fmbpt submitted, created time 1 year 3 months (pubs.acs.org)

Recently, Vakonakis and LiWang reported experimental evidence for stronger hydrogen bonds in RNA A:U than in DNA A:T base pairs. This conclusion is based on the observation that the deuterium isotope effect for H/D substitution at H3 of the pyrimidine base on the chemical shift of the adenine C2 atom is larger for A:U than for A:T. Such an isotope effect had previously been connected to hydroxyl torsional frequencies of intramolecularly hydrogen-bonded systems and empirical hydrogen-bond strengths

2 comments | Blog It | Email It | Keywords: hydrogen bonds hydrogen-bonded networks Watson-Crick base pairs RNA-DNA hybrid stability RNA, DNA,GENE NMR Hydrogen Density functional calculations DNA structure Computer silmulations

fmbpt submitted, created time 1 year 3 months (www3.interscience.wiley.com)

The hydrogen bond in DNA base pairs is, at variance with widespread belief, not a pure or essentially electrostatic phenomenon. Instead, as follows from our quantum chemical analyses, it has a substantial charge-transfer character caused by donor–acceptor orbital interactions (between O or N lone pairs and N-H sigma* acceptor orbitals) that are of the same order of magnitude as the electrostatic term. Polarization in the pi-electron system (i.e., "resonance assistance") provides an additional stabilizing term

1 comment | Blog It | Email It | Keywords: Molecular interactions Base-pairing similarities Charge transfer Density functional calculations DNA structures Hydrogen bonds Resonance assistance Orbital interactions Electronic structure Watson-Crick base pairs

fmbpt submitted, created time 1 year 3 months (www3.interscience.wiley.com)

Based on state-of-the-art computer simulations, we show that it is possible to build a supramolecular nanoswitch, based on the DNA base pair GC, that can be chemically switched between three states that differ in hydrogen-bond strength (weak, intermediate, strong) and geometrical shape (e.g. , GC bending in-plane “up”, “not”, and “down”). The chemical switching involves deprotonation or protonation of hydroxy and amino substituents at guanine C8 and cytosine C6. This behavior has been shown to persist under microsolvation conditions.

Submit comment | Blog It | Email It | Keywords: nanoswitches supramolecular switches DNA structure hydrogen bonds computer simulation density functional calculations guanine-cytosine

fmbpt submitted, created time 1 year 3 months (pubs.acs.org)

The structure of the DNA double helix's basic units, the Watson-Crick base pairs, is investigated using state-of-the-art computer simulations. We examine the Watson-Crick bond strength and geometry and, in particular, how it is affected: (i) by substituents at the nitrogens involved in glycosidic bonding; (ii) by geometrical strain stemming from the backbone; (iii) by solvent water molecules; and (iv) by sodium counter ions.

Submit comment | Blog It | Email It | Keywords: DNA structure hydrogen bonds backbone counter ion molecular recognition molecules structure RNA Double Helix DNA structure crystal structure | structure-function a