407D

STRUCTURAL BASIS FOR RECOGNITION OF A-T AND T-A BASE PAIRS IN THE MINOR GROOVE OF B-DNA

Summary for 407D

• Entry DOI: 10.2210/pdb407d/pdb
• Descriptor: DNA (5'-D(*CP*CP*AP*GP*TP*AP*CP*TP*GP*G)-3'), ~{N}-[5-[[5-[[5-[[3-[3-(dimethylamino)propylamino]-3-oxidanylidene-propyl]carbamoyl]-1-methyl-pyrrol-3-yl]carbamoyl]-1-methyl-pyrrol-3-yl]carbamoyl]-1-methyl-4-oxidanyl-pyrrol-3-yl]-1-methyl-imidazole-2-carboxamide, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ... (4 entities in total)
• Functional Keywords: drugs in the dna minor groove, dna
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 7539.60

Authors

Rees, D.C. (deposition date: 1998-06-24, release date: 1998-10-19, Last modification date: 2024-02-28)

Primary citation

Kielkopf, C.L.,White, S.,Szewczyk, J.W.,Turner, J.M.,Baird, E.E.,Dervan, P.B.,Rees, D.C.
A structural basis for recognition of A.T and T.A base pairs in the minor groove of B-DNA.
Science, 282:111-115, 1998

PubMed Abstract: Polyamide dimers containing three types of aromatic rings-pyrrole, imidazole, and hydroxypyrrole-afford a small-molecule recognition code that discriminates among all four Watson-Crick base pairs in the minor groove. The crystal structure of a specific polyamide dimer-DNA complex establishes the structural basis for distinguishing T.A from A.T base pairs. Specificity for the T.A base pair is achieved by means of distinct hydrogen bonds between pairs of substituted pyrroles on the ligand and the O2 of thymine and N3 of adenine. In addition, shape-selective recognition of an asymmetric cleft between the thymine-O2 and the adenine-C2 was observed. Although hitherto similarities among the base pairs in the minor groove have been emphasized, the structure illustrates differences that allow specific minor groove recognition.

PubMed: 9756473
DOI: 10.1126/science.282.5386.111

Experimental method

X-RAY DIFFRACTION (2.2 Å)