Sequence-specific protein-DNA

Sequence-specific protein-DNA interactions recognize operator regions... 

Figure 8.15 Sequence-specific protein-DNA interactions provide a general recognition signal for operator regions in 434 bacteriophage, (a) In this complex between 434 repressor fragment and a synthetic DNA there are two glutamine residues (28 and 29) at the beginning of the recognition helix in the helix-turn-helix motif that provide such interactions with the first three base pairs of the operator region.

The proteins impose precise distortions on the B-DNA in the complexes Sequence-specific protein-DNA interactions recognize operator regions... 

Ebright, Nature Struct. Biol, 3, 837 (1996). Aromatic Hydrogen Bond in Sequence-Specific Protein DNA Recognition. 

Hard T, Lundback T. Thermodynanucs of sequence-specific protein-DNA interactions. Biophys. Chem. 1996 62 121-139. Spolar RS, Record MT Jr. Coupling of local folding to site-specific binding of proteins to DNA. Science 1994 263 777-784. 

Ferdous, A., Akaike, T., Maruyama, A. Inhibition of sequence-specific protein-DNA interaction and restriction endonuclease cleavage via triplex stabilization by poly(L-lysine)-graft-dextran copolymer. Biomacromolecules 1, 186-193 (2000). doi 10.1021/ bm9900141... 

Bonham, A. J. Braun, G. Pavel, I. Moskovits, M. Reich, N. O. Detection of sequence-specific protein-DNA interactions via surface enhanced resonance Raman scattering. J. Am. Chem. Soc. 2007, 129, 14572-14573. 

Max and MyoD recognize the DNA HLH consensus sequence by different specific protein-DNA interactions... 

Dempsey LA, Hanakahi LA, Maizels N (1998) A specific isoform of hnRNP D interacts with DNA in the LRl heterodimer canonical RNA binding motifs in a sequence-specific duplex DNA binding protein. J Biol Chem 273 29224-29229... 

Bulyk ML. Analysis of sequence specificities of DNA-binding proteins with protein binding microarrays. Methods Enzymol. 2006 410 279-299. 

The principles of specific protein-DNA interactions were first discovered during the study of bacterial repressors. Many bacterial repressors are dimeric proteins in which an a helix from each monomer Inserts into a major groove in the DNA helix (Figure 11-20). This a helix is referred to as the recognition helix or sequence-reading helix because most of the amino acid side chains that contact DNA extend from this helix. The recognition helix that protrudes from the surface of bacterial repressors to enter the DNA major groove and make multiple, specific interactions with atoms in the DNA is usually supported in the protein structure in part by hydrophobic interactions with a second a helix just N-termlnal to it. This structural element, which is present in many bacterial repressors, is called a helix-turn-helix motif. 

The vast majority of p53 mutations are localized to the DNA binding domain and effect specific protein-DNA interactions. The dots show the distribution of p53 mutations across the entire protein-coding sequence and the boxes identify the most... 

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