Sequence-specific binding

Steitz, T.A. Stmctural studies of protein-nucleic acid interaction the sources of sequence-specific binding. 

Figure 9.19 shows the sequence of the DNA that was used for the structure determination of the p53-DNA complex the bases involved in sequence-specific binding to the protein are shaded. One molecule of the DNA-bind-ing domain of p53 binds to the minor and the major grooves of the DNA making sequence-specific interactions with both strands (Figure 9.20). 

Figure 10.5 Comparison of the sequence-specific binding to DNA of six different zinc fingers. Residues in the N-terminus of the a helix in the finger regions are numbered 1 to 6. The residue immediately preceding the a helix is numbered -1. Amino acid residues and nucleotides that make sequence-specific contacts are colored. In spite of the structural similarities between the zinc fingers and their overall mode of binding, there is no simple rule that governs which bases the fingers contact.

Zimarino, V. Wu, C. (1987). Induction of sequence-specific binding of Drosophila heat shock activator without protein synthesis. Nature 327, 727-730. 

Fig. 1.7. Basic leudne zipper and heltx-loop-heltx motif in complex with DNA. A) The basic leucine zipper of the transcription activator GCN4 of yeast consists of two slightly curved a-hehces, which dimerize with the help of the leucine zipper motif. The sequence specific binding of DNA occurs via the basic ends of the two helices. They insert themselves into the major groove of the DNA. B) The helix-loop-helix motif of the eucaryotic transcription factor Max complexed with DNA. Molscript drawing (Kraulis 1991).

TBP I 38 sequence specific binding to TATA box, recruitment of TFIIB... 

The possibility exists to condense DNA through proton donor and proton acceptor non-electrostatic interactions with DNA-grooves. This type of non-electrostatic complex has been developed for sequence-specific binding to DNA. Several prominent works were recently accomplished in this field (Dervan, 1997 Kiclkopf et al., 1998 Minchan et al, 2000). 

Malina J, Hannon MJ, Brabec V (2008) Interaction of dinuclear ruthenium(II) supramolecular cylinders with DNA sequence-specific binding, unwinding, and photocleavage. Chem Eur J 14 10408-10414... 

Many DDE transposases carry a DNA sequence-specific binding domain in their N-terminal regions and at least one domain involved in multimerization. Generally, the catalytic domain is located in the C-terminal part of the protein. The DDE domain is by far the most studied and best understood catalytic motif involved in transposition. It is found in many different types of transposon from retroviruses to Tc-Mariner, bacterial ISs, and transposons (4). 

T.K. Chiu and R E. Dickerson. 2000. 1 A crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium J. Mol. Biol. 301 915-945. (PubMed)... 

Figure 6 below, shows the normalized distributions for the values obtained from the simulations for AA/TT, AT and TA steps, for the six bps parameters. In all cases, the distributions belonging to TA steps are wider than those of the other steps, and we interpret that as a reflection of the greater flexibility of this step. Except for tilt, all these parameters are important for understanding sequence specific binding to TATA boxes [89,100,101,109], because TBP forces the conformation of DNA into regions of conformational space that are not well sampled by free DNA in the simulations or in the available free DNA structures contained in the NDB. It is also obvious from these plots that slide, rise and roll have a marked sequence dependence [110]. 

The sequence-specific binding of synthetic oligonucleotides and analogs to RNA and DNA is studied intensively in the examination of natural polynucleotides and for the development of potential therapeutics [69]. 

Furthermore, the TAFs are targets for protein-protein interactions with transcriptional activators and two of them are required for sequence-specific binding to the initiaion element of TATA-less promotors. TAFs also possess enzymatic activity. TAF]]250 has both a histone acetylase activity and a protein kinase activity. While the former presumably plays a role in the reorganization of the nucleosome, the latter can lead to phosphorylation of TFIIF. 

Figure 18.16. Sequence-specific binding of amino acid side chains to DNA base pairs, involving two hydrogen bonds.

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