Ant re-annealing of DNA is always be un-avoided. However the present study indicates that some degree of re-annealing occurrence together with helix-coil transitions has not affected the overall binding activity of the methylxanthines. Indeed it helped us to study the binding activity of MedChemExpress AZP-531 methylxanthines from double helical form of DNA to its denaturing state and enabled to derive and compare the increased binding activity of methylxanthines without changing the transition environment. This is mainly because of the fact that the binding activity of methylxanthines originally refereed to the double helical DNA would be invalid and may not that ease orFigure 7. Helix-coil transition analysis, Tm-profile. (A). UV spectra of Tm-DNA in the presence of methylxanthines at P/D 6. (B). A representative picture indicating the percentage of increased binding activity of methylxanthines with Tm-DNA at P/D 6. X1-theophylline, X2theobromine and X3-caffeine. Values are mean 6 SE with p,0.002 vs control. doi:10.1371/journal.pone.0050019.gInteraction of methylxanthines during helix-coil transitions of DNA by Tm/pH melting profilesInteraction of methylxanthines was studied during helix-coil transition of DNA, using higher temperature and pH as described in the methods section. The absorbance spectrum of heat melted DNA in the presence of drugs at varying P/D ratios was compared with heat melted free DNA (without drugs) and double helical (non-heat melted) DNA. Tm melting profile showed a significant increase of 24?0 in binding activity of methylxanthines (P/D 6) with DNA during helix-coil transition state rather than to a native double helical structure or in AZP-531 site absence of any helix-coil transitions (Figs. 7A ).Methylxanthines Binding with DNAFigure 8. Helix-coil transition analysis, pH melting profile. (A). pH melting profile of calf thymus DNA in 10 mM NaCl, 25 mM EDTA, produced by adding ml aliquots of 1M NaOH. pH melting curves of calf thymus DNA, which was preincubated with theophylline (X1) (B), theobromine (X2) (C) and Caffeine (X3) (D) at P/D 3 and 6. doi:10.1371/journal.pone.0050019.greliable to compare and derive its increased binding activity in the case of pure form of single stranded DNA environment. Thus the understanding of nucleic acid structure and their interactions with small molecule drugs as evinced by above methods gain importance mainly because of targeting drugs of our interest could easily modulate the expression of nucleic acids functions. As these naturally occurring methylxanthines are the derivatives of xanthines and/or base analogs of purine 1407003 nucleotides, the present study accentuated for its interaction with DNA both in the presence and absence of divalent metal ions or during helixcoil transitions depicting a platform for the development of methylxanthines as co-enhancers for targeted drug delivery and therapeutic innovations.AcknowledgmentsWe thank Prof. N. Yathindra, Dept. of Biophysics, University of Madras, Chennai 600025, India for providing the Varian, Cary, 1E UV/visible spectrophotometer facility. We are indebted to Dr. S.M.S. Kumar Felix and Dr. Mohan for their timely help to get the methylxanthines from Sigma, USA. We acknowledge the Sophisticated Analytical Instruments Facility at the Indian Institute of Technology Madras, Chennai, India for assistance in FTIR spectroscopy.Author ContributionsConceived and designed the experiments: IMJ HP RM. Performed the experiments: IMJ HP RM. Analyzed the data: IMJ HP JP RR RM.Ant re-annealing of DNA is always be un-avoided. However the present study indicates that some degree of re-annealing occurrence together with helix-coil transitions has not affected the overall binding activity of the methylxanthines. Indeed it helped us to study the binding activity of methylxanthines from double helical form of DNA to its denaturing state and enabled to derive and compare the increased binding activity of methylxanthines without changing the transition environment. This is mainly because of the fact that the binding activity of methylxanthines originally refereed to the double helical DNA would be invalid and may not that ease orFigure 7. Helix-coil transition analysis, Tm-profile. (A). UV spectra of Tm-DNA in the presence of methylxanthines at P/D 6. (B). A representative picture indicating the percentage of increased binding activity of methylxanthines with Tm-DNA at P/D 6. X1-theophylline, X2theobromine and X3-caffeine. Values are mean 6 SE with p,0.002 vs control. doi:10.1371/journal.pone.0050019.gInteraction of methylxanthines during helix-coil transitions of DNA by Tm/pH melting profilesInteraction of methylxanthines was studied during helix-coil transition of DNA, using higher temperature and pH as described in the methods section. The absorbance spectrum of heat melted DNA in the presence of drugs at varying P/D ratios was compared with heat melted free DNA (without drugs) and double helical (non-heat melted) DNA. Tm melting profile showed a significant increase of 24?0 in binding activity of methylxanthines (P/D 6) with DNA during helix-coil transition state rather than to a native double helical structure or in absence of any helix-coil transitions (Figs. 7A ).Methylxanthines Binding with DNAFigure 8. Helix-coil transition analysis, pH melting profile. (A). pH melting profile of calf thymus DNA in 10 mM NaCl, 25 mM EDTA, produced by adding ml aliquots of 1M NaOH. pH melting curves of calf thymus DNA, which was preincubated with theophylline (X1) (B), theobromine (X2) (C) and Caffeine (X3) (D) at P/D 3 and 6. doi:10.1371/journal.pone.0050019.greliable to compare and derive its increased binding activity in the case of pure form of single stranded DNA environment. Thus the understanding of nucleic acid structure and their interactions with small molecule drugs as evinced by above methods gain importance mainly because of targeting drugs of our interest could easily modulate the expression of nucleic acids functions. As these naturally occurring methylxanthines are the derivatives of xanthines and/or base analogs of purine 1407003 nucleotides, the present study accentuated for its interaction with DNA both in the presence and absence of divalent metal ions or during helixcoil transitions depicting a platform for the development of methylxanthines as co-enhancers for targeted drug delivery and therapeutic innovations.AcknowledgmentsWe thank Prof. N. Yathindra, Dept. of Biophysics, University of Madras, Chennai 600025, India for providing the Varian, Cary, 1E UV/visible spectrophotometer facility. We are indebted to Dr. S.M.S. Kumar Felix and Dr. Mohan for their timely help to get the methylxanthines from Sigma, USA. We acknowledge the Sophisticated Analytical Instruments Facility at the Indian Institute of Technology Madras, Chennai, India for assistance in FTIR spectroscopy.Author ContributionsConceived and designed the experiments: IMJ HP RM. Performed the experiments: IMJ HP RM. Analyzed the data: IMJ HP JP RR RM.
