Nuclease, function

Another class of DNA-binding proteins are the polymerases. These have a nonspecific interaction with DNA because the same protein acts on all DNA sequences. DNA polymerase performs the dual function of DNA repHcation, in which nucleotides are added to a growing strand of DNA, and acts as a nuclease to remove mismatched nucleotides. The domain that performs the nuclease activity has an a/P-stmcture, a deep cleft that can accommodate double-stranded DNA, and a positively charged surface complementary to the phosphate groups of DNA. The smaller domain contains the exonuclease active site at a smaller cleft on the surface which can accommodate a single nucleotide. 

Pyridyl functionalized tris(pyrazolyl)borate ligands show some interesting properties including the formation of polynuclear zinc complexes.23,1 Some of these contain extensive H bonding and have potential as models for multinuclear zinc enzymes such as phospholipase C or PI nuclease.235 A bis-ligand complex of the hydrotris(5-methyl-3-(3-pyridyl)pyrazolyl)borate ligand (23) shows octahedral coordination of all six pyrazole nitrogen donors despite the steric bulk. 

The changes in structure of denatured nuclease as a function of urea concentration (Fig. 3) suggest that, as hydrophobic interactions are weakened and the backbone becomes more highly solvated, the chain expands gradually. The data presented by Millet et al. in this volume suggest that this expansion does not continue asymptotically as predicted by simple polymer physical chemistry. This is the behavior expected for a polypeptide chain trapped in a small region of conformation space. Most, perhaps all, of the conformations accessible in the expanded denatured state may have a native-like topology. 

The Klenow fragment. The DNA polymerase 1 molecule contains its polymerase and nuclease activities on different parts of the enzyme molecule. These two parts can be separated by treatment with the enzyme sub-tilisin. The part which retains the polymerase function is known as the Klenow fragment. This enzyme sythesizes a new DNA strand complementary to the single strand of DNA (the template) only. It is used to create blunt ends in dsDNA and in the dideoxy method of DNA sequencing. 

Similar results were obtained from reconstitution experiments with DNA and a non-cross-linked octamer (Thomas and Butler, 1978). Nucleosome-like particles were observed in the EM and a pattern of histone cross-linking comparable to that of native chromatin was obtained. However, only 140-base-pair repeats were obtained upon micrococcal nuclease digestion instead of 200-base-pair repeats obtained for native rat liver chromatin (Noll and Komberg, 1977). This indicates that, in the absence of HI, only core particles can be reconstituted. Nevertheless, these studies with both cross-linked and reassembled un-cross-linked histones demonstrate that the octamer is a complete biological functional unit retaining the information for folding the DNA around the histone core. 

Nucleosomes core particles containing H2A only have 118 base pairs of DNA incorporated compared to the canonical nucleosomes protecting about 147 base pairs from micrococcal nuclease (Bao et al. 2004). These nucleosomes are more flexible in structure and might facilitate passage of RNA polymerase II. However, the function of this histone variant in mammalian cells is not fully understood. As... 

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