Studies On The Properties Of Nonnormal Nucleotide Base Pairs

The functions of DNA are vital for inheritance,coding for proteins and the genetic blueprint of life.With the self-assembled structure,the DNA double helix is very stable and provides potential for nanotechnological molecular-wires. However,oxidative and radiation damage from the surrounding environment may bring about significant changes in the geometry of the base pair and overall shape of the DNA strand.Then cell death or even human lesions may happen if these damaged bases are unrepaired or incorrectly repaired.Moreover,metal counter-ions may also have an impact on DNA conformation by neutralizing the charged phosphate backbone or artificial modification for special applications. My thesis addresses the effects of the metal counter-ions,oxidation and radiation damage,size-expanded modification of DNA properties,and discusses possible practical implications of our findings.Some significant progresses have been made,which can be described as follows:1.The effects of metal ion binding on the ^2hJ_NN-coupling andδ(¹H)/Δδ(¹⁵N) chemical shifts of N-H...N H-bond units in internucleotide base pairs were explored by a combination of density functional theory calculations and molecular dynamics(MD) simulations.Results indicate that the NMR parameters vary considerably upon cation binding to the natural G-C or A-T base pairs,and thus can be used to identify the status of the base pairs,if cation-perturbed.The basic trend is that cation perturbation causes ^2hJ_NN to increase,Δδ(¹⁵N) to decrease,andδ(¹H) to shift upfield for G-C,and in the opposite directions for A-T.The magnitudes of variation are closely related to the Lewis acidity of the metal ions. For both base pair series(M^z+GC and M^z+AT),these NMR parameters are linearly correlated among themselves.Their values depend strongly on the energy gaps (ΔE_{LP→σ^*}) and the second-order interaction energies(E(2)) between the donor N lone-pair(LP_N) and the acceptorσ_N-H^* localized NBO orbitals.In addition,the ^2hJ_NN changes are also sensitive to the amount of charge transfer from LP_N toσ_N-H^* NBOs or from the purine to the pyrimidine moieties.The different trends are a consequence of the different H-bond patterns,and thus the different charge transfer directions in the cationized M^z+ AT series,M^z+←A→T,and the cationized M^z+GC series,M^z+←G←C.The predicted cation-induced systematic trends of ^2hJ_NN andδ(¹⁵N,¹H) in N-H...N H-bond units may provide a new approach to the determination of H-bond structure and strength in Watson-Crick base pairs,and provide an alternative probe of the heterogeneity of DNA sequences.2.On the basis of the ¹⁵N NMR HN-COSY method,NMR parameters including intemucleotide ^2hJ_NN spin-spin couplings and chemical shifts(δ(¹H) andΔδ(¹⁵N)) of N-H...N H-bond units in natural and damaged base pairs(viz., mismatched pairs,GC^·- and GC^·+ radicals,dehydrogenated and deprotonated G-C pairs) were predicted using the appropriated density functional theory calculations with a large basis set.For those damaged base pairs,their ^2hJ_NN,δ(¹H) andΔδ(¹⁵N) associated the N-H...N H-bond pattern are considerably different from those of the natural canonical G-C and A-T,and may be taken as the important indexed for prejudging if G-C and A-T are damaged.Similar with the results in above work,detailed NBO analysis shows that ^2hJ_NN couplings are strongly interrelated with the energy gaps(ΔE_{LP→σ^*}) between the donor N lone-pair(LP_N) and the acceptorσ_N-H^* localized NBO orbitals,and also are sensitive to the electron density distributions over theσ_(N-H)^* orbital,indicating that ^2hJ_NN couplings across the N-H...N H-bonds are charge-transfer-controlled.This is well supported by variation of the electrostatic potential surfaces and corresponding charge transfer amount between G and C moieties.The present data indicate that measurements of NMR parameters associated with the N-H...N H-bond may be used to discriminate between natural G-C pair and the radiation-damaged G-C pairs.3.Considering homo/hetero ring-expanded DNA analogues are rationally-modified DNA motifs with improved physical or biological properties, the stability of these artificial DNA base pairs was examined with regard to three aspects associated with DNA damage;namely deprotonation,H-abstraction and H^·-radical addition using density functional theory.The effect of size-expansion on C8 activity was investigated because C8-oxidative guanine(G) is one of the most important products of DNA damage.Computational results indicate that the insertion of an aromatic spacer ring in G considerably decreases the electron density over the C8 site,leading to easier deprotonation or H-abstraction from the C8 site and more difficult H^·-radical attack on the C8 site.However,the opposite phenomenon is observed if the spacer ring is antiaromatic,because of the increased electron density over the C8 site.Moreover,these effects are more prominent the larger the aromaticity or antiaromaticity of the spacer ring. Further analyses,using natural bond orbitals and the nucleus-independent chemical shift index of aromaticity,indicate that the changes of the electron distribution over the C8 site arise because the aromatic spacer ring,involved in conjugation structure,increases the electron delocalization from the electron-rich imidazole ring to the diatropic six-membered rings,while the antiaromatic spacer ring acts as an electron-donating group,not only inhibiting the above electron delocalization,but also slightly increasing the electron density over the C8 site. The improved stability of these size-expanded bases pairs in different DNA-damaged environments may encourage their use in practical applications.4.Electron hole(radical cation) migration in rationally-designed size-expanded DNAs(named sDNA here),where the quantum transport of an injected charge is coupled with the double proton transfer in isolated sGC pair,is described here.Classical molecular dynamics simulations in conjunction with large-scale density functional theory calculations reveal that the distribution of highest occupied molecular orbital(HOMO) in size-expanded duplex sDNA is similar with that in B-form DNA,that is,the HOMO of stacked 5'-sGTsGsGsG-3' sequence is especially high in energy and largely localized on the 5'-sG of the sGsGsG triplet,with no HOMO at the single sG base.As a consequence, one-electron oxidation and electrophilic attacks are favored at the 5'-sG site of the sGsGsG triplet as that in natural DNA duplex.It is also demonstrated that a charge sink from the sGsGsG triplet can be created by modification of the isolated sG base(viz.,double proton transfer in the isolated sGC pair induces correlated changes in the special distribution of the hole,with concomitant charge transport along the sDNA double helix).The ion potential(IP) energy of the sG tautomer generated by double proton transfer is lower than that of an isolated sG,thus making the site an effective hole trap.The charge sink phenomenon in sDNA matches very well with theoretical and experimental research for the double proton coupled charge transfer in natural DNA base pairs(Gervasio et al.Angew. Chem.Int.Ed.2006,45,5606),implying that the charge can hop reversibly between all size-expanded guanines in sDNA sequences containing isolated sGC sites between the source and sink.Moreover,future detailed calculation results show that the proton transfer activity energies(Ea) as well as IPs of the sGC base pairs are lower than those of natural G-C base pair.That means the double proton coupled charge transfer in size-expanded DNAs is easier than that in natural DNA double helix.Double proton coupled proton transfer discussed here provide a new evidence that the size-expanded DNA double helix can also mediates charge transport over a distance.Associated with the fact that the size-expanded DNAs have strongerÏ€-Ï€stacking interactions and lower HOMO-LUMO gaps than natural DNAs,it can be concluded that size-expanded DNAs could be a good plausible candidate for molecular-wire application,which is not directly accessible to experimental probes.