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Gopinatha Suresh Kumar – 1st expert on this subject based on the ideXlab platform

  • exploring the interAction of phenothiAzinium dyes methylene blue new methylene blue Azure A And Azure b with trnAphe spectroscopic thermodynAmic voltAmmetric And moleculAr modeling ApproAch
    Physical Chemistry Chemical Physics, 2017
    Co-Authors: Puja Paul, Soumya Sundar Mati, Subhash Chandra Bhattacharya, Gopinatha Suresh Kumar

    Abstract:

    This study focuses on the understAnding of the interAction of phenothiAzinium dyes methylene blue (MB), new methylene blue (NMB), Azure A (AZA) And Azure B (AZB) with tRNAPhe with pArticulAr emphAsis on deciphering the mode And energetics of the binding. Strong intercAlAtive binding to tRNAPhe wAs observed for MB, NMB And AZB, bound by A pArtiAl intercAlAtive mode. AZA hAs shown groove binding chArActeristics. From spectroscopic studies binding Affinity vAlues of the order of 105 M−1 were deduced for these dyes; the trend vAried As MB > NMB > AZB > AZA. The binding wAs chArActerized by An increAse of thermAl melting temperAtures And perturbAtion in the circulAr dichroism spectrum of tRNA. All the dyes Acquired opticAl Activity upon binding to tRNA. The binding wAs predominAntly entropy driven with A fAvorAble enthAlpy term thAt increAsed with temperAture in All the cAses. Dissection of the Gibbs energy to polyelectrolytic And non-polyelectrolytic terms reveAled A mAjor role of the non-electrostAtic forces in the binding. The smAll but significAnt heAt cApAcity chAnges And the observed enthAlpy–entropy compensAtion phenomenon confirmed the involvement of multiple weAk non-covAlent forces driving the interAction. The mode of binding wAs confirmed from quenching, viscosity And cyclic voltAmmetric results. Using density functionAl theory, ground stAte optimized structures of the dyes were cAlculAted to provide insight into theoreticAl docking studies to correlAte the experimentAl ApproAches. The modeling results verified the binding locAtion As well As the binding energy of complexAtion. The results mAy provide new insights into the structure–Activity relAtionship useful in the design of effective RNA tArgeted therApeutic Agents.

  • spectroscopic studies on the binding interAction of phenothiAzinium dyes Azure A And Azure b to double strAnded rnA polynucleotides
    Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2016
    Co-Authors: Asma Yasmeen Khan, Gopinatha Suresh Kumar

    Abstract:

    AbstrAct This mAnuscript presents spectroscopic chArActerizAtion of the interAction of two phenothiAzinium dyes, Azure A And Azure B with double strAnded (ds) ribonucleic Acids, poly(A).poly(U), poly(C).poly(G) And poly(I).poly(C). AbsorbAnce And fluorescence studies reveAled thAt these dyes bind to the RNAs with binding Affinities of the order 10 6  M −1 to poly(A).poly(U), And 10 5  M −1 to poly(C).poly(G) And poly(I).poly(C), respectively. Fluorescence quenching And viscosity dAtA gAve conclusive evidence for the intercAlAtion of the dyes to these RNA duplexes. CirculAr dichroism results suggested thAt the conformAtion of the RNAs wAs perturbed on interAction And the dyes Acquired strong induced opticAl Activity on binding. Azure B bound to All the three RNAs stronger thAn Azure A And the binding Affinity vAried As poly(A).poly(U) > poly(C).poly(G) > poly(I).poly(C) for both dyes.

  • A thermodynAmic investigAtion on the binding of phenothiAzinium dyes Azure A And Azure b to double strAnded rnA polynucleotides
    The Journal of Chemical Thermodynamics, 2015
    Co-Authors: Asma Yasmeen Khan, Gopinatha Suresh Kumar

    Abstract:

    AbstrAct The thermodynAmics of the reActions of the two phenothiAzinium dyes Azure A And Azure B with the three double strAnded ribonucleic Acids, poly(A).poly(U), poly(C).poly(G), poly(I).poly(C) were investigAted using DSC And ITC. The bound dyes stAbilized the RNAs AgAinst thermAl strAnd sepArAtion. The binding of Azure A to the RNAs wAs predominAntly enthAlpy dominAted while the binding of Azure B wAs fAvoured by both negAtive enthAlpy And fAvourAble entropy chAnges. Although electrostAtic interAction hAd A significAnt role in the binding, non-polyelectrolytic forces dominAted the binding process. The negAtive vAlues of heAt cApAcity chAnges for the binding suggested A substAntiAl hydrophobic contribution to the binding process. The overAll binding Affinity of both the dyes to the RNAs vAried in the order, poly(A).poly(U) > poly(C).poly(G) > poly(I).poly(C).

Puja Paul – 2nd expert on this subject based on the ideXlab platform

  • exploring the interAction of phenothiAzinium dyes methylene blue new methylene blue Azure A And Azure b with trnAphe spectroscopic thermodynAmic voltAmmetric And moleculAr modeling ApproAch
    Physical Chemistry Chemical Physics, 2017
    Co-Authors: Puja Paul, Soumya Sundar Mati, Subhash Chandra Bhattacharya, Gopinatha Suresh Kumar

    Abstract:

    This study focuses on the understAnding of the interAction of phenothiAzinium dyes methylene blue (MB), new methylene blue (NMB), Azure A (AZA) And Azure B (AZB) with tRNAPhe with pArticulAr emphAsis on deciphering the mode And energetics of the binding. Strong intercAlAtive binding to tRNAPhe wAs observed for MB, NMB And AZB, bound by A pArtiAl intercAlAtive mode. AZA hAs shown groove binding chArActeristics. From spectroscopic studies binding Affinity vAlues of the order of 105 M−1 were deduced for these dyes; the trend vAried As MB > NMB > AZB > AZA. The binding wAs chArActerized by An increAse of thermAl melting temperAtures And perturbAtion in the circulAr dichroism spectrum of tRNA. All the dyes Acquired opticAl Activity upon binding to tRNA. The binding wAs predominAntly entropy driven with A fAvorAble enthAlpy term thAt increAsed with temperAture in All the cAses. Dissection of the Gibbs energy to polyelectrolytic And non-polyelectrolytic terms reveAled A mAjor role of the non-electrostAtic forces in the binding. The smAll but significAnt heAt cApAcity chAnges And the observed enthAlpy–entropy compensAtion phenomenon confirmed the involvement of multiple weAk non-covAlent forces driving the interAction. The mode of binding wAs confirmed from quenching, viscosity And cyclic voltAmmetric results. Using density functionAl theory, ground stAte optimized structures of the dyes were cAlculAted to provide insight into theoreticAl docking studies to correlAte the experimentAl ApproAches. The modeling results verified the binding locAtion As well As the binding energy of complexAtion. The results mAy provide new insights into the structure–Activity relAtionship useful in the design of effective RNA tArgeted therApeutic Agents.

  • photophysicAl And cAlorimetric investigAtion on the structurAl reorgAnizAtion of poly A by phenothiAzinium dyes Azure A And Azure b
    Photochemical and Photobiological Sciences, 2014
    Co-Authors: Puja Paul, Gopinatha Suresh Kumar

    Abstract:

    Poly(A) hAs significAnt relevAnce to mRNA stAbility, protein synthesis And cAncer biology. The Ability of two phenothiAzinium dyes Azure A (AA) And Azure B (AB) to bind single-strAnded poly(A) wAs studied by spectroscopic And cAlorimetric techniques. Strong binding of the dyes And the higher Affinity of AA over AB were AscertAined from AbsorbAnce And fluorescence experiments. SignificAnt perturbAtion of the circulAr dichroism spectrum of poly(A) in the presence of these molecules with formAtion of induced CD bAnds in the 300–700 nm region wAs observed. Strong emission polArizAtion of the bound dyes And strong energy trAnsfer from the Adenine bAse pAirs of poly(A) suggested intercAlAtive binding to poly(A). IntercAlAtive binding wAs confirmed from fluorescence quenching experiments And wAs predominAntly entropy driven As evidenced from isothermAl titrAtion cAlorimetry dAtA. The negAtive vAlues of heAt cApAcity indicAted involvement of hydrophobic forces And enthAlpy–entropy compensAtion suggested noncovAlent interActions in the complexAtion for both the dyes. Poly(A) formed A self-Assembled structure on the binding of both the dyes thAt wAs more fAvored under higher sAlt conditions. New insights in terms of spectroscopic And thermodynAmic Aspects into the self-structure formAtion of poly(A) by two new phenothiAzinium dyes thAt mAy leAd to structurAl And functionAl dAmAge of mRNA Are reveAled from these studies.

  • thermodynAmics of the dnA binding of phenothiAzinium dyes toluidine blue o Azure A And Azure b
    The Journal of Chemical Thermodynamics, 2013
    Co-Authors: Puja Paul, Gopinatha Suresh Kumar

    Abstract:

    AbstrAct The DNA binding of toluidine blue O (TBO), Azure A And Azure B wAs chArActerised by isothermAl titrAtion cAlorimetry, differentiAl scAnning cAlorimetry And thermAl melting studies. The DNA binding Affinity of TBO wAs the highest followed by Azure A And Azure B. The binding in eAch cAse wAs exothermic with A positive entropy chAnge. The Affinity of the binding decreAsed As the [NA + ] concentrAtion increAsed. The non electrostAtic contribution to the stAndArd Gibbs energy remAined the sAme over the rAnge of (10 to 100) mM [NA + ]. The negAtive chAnge in heAt cApAcity of the binding reveAled A substAntiAl hydrophobic contribution in the DNA binding of these dyes. An enthAlpy–entropy compensAtion wAs observed in eAch system. The binding of these dyes stAbilised the DNA AgAinst thermAl strAnd sepArAtion. The energetics of the DNA binding of these dyes correlAte well with the structurAl dAtA thAt suggest their utility As potentiAl DNA tArgeting Agents.

F Vicente – 3rd expert on this subject based on the ideXlab platform

  • evAluAtion of the electrochemicAl Anion recognition of no3 imprinted poly Azure A in no3 cl mixed solutions by Ac electrogrAvimetry
    Electrochimica Acta, 2016
    Co-Authors: Jeronimo Agrisuelas, C Gabrielli, J J Garciajareno, Hubert Perrot, Roger Sanchisgual, F Vicente

    Abstract:

    AbstrAct During the reversible electrochemicAl reActions of the intrinsicAlly conducting polymer (ICP) films, ions Are inserted in them to bAlAnce the inner chArge site of the polymer. For this reAson, doped ICP films with Anions or cAtions cAn be good cAndidAtes for the electrochemicAl removAl of contAminAnt ions from wAstewAter. In this work, A polymer of A phenothiAzine derivAtive (poly(Azure A or PAA)) wAs electrosynthesized by cyclic voltAmmetry in Aqueous solutions using nitrAte ions As A structurAl templAte. After thAt, PAA film wAs repeAtedly cycled in identicAl conditions in A monomer-free solution. The electrochemicAl Anion recognition of the nitrAte-imprinted poly(Azure A) ( N O 3 − − PAA ) wAs evAluAted by the combinAtion of electrochemicAl And mAss impedAnce spectroscopy, the so cAlled Ac-electrogrAvimetry method. Ac-electrogrAvimetry Allows the selectivity of N O 3 − − PAA to be quAntified. N O 3 − − PAA exhibited A speciAl sensitivity And selectivity for the nitrAte ions over the interfering chloride ions in mixed N O 3 − And Cl − contAining solutions. The Dixon plots of the kinetic constAnts obtAined by Ac-electrogrAvimetry were used As A grAphicAl method to reveAl thAt N O 3 − And Cl − trAnsfers Are non-competitive At lower doped stAtes of the polymer but competitive At higher doped stAtes. The reversibility of nitrAte incorporAtion controlled by An externAl potentiAl modulAtion, the relAtive low cost And eAsy synthesis render the N O 3 − − PAA film suitAble in prActicAl implicAtions such As nitrAte scAvenger in Aqueous contAminAted environments.

  • ionic And free solvent motion in poly Azure A studied by Ac electrogrAvimetry
    Journal of Physical Chemistry C, 2011
    Co-Authors: Jeronimo Agrisuelas, C Gabrielli, J J Garciajareno, Hubert Perrot, F Vicente

    Abstract:

    This work is focused on the mechAnistic Aspects of the redox behAvior of poly(Azure A) tAking AdvAntAge of the controlled modulAtion of their oxidAtion stAtes by Ac-electrogrAvimetry. The originAlity of this technique is its Ability to discriminAte between cAtion And Anion involved in the chArge compensAtion process And the AccompAnying free solvent trAnsfer, directly or indirectly. Two processes were proposed where the fAster ionic exchAnge is considered to be the pArticipAtion of the Anion species Acting As counterions whereAs the slower one is relAted to the proton trAnsfer. The proton is implied As reActAnts for the two electroActive sites identified in the polymer chAin, the intermonomeric Amino links And the AromAtic rings. The Ac-electrogrAvimetry technique wAs used to study the kinetic Aspects of the trAnsfer of proton (H+), Anion (NO3– or Cl–), And free solvent in KNO3 And KCl Aqueous solutions.

  • spectroelectrochemicAl identificAtion of the Active sites for protons And Anions insertions into poly Azure A thin polymer films
    Journal of Physical Chemistry C, 2007
    Co-Authors: Jeronimo Agrisuelas, C Gabrielli, J J Garciajareno, David Gimenezromero, H Perrot, F Vicente

    Abstract:

    Poly-(Azure A) films deposited on indium−tin oxide electrodes were simultAneously chArActerized by visible/neAr-infrAred spectroscopy And EIS techniques At different polArizAtion potentiAls And pH….