Single-stranded binding proteins

The amplification of genetic information, i.e., the replication of parent DNA molecules, is achieved by means of an entire set of enzymes. The major players are a DNA-gyrase for unwinding of the double helix, proteins to separate the two antiparallel DNA strands at the replicational junction, single-stranded binding proteins (SSB) that prevent the... 

Examples (a) nucleosome K Huger, AW Mader, RK Richmond, DF Sargent, TJ Richmond. Nature 389 251-260, 1997 (b) DNA polymerases CA Brautigam, TA Steitz. Curr. Opin. Struct. Biol. 8 54-63, 1998 (c) single-stranded binding protein Y Shamoo, AM Friedman, MR Parsons, WH Konigsberg, TA Steitz. Nature 376 362-366, 1995 (d) restriction endonucleases RA Kovall, BW Matthews. Curr. Opin. Chem. Biol. 3 578-583, 1999 (e) DNA lig-ase S Shuman. Structure 4 653-656, 1996 (f) DNA helicases MC Hall, SW Matson. Mol. Microbiol. 34 867-877, 1999 (g) zinc-finger proteins Y Choo, JW Schwabe. Nat. Struct. Biol. 5 253-255, 1998. 

Single-strand binding proteins Prevent premature reannealing of dsDNA... 

The E. coli single-strand binding protein, another helix-destabilizing protein that is usually called simply SSB, is a tetramer of 18.5-kDa subunits.265,3,2,313 It is essential to DNA replication. About 35 nucleotides may bind to each tetramer.314 The situation is not as clear in eukaryotes where DNA is largely coiled around histones in the nucleosomes. Several singlestrand binding proteins have been identified,315 but the need for SSB proteins in eukaryotic nuclear replication is uncertain.316 A human mitochondrial SSB resembles that of E. coli.317... 

Single-strand binding protein (SSB) is found in abundance in E. coli, and it is believed to be bound in mass at the replication fork. This fact and other evidence described later on indicate that it plays an important role at the growth fork. 

Lohman, T. M., W. Bujalowski, and L. B. Overman, E. coli single strand binding protein. Trends Biochem. Sci. 13 250-255, 1988. 

Why is a single-strand binding protein or a DNA helicase not required for transcription as they are for replication ... 

K. Kerman, Y. Morita, Y. Takamura and E. Tamiya, Escherichia coli single-strand binding protein-DNA interactions on carbon nanotube-modified electrodes form a label-free electrochemical hybridization sensor, Anal. Bioanal. Chem., 381 (2005) 1114-1121. 

Initiation sequences contain a set of repeated sequences, which bind the essential initiator protein, DnaA. The DnaA protein opens the helix to make a short region of separated strands. Then a specialized single-strand binding protein binds to the DNA strands to keep them apart. This process makes a template, but replication can t happen because no primer yet exists. See Figure 8-10b. 

Know the roles of DNA polymerase I, II, III, and eukaryotic DNA polymerases, the roles of primers, helicases, single-stranded binding proteins (SSB), topoisomerases (gyrase), ligases, primase, and RNA polymerases, and the differences between the leading and lagging strands of DNA. 

SSB Single-stranded binding protein (helix destabilizing)... 

Figure 11.5 Simultaneous synthesis of leading and lagging templates. P = RNA primer SSB = single-stranded binding protein.

Although protein microheterogeneity usually disrupts crystal formation, it can occasionally promote crystallization. For example, crystals of Escherichia coli single-stranded binding protein contain a 1 1 mixture of intact and proteolyzed protein (Ollis et ai, 1983). While crystallization experiments were initially conducted with intact protein, crystals grew only when enough molecules to form the mixed crystals had been cleaved by contaminating proteases. 

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