Mediated Base Pairing in DNA

IV. METAL-MEDIATED BASE PAIRING IN DNA A. Basic Concept... 

Y. Miyake, H. Togashi, M. Tashiro, H. Yamaguchi, S. Oda, M. Kudo, Y. Tanaka, Y. Kondo, R. Sawa, T. Fujimoto, T. Machinami, A. Ono, Mercuryll-mediated formation of thymine-Hgll-thymine base pairs in DNA duplexes, J. Am. Chem. Soc. 128 (7) (2006) 2172-2173. 

Histones are small, basic proteins required to condense DNA into chromatin. They have been first described and named in 1884 by Albrecht Kossel. There are five main histones HI, H2A, H2B, H3 andH4. An octamer of core histones H2A, H2B, H3 andH4 is located inside a nucleosome, the central building block of chromatin, with about 150 base pairs of DNA wrapped around. The basic nature of histones, mediated by the high content of lysine and arginine residues, allows a direct interaction with the acidic phosphate back bone of DNA. The fifth histone HI is located outside at the junction between nucleosomes and is referred to as the linker histone. Besides the main histones, so-called histone variants are known, which replace core histones in certain locations like centromers. 

In many investigations of CT, pendant redox probes interact with both bases of abase pair. However, studies of base-base charge transfer can differentiate between discrete intra- and interstrand reactions (Fig. 7). These investigations further attest to the critical role of base stacking in DNA-mediated CT. In B-DNA duplexes, stacking interactions are largely restricted to... 

A very different but equally direct mechanism is used to repair 1-methyladenine and 3-methylcytosine. The amino groups of A and C residues are sometimes methylated when the DNA is single-stranded, and the methylation directly affects proper base pairing. In E. coli, oxidative demethylation of these alkylated nucleotides is mediated by the AllcB protein, a member of the a-ketoglutarate-Fe2+-dependent dioxygenase superfamily (Fig. 25-27). (See Box 4-3 for a description of another member of this enzyme family.)... 

Biochemically, apoptosis is characterized by the internucleosomal degradation of chromosomal DNA to form a series of double-stranded fragments that are multiples of 180 200 base pairs in length. These fragments give a characteristic DNA ladder pattern on gel electrophoresis [91, 92] and can be detected by several cytochemical methods, the most extensively used being the terminal deoxynucleotidyl transferase (TdT)-mediated biotinylated dUTP nick end labeling (TUNEL) [93-95], The detection of ladder pattern and TUNEL positivity has been adopted as a marker of apoptosis. 

Santangelo MG, Antoni PM, Spingler B, Jeschke G (2010) Can copper(II) mediate Hoogsteen base-pairing in a left-handed DNA duplex A pulse EPR study. Chemphyschem 11(3) 599-606. doi 10.1002/cphc.200900672... 

In eukaryotes, transcriptional regulation is mediated within the context of nucleosomes, the repeating subunits of chromatin. The core nucleo-some particle consists of 147 base pairs of DNA wrapped around the histone octamer composed of two copies of each of the four core histones H2A, H2B, H3, and H4. Each core histone is composed of a globular domain and an unstructured amino-terminal tail of 25-40 residues. This... 

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