Comparative studies between hydrated hydrogen bonded and stacked DNA base pair

Sivanesan, D.; Sumathi, I; Welsh, William J.

doi:10.1016/s0009-2614(02)01704-9

Cited by 54 publications

(49 citation statements)

References 25 publications

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“…They also concluded that up to 6 water molecules are needed to solvate the GC base pair. 91 In (AT‚5H 2 O) and (AT‚5H 2 O) -, the planes of some water molecules are nearly vertical to the AT ring plane ( Figure 1). Further, three water molecules W1, W2, and W3 are linked to each other by hydrogen bonds on the major groove side, whereas the other two water molecules (W4 and W5) are located on the minor groove side ( Figure 1).…”

Section: Resultsmentioning

confidence: 99%

Adiabatic Electron Affinities of the Polyhydrated Adenine−Thymine Base Pair: A Density Functional Study

2005

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Adiabatic electron affinities (AEAs) of the adenine-thymine (AT) base pair surrounded by 5 and 13 water molecules have been studied by density functional theory (DFT). Geometries of neutral AT x nH2O and anionic (AT x nH2O)- complexes (n = 5 and 13) were fully optimized, and vibrational frequency analysis was performed at the B3LYP/6-31+G** level of theory. The optimized structures of the neutral (AT x nH2O) and (AT x nH2O)- complexes were found to be somewhat nonplanar. Some of the water molecules are displaced away from the AT ring plane and linked with one another by hydrogen bonds. The optimized structures of the complexes are found to be in a satisfactory agreement with the observed experimental and molecular dynamics simulation results. In the optimized anionic complexes, the thymine (T) moiety was found to be puckered, whereas the adenine (A) moiety remained almost planar. Natural population analysis (NPA) performed using the B3LYP/6-31+G** method shows that the thymine moiety in the anionic (AT x nH2O)- complexes (n = 5 and 13) has most of the excess electronic charge, i.e., approximately -0.87 and approximately -0.81 (in the unit of magnitude of the electronic charge), respectively. The zero-point energy corrected adiabatic electron affinities of the hydrated AT base pair were found to be positive both for n = 5 and 13 and have the values of 0.97 and 0.92 eV, respectively, which are almost three times the AEA of the AT base pair. The results show that the presence of water molecules appreciably enhances the EA of the base pair.

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Section: Resultsmentioning

confidence: 99%

Adiabatic Electron Affinities of the Polyhydrated Adenine−Thymine Base Pair: A Density Functional Study

2005

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“…In π-stacked quadruply H-bonded dimers of ureidopyrimidone, π-stacking was observed to strengthen the hydrogen bonds by increasing charge-transfer between H-bonded partners (44). Electrostatics based studies on hydrated DNA base pairs show that the stacked base pairs hydrate better than the corresponding H-bonded base pairs (45). Apart from the fact that more binding sites for water molecules are present in the stacked conformation, the most negative values of the MEP show up in the stacked conformations in contrast to the H-bonded ones.…”

Section: Introductionmentioning

confidence: 99%

Influence of the - interaction on the hydrogen bonding capacity of stacked DNA/RNA bases

Mignon

Loverix²,

Steyaert³

et al. 2005

Nucleic Acids Research

228

157

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The interplay between aromatic stacking and hydrogen bonding in nucleobases has been investigated via high-level quantum chemical calculations. The experimentally observed stacking arrangement between consecutive bases in DNA and RNA/DNA double helices is shown to enhance their hydrogen bonding ability as opposed to gas phase optimized complexes. This phenomenon results from more repulsive electrostatic interactions as is demonstrated in a model system of cytosine stacked offset-parallel with substituted benzenes. Therefore, the H-bonding capacity of the N3 and O2 atoms of cytosine increases linearly with the electrostatic repulsion between the stacked rings. The local hardness, a density functional theory-based reactivity descriptor, appears to be a key index associated with the molecular electrostatic potential (MEP) minima around H-bond accepting atoms, and is inversely proportional to the electrostatic interaction between stacked molecules. Finally, the MEP minima on surfaces around the bases in experimental structures of DNA and RNA–DNA double helices show that their hydrogen bonding capacity increases when taking more neighboring (intra-strand) stacking partners into account.

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“…Despite that there exist a number of literatures reporting experimental and theoretical findings on these interactions, [32][33][34][35][36][37][38][39][40][41][42] the natures of delocalized vibrational excitons in base pairs and DNA oligomers have not been fully understood nor described in terms of vibrational basis modes. Despite that there exist a number of literatures reporting experimental and theoretical findings on these interactions, [32][33][34][35][36][37][38][39][40][41][42] the natures of delocalized vibrational excitons in base pairs and DNA oligomers have not been fully understood nor described in terms of vibrational basis modes.…”

Section: Introductionmentioning

confidence: 99%

Vibrational dynamics of DNA. I. Vibrational basis modes and couplings

Lee

Park²,

Cho³

2006

The Journal of Chemical Physics

104

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Carrying out density functional theory calculations of four DNA bases, base derivatives, Watson-Crick (WC) base pairs, and multiple-layer base pair stacks, we studied vibrational dynamics of delocalized modes with frequency ranging from 1400 to 1800 cm(-1). These modes have been found to be highly sensitive to structure fluctuation and base pair conformation of DNA. By identifying eight fundamental basis modes, it is shown that the normal modes of base pairs and multilayer base pair stacks can be described by linear combinations of these vibrational basis modes. By using the Hessian matrix reconstruction method, vibrational coupling constants between the basis modes are determined for WC base pairs and multilayer systems and are found to be most strongly affected by the hydrogen bonding interaction between bases. It is also found that the propeller twist and buckle motions do not strongly affect vibrational couplings and basis mode frequencies. Numerically simulated IR spectra of guanine-cytosine and adenine-thymine bases pairs as well as of multilayer base pair stacks are presented and described in terms of coupled basis modes. It turns out that, due to the small interlayer base-base vibrational interactions, the IR absorption spectrum of multilayer base pair system does not strongly depend on the number of base pairs.

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Comparative studies between hydrated hydrogen bonded and stacked DNA base pair

Cited by 54 publications

References 25 publications

Adiabatic Electron Affinities of the Polyhydrated Adenine−Thymine Base Pair: A Density Functional Study

Adiabatic Electron Affinities of the Polyhydrated Adenine−Thymine Base Pair: A Density Functional Study

Influence of the - interaction on the hydrogen bonding capacity of stacked DNA/RNA bases

Vibrational dynamics of DNA. I. Vibrational basis modes and couplings

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