This study investigates the effect of Mg(2+) bound to the DNA major groove on DNA structure and dynamics. The analysis of a comprehensive dataset of B-DNA crystallographic structures shows that divalent cations are preferentially located in the DNA major groove where they interact with successive bases of (A/G)pG and the phosphate group of 5'-CpA or TpG. Based on this knowledge, molecular dynam...

potential relationships between amino acid motifs in the antigen binding groove of various alleles of the bovine major histocompatibility complex dr (bola-dr) molecule and peripheral blood mononuclear cell (pbmc) proliferation, in response to s. aureus and phytohemaglutinin, were investigated. the animals included in the study were approximately of the same age and comprised of pure holstein-fr...

Upon interaction with calf thymus DNA the ∆,∆-enantiomer of the semirigid binuclear ruthenium complex [μ-(11,11’-bidppz)(phen)4Ru2] has previously been shown to reorganize, from an initial groove bound geometry, into an intercalative binding mode, threading one of its bulky Ru(phen)2 moieties through the core of the DNA. We have now found that all three stereoisomers, ∆,∆, Λ,Λ, and ∆,Λ (meso), ...

Cationic calix[6]arene and calix[4]arene derivatives non-covalently bind into a DNA minor groove or RNA major form tweezer-like complexes with nucleotides.

RNA 5-methyl and 5-propynyl pyrimidine analogs were substituted into short interfering RNAs (siRNAs) to probe major groove steric effects in the active RNA-induced silencing complex (RISC). Synthetic RNA guide strands containing varied combinations of propynyl and methyl substitution revealed that all C-5 substitutions increased the thermal stability of siRNA duplexes containing them. Cellular ...

DNA sequence-dependent conformational changes induced by the minor groove binder, distamycin, have been evaluated by polyacrylamide gel electrophoresis. The distamycin binding affinity, cooperativity, and stoichiometry with three target DNA sequences that have different sizes of alternating AT sites, ATAT, ATATA, and ATATAT, have been determined by mass spectrometry and surface plasmon resonanc...

Zinc finger proteins of the Cys2His2 class are DNA sequence-specific transcription factors. Previous structural studies of zinc finger protein-DNA complexes have shown that amino acids in the finger tip and alpha-helix regions within individual finger domains make base-specific contacts with the major groove of DNA. The nine finger protein transcription factor IIIA (TFIIIA) from Xenopus oocytes...

The crystal structure of [d(CGCAAATTTGCG)]2 has been determined to 1.5 A resolution, representing the first high-resolution structure of this DNA fragment. The ion interactions are novel. A spermine molecule replaces a Mg2+ observed in analogous structures. Unlike lower-resolution structures, the minor groove is narrow and the major groove lacks extra Watson-Crick hydrogen bonds. In addition, a...