (CD), and electrochemical and gel electrophoresis methods. The changes of the absorption spectra during the titration of these complexes with Polynucleotides revealed a shift in the absorption maxima and a hypochromicity of the porphyrin Soret bands. The intrinsic binding constants were found to be in the range of 105−106 M-1. These values were higher for the more electron-deficient (Br8TMPyP)Co. Induced CD bands were noticed in the Soret region of the complexes due to the interaction of these complexes with different Polynucleotides, and an analysis of the CD spectra supported a mainly external mode of binding. Electrochemical studies revealed the cleavage of Polynucleotides by (TMPyP)Co and (Br8TMPyP)Co in the presence of ox...
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binding electrochemical activation and cleavage of dna by cobalt ii tetrakis n methylpyridyl porphyrin and its β pyrrole brominated derivative
Bioconjugate Chemistry, 2006Co-Authors: Shivaraj Yellappa, Jaldappagari Seetharamappa, Lisa M Rogers, Raghu Chitta, Ram P Singhal, Francis DsouzaAbstract:The binding of nucleic acids by water-soluble cobalt(II) tetrakis-N-methylpyridyl porphyrin, (TMPyP)Co, and its highly electron-deficient derivative cobalt(II) tetrakis-N-methyl pyridyl-beta-octabromoporphyrin, (Br(8)TMPyP)Co, was investigated by UV-visible absorption, circular dichroism (CD), and electrochemical and gel electrophoresis methods. The changes of the absorption spectra during the titration of these complexes with Polynucleotides revealed a shift in the absorption maxima and a hypochromicity of the porphyrin Soret bands. The intrinsic binding constants were found to be in the range of 10(5)-10(6) M(-1). These values were higher for the more electron-deficient (Br(8)TMPyP)Co. Induced CD bands were noticed in the Soret region of the complexes due to the interaction of these complexes with different Polynucleotides, and an analysis of the CD spectra supported a mainly external mode of binding. Electrochemical studies revealed the cleavage of Polynucleotides by (TMPyP)Co and (Br(8)TMPyP)Co in the presence of oxygen preferentially at the A-T base pair region. Gel electrophoresis experiments further supported the cleavage of nucleic acids. The results indicate that the beta-pyrrole brominated porphyrin, (Br(8)TMPyP)Co, binds strongly and cleaves nucleic acids efficiently as compared with (TMPyP)Co. This electrolytic procedure offers a unique tool in biotechnology for cleaving double-stranded DNA with specificity at the A-T regions.
Gopinatha Suresh Kumar - One of the best experts on this subject based on the ideXlab platform.
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sequence selective binding of phenazinium dyes phenosafranin and safranin o to guanine cytosine deoxyriboPolynucleotides spectroscopic and thermodynamic studies
Journal of Physical Chemistry B, 2010Co-Authors: Ishita Saha, Maidul Hossain, Gopinatha Suresh KumarAbstract:The sequence selectivity of the DNA binding of the phenazinium dyes phenosafranin and safranin O have been investigated with four sequence-specific deoxyriboPolynucleotides from spectroscopic and calorimetric studies. The alternating guanine−cytosine sequence selectivity of the dyes has been revealed from binding affinity values, circular dichroism, thermal melting, competition dialysis, and calorimetric results. The binding affinities of both the dyes to the Polynucleotides were of the order of 105 M−1, but the values were higher for the guanine−cytosine Polynucleotides over adenine−thymine ones. Phenosafranin had a higher binding affinity compared to safranin O. Isothermal titration calorimetric studies revealed that the binding reactions were exothermic and favored by negative enthalpy and predominantly large positive entropy contributions in all cases except poly(dA)·poly(dT) where the profile was anomalous. Although charged, nonpolyelectrolytic contribution was revealed to be dominant to the free ene...
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dna intercalation of methylene blue and quinacrine new insights into base and sequence specificity from structural and thermodynamic studies with Polynucleotides
Molecular BioSystems, 2009Co-Authors: Maidul Hossain, Gopinatha Suresh KumarAbstract:The binding of the known DNA intercalators methylene blue and quinacrine with four sequence specific Polynucleotides, viz. poly(dG-dC).poly(dG-dC), poly(dG).poly(dC), poly(dA-dT).poly(dA-dT) and poly(dA).poly(dT), have been compared using absorbance, fluorescence, competition dialysis and thermal melting and the thermodynamic aspects of the interaction studied. In all the cases, non-cooperative binding phenomena obeying neighbor exclusion principle was observed though the affinity was remarkably higher for quinacrine and the nature of the binding was characterized to be true intercalation. The data on the salt dependence of binding derived from the plot of log Kvs. log[Na+] revealed a slope of around 1.0, consistent with the values predicted by the theories for the binding of monovalent cations, and contained contributions from polyelectrolytic and non-polyelectrolytic forces. The bindings were characterized by strong stabilization of the Polynucleotides against thermal strand separation in both optical melting as well as differential scanning calorimetry studies. The data analyzed from the thermal melting and isothermal titration calorimetry studies were in close proximity to those obtained from absorption spectral titration data. Isothermal titration calorimetry results revealed the bindings to poly(dG-dC).poly(dG-dC), poly(dG).poly(dC) and poly(dA-dT).poly(dA-dT) to be exothermic and favoured by both negative enthalpy and large favourable positive entropy changes, while that to poly(dA).poly(dT) was endothermic and entropy driven. The heat capacity changes obtained from temperature dependence of enthalpy gave negative values to all Polynucleotides. New insights on the molecular aspects of interaction of these molecules to DNA have emerged from these studies.
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molecular recognition of dna by small molecules at base pair specific intercalative binding of cytotoxic plant alkaloid palmatine
Biochimica et Biophysica Acta, 2007Co-Authors: Kakali Bhadra, Motilal Maiti, Gopinatha Suresh KumarAbstract:Abstract The base dependent binding of the cytotoxic alkaloid palmatine to four synthetic Polynucleotides, poly(dA).poly(dT), poly(dA–dT).poly(dA–dT), poly(dG).poly(dC) and poly(dG–dC).poly(dG–dC) was examined by competition dialysis, spectrophotometric, spectrofluorimetric, thermal melting, circular dichroic, viscometric and isothermal titration calorimetric (ITC) studies. Binding of the alkaloid to various Polynucleotides was dependent upon sequences of base pairs. Binding data obtained from absorbance measurements according to neighbour exclusion model indicated that the intrinsic binding constants decreased in the order poly(dA).poly(dT) > poly(dA–dT).poly(dA–dT) > poly(dG–dC).poly(dG–dC) > poly(dG).poly(dC). This affinity was also revealed by the competition dialysis, increase of steady state fluorescence intensity, increase in fluorescence quantum yield, stabilization against thermal denaturation and perturbations in circular dichroic spectrum. Among the Polynucleotides, poly(dA).poly(dT) showed positive cooperativity at binding values lower than r = 0.05. Viscosity studies revealed that in the strong binding region, the increase of contour length of DNA depended strongly on the sequence of base pairs being higher for AT polymers and induction of unwinding–rewinding process of covalently closed superhelical DNA. Isothermal titration calorimetric data showed a single entropy driven binding event in the AT homo polymer while that with the hetero polymer involved two binding modes, an entropy driven strong binding followed by an enthalpy driven weak binding. These results unequivocally established that the alkaloid palmatine binds strongly to AT homo and hetero polymers by mechanism of intercalation.
Daniel Branton - One of the best experts on this subject based on the ideXlab platform.
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rapid nanopore discrimination between single polynucleotide molecules
Proceedings of the National Academy of Sciences of the United States of America, 2000Co-Authors: Amit Meller, Lucas G Nivon, Eric Brandin, Jene Andrew Golovchenko, Daniel BrantonAbstract:A variety of different DNA polymers were electrophoretically driven through the nanopore of an alpha-hemolysin channel in a lipid bilayer. Single-channel recording of the translocation duration and current flow during traversal of individual Polynucleotides yielded a unique pattern of events for each of the several polymers tested. Statistical data derived from this pattern of events demonstrate that in several cases a nanopore can distinguish between Polynucleotides of similar length and composition that differ only in sequence. Studies of temperature effects on the translocation process show that translocation duration scales as approximately T(-2). A strong correlation exists between the temperature dependence of the event characteristics and the tendency of some polymers to form secondary structure. Because nanopores can rapidly discriminate and characterize unlabeled DNA molecules at low copy number, refinements of the experimental approach demonstrated here could eventually provide a low-cost high-throughput method of analyzing DNA Polynucleotides.
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rapid nanopore discrimination between single polynucleotide molecules
Proceedings of the National Academy of Sciences of the United States of America, 2000Co-Authors: Amit Meller, Lucas G Nivon, Eric Brandin, Jene Andrew Golovchenko, Daniel BrantonAbstract:A variety of different DNA polymers were electrophoretically driven through the nanopore of an α-hemolysin channel in a lipid bilayer. Single-channel recording of the translocation duration and current flow during traversal of individual Polynucleotides yielded a unique pattern of events for each of the several polymers tested. Statistical data derived from this pattern of events demonstrate that in several cases a nanopore can distinguish between Polynucleotides of similar length and composition that differ only in sequence. Studies of temperature effects on the translocation process show that translocation duration scales as ∼T−2. A strong correlation exists between the temperature dependence of the event characteristics and the tendency of some polymers to form secondary structure. Because nanopores can rapidly discriminate and characterize unlabeled DNA molecules at low copy number, refinements of the experimental approach demonstrated here could eventually provide a low-cost high-throughput method of analyzing DNA Polynucleotides.
Ram P Singhal - One of the best experts on this subject based on the ideXlab platform.
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binding electrochemical activation and cleavage of dna by cobalt ii tetrakis n methylpyridyl porphyrin and its β pyrrole brominated derivative
Bioconjugate Chemistry, 2006Co-Authors: Shivaraj Yellappa, Jaldappagari Seetharamappa, Lisa M Rogers, Raghu Chitta, Ram P Singhal, Francis DsouzaAbstract:The binding of nucleic acids by water-soluble cobalt(II) tetrakis-N-methylpyridyl porphyrin, (TMPyP)Co, and its highly electron-deficient derivative cobalt(II) tetrakis-N-methyl pyridyl-β-octabromoporphyrin, (Br8TMPyP)Co, was investigated by UV−visible absorption, circular dichroism (CD), and electrochemical and gel electrophoresis methods. The changes of the absorption spectra during the titration of these complexes with Polynucleotides revealed a shift in the absorption maxima and a hypochromicity of the porphyrin Soret bands. The intrinsic binding constants were found to be in the range of 105−106 M-1. These values were higher for the more electron-deficient (Br8TMPyP)Co. Induced CD bands were noticed in the Soret region of the complexes due to the interaction of these complexes with different Polynucleotides, and an analysis of the CD spectra supported a mainly external mode of binding. Electrochemical studies revealed the cleavage of Polynucleotides by (TMPyP)Co and (Br8TMPyP)Co in the presence of ox...
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binding electrochemical activation and cleavage of dna by cobalt ii tetrakis n methylpyridyl porphyrin and its β pyrrole brominated derivative
Bioconjugate Chemistry, 2006Co-Authors: Shivaraj Yellappa, Jaldappagari Seetharamappa, Lisa M Rogers, Raghu Chitta, Ram P Singhal, Francis DsouzaAbstract:The binding of nucleic acids by water-soluble cobalt(II) tetrakis-N-methylpyridyl porphyrin, (TMPyP)Co, and its highly electron-deficient derivative cobalt(II) tetrakis-N-methyl pyridyl-beta-octabromoporphyrin, (Br(8)TMPyP)Co, was investigated by UV-visible absorption, circular dichroism (CD), and electrochemical and gel electrophoresis methods. The changes of the absorption spectra during the titration of these complexes with Polynucleotides revealed a shift in the absorption maxima and a hypochromicity of the porphyrin Soret bands. The intrinsic binding constants were found to be in the range of 10(5)-10(6) M(-1). These values were higher for the more electron-deficient (Br(8)TMPyP)Co. Induced CD bands were noticed in the Soret region of the complexes due to the interaction of these complexes with different Polynucleotides, and an analysis of the CD spectra supported a mainly external mode of binding. Electrochemical studies revealed the cleavage of Polynucleotides by (TMPyP)Co and (Br(8)TMPyP)Co in the presence of oxygen preferentially at the A-T base pair region. Gel electrophoresis experiments further supported the cleavage of nucleic acids. The results indicate that the beta-pyrrole brominated porphyrin, (Br(8)TMPyP)Co, binds strongly and cleaves nucleic acids efficiently as compared with (TMPyP)Co. This electrolytic procedure offers a unique tool in biotechnology for cleaving double-stranded DNA with specificity at the A-T regions.