Methylating agents introduce cytotoxic 1-methyladenine (1-meA) and 3-methylcytosine (3-meC) residues into nucleic acids, and it was recently demonstrated that the Escherichia coli AlkB protein and two human homologues, hABH2 and hABH3, can remove these lesions from DNA by oxidative demethylation. Moreover, AlkB and hABH3 were also found to remove 1-meA and 3-meC from RNA, suggesting that cellul...

It is well known that during homology recognition and strand exchange the double stranded DNA (dsDNA) in DNA/RecA filaments is highly extended, but the functional role of the extension has been unclear. We present an analytical model that calculates the distribution of tension in the extended dsDNA during strand exchange. The model suggests that the binding of additional dsDNA base pairs to the...

Homologous recombination is essential for the accurate repair of double-stranded DNA breaks (DSBs). Initially, RecBCD complex resects ends DSB into 3′ single-stranded on which a RecA filament assembles. Next, locates homologous template sister chromosome. Here we directly visualize DSBs in single cells, using high-throughput microfluidics and fluorescence microscopy. We find that, Escherichia c...

Yeast RAD51 gene functions in genetic recombination and DNA double-strand break repair. In vitro, in the presence of ATP and replication protein A, RAD51 protein pairs single-stranded DNA (ssDNA) with homologous double-stranded DNA (dsDNA) and catalyzes strand exchange between the synapsed DNA partners. Electron microscopic analyses show that RAD51 forms helical filaments on both ssDNA and dsDN...

The phage lambda-derived Red recombination system is a powerful tool for making targeted genetic changes in Escherichia coli, providing a simple and versatile method for generating insertion, deletion, and point mutations on chromosomal, plasmid, or BAC targets. However, despite the common use of this system, the detailed mechanism by which lambda Red mediates double-stranded DNA recombination ...

A phenomenological model based on the three-dimensional theory of nonlinear elasticity is developed to describe phenomenon overstretching in force-extension curve for double-stranded DNA (dsDNA). By using concept a material with multiple reference configurations single formula obtained fit curve.

The surface of an electrochemical glassy carbon electrode was modified with a layer of double-stranded DNA (dsDNA) or with double-stranded DNA conditioned in single-stranded DNA (ssDNA) and was used to investigate mitoxantrone-DNA interactions. Differential pulse and square wave voltammetry were applied to develop an electroanalytical procedure for the determination of mitoxantrone and evaluate...

Using the pulse injection method, single-stranded DNA and double-stranded plasmid DNA have been deposited on well-defined Cu(111) surfaces under ultrahigh vacuum (UHV ) conditions to obtain high-resolution scanning tunneling microscope (STM) images. These particular UHV-STM images have revealed that DNA molecules are adsorbed directly onto a clean Cu(111) surface and exhibited the detailed stru...

The basic regularity of chromatin substructure that has been reported in rat liver chromatin (Hewish & Burgoyne, 1973b) was also detected in mouse chromatin. The regular series of DNA fragments produced by the action of Ca-Mg endonuclease on rat chromatin were studied further. The smallest single-stranded class has a molecular weight of approx. 45000-63000 and the smallest double-stranded class...

Alternatives for sequencing of PCR products essentially fall into one of two categories; generation of single-stranded DNA for sequencing or the direct sequencing of double-stranded product. Of the two alternatives, sequencing of double-stranded PCR products is likely to be of greatest immediate significance in terms of general applicability and rapidity. Double-stranded sequencing allows the u...