The specific folding pattern and function of RNA molecules lies in various weak interactions, in addition to the strong base-base pairing and stacking. One of these relatively weak interactions, characterized by the stacking of the O4' atom of a ribose on top of the heterocycle ring of a nucleobase, has been known to occur but has largely been ignored in the description of RNA structures. We id...

A variable temperature-dependent H NMR conformational analysis of JHH coupling constants and NOE enhancements of a series of 8-aza-3-deaza modified guanine nucleosides 2 and 4–8 has been performed in DMSO-d6 and the results compared to those for natural nucleosides dG (1) and G (3). 8-Aza-3-deaza nucleobase modification leads to the stabilization of N-type conformers by ∆∆H of 3.1 kJ mol , whic...

In the ribozyme from the hepatitis delta virus (HDV) genomic strand RNA, a cytosine side chain is proposed to facilitate proton transfer in the transition state of the reaction and, thus, act as a general acid-base catalyst. Mutation of this active-site cytosine (C75) reduced RNA cleavage rates by as much as one million-fold, but addition of exogenous cytosine and certain nucleobase or imidazol...

DNA oxidation by reactive oxygen species is nonrandom, potentially leading to accumulation of nucleobase damage and mutations at specific sites within the genome. We now present the first quantitative data for sequence-dependent formation of structurally defined oxidative nucleobase adducts along p53 gene-derived DNA duplexes using a novel isotope labeling-based approach. Our results reveal tha...

Nucleobase modifications dramatically alter nucleic acid structure and thermodynamics. 2-thiouridine (s(2)U) is a modified nucleobase found in tRNAs and known to stabilize U:A base pairs and destabilize U:G wobble pairs. The recently reported crystal structures of s(2)U-containing RNA duplexes do not entirely explain the mechanisms responsible for the stabilizing effect of s(2)U or whether this...

Recent studies have considerably clarified the mechanism ofhydrolysis of ribonucleic acids (RNA) by pancreatic ribonuclease and by spleen phosphodiesterase. Digestion ofRNA with ribonuclease results in the splitting of all pyrimidine-pyrimidine internucleotidic links and of those pyrimidine-purine internucleotidic links which involve C(3w) of the pyrimidine nucleotide (Schmidt et al. 1951; Mark...

We propose a DNA sequencing scheme based on silicene nanopores. Using first principles theory, we compute the electrical properties of such pores in the absence and presence of nucleobases. Within a two-terminal geometry, we analyze the current-voltage relation in the presence of nucleobases with various orientations. We demonstrate that when nucleobases pass through a pore, even after sampling...

In this contribution several new coordination compounds on the basis of cadmium(II) thio- and selenocyanate with pyrimidine as co-ligand were prepared and investigated for their structural, thermal and spectroscopic properties. The reaction of cadmium(II) thiocyanate with pyrimidine leads to the formation of four compounds, which from a structural point of view are closely related. In the most ...