1CVX

CRYSTAL STRUCTURE OF POLYAMIDE DIMER (IMPYHPPYBETADP)2 BOUND TO B-DNA DECAMER CCAGATCTGG

Summary for 1CVX

• Entry DOI: 10.2210/pdb1cvx/pdb
• Descriptor: 5'-D(*CP*CP*AP*GP*AP*TP*CP*TP*GP*G)-3', HYDROXYPYRROLE-IMIDAZOLE-PYRROLE POLYAMIDE (3 entities in total)
• Functional Keywords: polyamide, minor groove recognition, ta recognition, double drug in minor groove, dna
• Total number of polymer chains: 2
• Total formula weight: 7417.46

Authors

Kielkopf, C.L.,Bremer, R.E.,White, S.,Baird, E.E.,Dervan, P.B.,Rees, D.C. (deposition date: 1999-08-24, release date: 2000-01-15, Last modification date: 2024-02-07)

Primary citation

Kielkopf, C.L.,Bremer, R.E.,White, S.,Szewczyk, J.W.,Turner, J.M.,Baird, E.E.,Dervan, P.B.,Rees, D.C.
Structural effects of DNA sequence on T.A recognition by hydroxypyrrole/pyrrole pairs in the minor groove.
J.Mol.Biol., 295:557-567, 2000

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.

PubMed: 10623546
DOI: 10.1006/jmbi.1999.3364

Experimental method

X-RAY DIFFRACTION (2.27 Å)