Download MendeleyStructural effects of DNA sequence on T.A recognition by hydroxypyrrole/pyrrole pairs in the minor groove.
Kielkopf, C.L., Bremer, R.E., White, S., Szewczyk, J.W., Turner, J.M., Baird, E.E., Dervan, P.B., Rees, D.C.(2000) J Mol Biol 295: 557-567
- PubMed: 10623546
- DOI: https://doi.org/10.1006/jmbi.1999.3364
- Primary Citation of Related Structures:
1CVX, 1CVY - PubMed Abstract:
Synthetic polyamides composed of three types of aromatic amino acids, N-methylimidazole (Im), N-methylpyrrole (Py) and N-methyl-3-hydroxypyrrole (Hp) bind specific DNA sequences as antiparallel dimers in the minor groove. The side-by-side pairings of aromatic rings in the dimer afford a general recognition code that allows all four base-pairs to be distinguished. To examine the structural consequences of changing the DNA sequence context on T.A recognition by Hp/Py pairs in the minor groove, crystal structures of polyamide dimers (ImPyHpPy)(2) and the pyrrole counterpart (ImPyPyPy)(2) bound to the six base-pair target site 5'-AGATCT-3' in a ten base-pair oligonucleotide have been determined to a resolution of 2.27 and 2.15 A, respectively. The structures demonstrate that the principles of Hp/Py recognition of T.A are consistent between different sequence contexts. However, a general structural explanation for the non-additive reduction in binding affinity due to introduction of the hydroxyl group is less clear. Comparison with other polyamide-DNA cocrystal structures reveals structural themes and differences that may relate to sequence preference.
Organizational Affiliation:
Division of Chemistry, California Institute of Technology, Pasadena, CA, 91125, USA.
