Ionic Interactions Between PT-DNA And Organic Cation

Phosphorothioated DNA(PT-DNA),a non-bridging phosphate oxygen atom substituted by sulfur atom on DNA backbone structure,is widespread among a variety of bacterial species.As a unique type of natural DNA modification,DNA phosphorothioation confers the bacteria both antioxidant activity and protection itself from exogenous DNA by a restriction-modification(R-M)system.It has been reported that positivelycharged side-chain of lysine residue forms ion-pairs with anionic phosphorothioate group in PT-DNA-protein complexation,which increases entropy change during the molecular recognition.In particular,the Dnd FGH restriction systems in E.coli HST04 and E.coli B7 A dnd BCDE-deficient mutant WXY-1 are thermoregulated under 15-37?.However,thermodynamic parameters of this temperature-dependent intermolecular recognition are not elucidated yet.In this work,an interdisciplinary approach including molecular spectroscopy,mathematical modeling,and molecular simulations are used to understand subtle changes caused by PT-modification in the interactions between PT-DNA and cation.First,an organic cation TMP [5,10,15,20-Tetra-(N-methyl-4-pyridyl)porphyrin] was chose as an optical probe to detect interacting spectroscopy of 10-mer oligonucleotides and the cation.Thereafter,the multivariate analysis method(MCR-ALS)was used to extract concentration profiles from spectroscopic data,and then the hostmultiguest Mc Ghee-Von Hippel cooperative model was used to calculate binding constants for the four different PT-DNA double-stranded systems,thus enthalpic and entropic changes were derived during the interaction between PT-DNA and cation.As a result,compared with normal DNA,entropic change increases by 8.6 J/(mol·K)while enthalpic change decreases by 2.6 k J/mol.Therefore,the enthalpy-entropy balance point for the interactions between PT-DNA and cation is about 302 K(i.e.29 ?),which locates in range of 4-60 ? as the ambient temperature for most of microbes.The findings are in good agreement with thermoregulation,indicating that PT-modification could be a thermal regulator during molecular recognition.Then molecular docking and molecular dynamics simulation are employed to analyze Rp and Sp chiral-specificity of PT-DNA during the interactions.According to calculations,local micro-environment around the PT site enhance desolvation,which may be accounted for the entropic change.Moreover,TMP molecules cluster in the minor groove of doublestrand PT-DNA in molecular docking.Natural Rp-phosphorothioation seems to allow abundant TMP orientations that can contribute higher entropic change.However,the ion-pair interactions unlikely distinguishes the chiralspecificity of PT-DNA.Take it together,the structural information from NMR and crystallization data provides a good chance to understand physiochemical origin of molecular recognitionbetween PT-DNA and protein.In this work,thermodynamic parameters have been carefully measured and the thermoregulation has been interpreted at the molecular level for temperature-dependent R+-M+ bacteria.Our findings indicate that PTmodification is able to serve as a thermo-controller in the functional selfprotection of bacteria,while more detailed microscopic mechanism for the thermo-regulating process still needs further investigation.