The behavior of the complexes of echinomycin with the DNA tetramers d(ACGT)2 and d(TCGA)2, in which the terminal AT base pairs are in either a Hoogsteen or a Watson-Crick conformation, has been explored by molecular dynamics taking into account experimental data from NMR studies (Gao and Patel. Biochemistry 1988,27,1744-1751). The DNA binding specificity of echinomycin appears to be the result ...

The discovery of uncommon DNA structures and speculation about their potential functions in genes has brought attention to specific DNA structure recognition. G-quadruplexes are four-stranded nucleic acid structures formed by G-rich DNA (or RNA) sequences. G-rich sequences with a high potential to form G-quadruplexes have been found in many important genomic regions. Porphyrin derivatives with ...

The double helix of DNA, when composed of dinucleotide purine-pyrimidine repeats, can adopt a left-handed helical structure called Z-DNA. For reasons not entirely understood, such dinucleotide repeats in genomic sequences have been associated with genomic instability leading to cancer. Adoption of the left-handed conformation results in the formation of conformational junctions: A B-to-Z juncti...

A coarse-grained lattice model of DNA oligonucleotides is proposed to investigate the general mechanisms by which single-stranded oligonucleotides hybridize to their complementary strands in solution. The model, based on a high-coordination cubic lattice, is simple enough to allow the direct simulation of DNA solutions, yet capturing how the fundamental thermodynamic processes are microscopical...

The different triplet sequences in high molecular weight aromatic copolyimides comprising pyromellitimide units ("I") flanked by either ether-ketone ("K") or ether-sulfone residues ("S") show different binding strengths for pyrene-based tweezer-molecules. Such molecules bind primarily to the diimide unit through complementary π-π-stacking and hydrogen bonding. However, as shown by the magnitude...

Reaction between LiH and the A(n)B(n-1)O(3n) cation deficient perovskite phases Ba(5)Nb(4)O(15), Ba(6)TiNb(4)O(18) and Ba(3)LaNb(3)O(12) proceeds by reductive lithium insertion, leading to the formation of Ba(5)LiNb(4)O(15), Ba(6)LiTiNb(4)O(18) and Ba(3)LaLiNb(3)O(12) respectively. During lithium insertion into Ba(5)Nb(4)O(15) and Ba(6)TiNb(4)O(18) the respective ccchh and cccchh stacking seque...

A regular right part grammar (RRPG) is a context-free grammar, in which right parts of productions are finite automata to extend the descriptive power of context-free grammar by including notations for describing repetitions and alternations [6,8]. On LR parsing of RRPGs, extra work is required to identify the left end of a handle at reduction time because a nonterminal can derive potentially i...

The low-energy electronic properties of a few graphite layers with AA and ABC stacking under application of the electric field (F), perpendicular to the layers, are explored through the tight-binding model. They strongly depend on the interlayer interactions, the stacking sequences, the layer numbers, and the field strength. In the absence or presence of F, the AA-stacked N-layer graphites (N 1...