Molecular models of DNA

About: Molecular models of DNA is a research topic. Over the lifetime, 300 publications have been published within this topic receiving 16805 citations.

Thermodynamics and kinetics of DNA-protein interactions from single molecule force spectroscopy

Abstract: The process of replication requires the cooperation of many proteins which associate with each other at the replication fork to form a highly efficient replication machine. Bacterium E. coli and bacteriophages that infect it (T4 and T7) have been used extensively in molecular biology research and provide excellent model systems for analyzing the DNA replication. In this work we use single DNA molecule stretching to investigate the degree of alteration in the structure and stability of DNA in the presence of DNA binding proteins which help us to quantify thermodynamics and kinetics of protein-protein and protein-nucleic acid interactions and obtain new insights into the function of proteins in these specific biological system. Because the nature of the overstretching transition in DNA stretching experiments continues to generate controversy we have undertaken studies of DNA stretching in the presence of glyoxal to solve this dilemma which brought new evidence in favor of force-induced melting theory against the alternative S-DNA model. One of the classic paradigms of single-stranded DNA binding proteins is bacteriophage T7 gene 2.5 protein (gp2.5), known to have essential roles in DNA replication and recombination in phage-infected cells by binding preferentially to single-stranded DNA and establishing electrostatic interactions with other proteins, recruiting them at the site of the ssDNA and regulating their activity. Varying solution conditions and the pulling dynamics, we could obtain binding affinities to single- and double-stranded DNA for gp2.5 and its deletion mutant lacking 26 C-terminal residues, gp2.5-Δ26C, over a range of salt concentration not available to ensemble studies. We also

DNA Computer Principle,Advances and Difficulties (III):The Structure and Character of “Data” in DNA Computing

Abstract: Biomolecular computing,including DNA computing,RNA computing and protein computing,is a kind of computing mode of information processing whose “data” is biomolecule.In addition,the biomolecular computing mode using PNA molecule as “data” was presented.This paper does not discuss PNA computing,RNA computing and protein computing because their research results are less.Clearly,it is a foundation problem to know well the structure and character of the “data”(that is DNA molecules)in DNA computing.So,this paper mainly discusses the structure and characters of several type of DNA molecule.We usually adopt different DNA molecule for different problem or models.Now,the main kinds of DNA molecules used in DNA computing are single,double and sticker terminal DNA molecules.Secondly,the DNA molecules used in DNA computing have also hairpin DNA molecules and plasmid DNA molecule.Especially,the relationship between the “data”(DNA molecule)and corresponding biomolecular model is disscuss.

Generating Crystallographic Models of DNA Dodecamers from Structures of RNase H:DNA Complexes.

Abstract: The DNA dodecamer 5'-d(CGCGAATTCGCG)-3' is arguably the best studied oligonucleotide and crystal structures of duplexes with this sequence account for a considerable portion of the total number of oligo-2'-deoxynucleotide structures determined over the last 30 years. The dodecamer has commonly served as a template to analyze the effects of sequence on DNA conformation, the conformational properties of chemically modified nucleotides, DNA-ligand interactions as well as water structure and DNA-cation binding. Although molecular replacement is the phasing method of choice given the large number of available models of the dodecamer, this strategy often fails as a result of conformational changes caused by chemical modification, mismatch pairs, or differing packing modes. Here, we describe an alternative approach to determine crystal structures of the dodecamer in cases where molecular replacement does not produce a solution or when crystals of the DNA alone cannot be grown. It is based on the discovery that many dodecamers of the above sequence can be readily co-crystallized with Bacillus halodurans RNase H, whereby the enzyme is unable to cleave the DNA. Determination of the structure of the complex using the protein portion as the search model yields a structural model of the DNA. Provided crystals of the DNA alone are also available, the DNA model from the complex then enables phasing their structures by molecular replacement.