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Conversation 11: No. 2

category image Volume: Conversation 11
Issue Number 2
May 2000
ISBN 0-940030-81-0

DNA Sequence Recognition of a Cross-Linked Polyamide: CD Studies, Footprinting and Effects on the Activity of DNA Gyrase

Using circular dichroism the binding ability of a cross-linked thiazole-lexitropsin, composed of two polyamide strands (with the base binding residues thiazole-imidazole-pyrrole) to a series of dodecamer duplexes containing different central sequences, has been examined. The binding of the dimer with a heptanediyl linker (C7 dimer) was compared with that of the lexitropsin monomer at 200 mM NaCl and 2 M NaCl. The C7 dimer exhibits a clear-cut different binding tendency to various dodecamers at 2 M NaCl indicating that sequence specificity becomes apparent at high salt concentration. The highest binding preference occurs to the dodecamers with the central sequences: AACGTT, AAGTTT and ATCGTA but almost no affinity was observed at 2 M NaCl for AGCGCT, ATCGAT and AAATTT. From the results it appears that the sequence selectivity of the dimer can be ascribed to the side-by-side binding mode of the cross-linked polyamide strands in the minor groove. In contrast no similar variation was found in the binding behavior for the lexitropsin monomer. Modification of the leading residue on the thiazoles of the dimer significantly lowers (or even abolishs) the binding ability, e.g. if the amino group is replaced by formyl or an acetyl residue. Footprinting and melting temperature data are in agreement with the CD results. Comparative in vitro studies on the influence of the lexitropsins on DNA gyrase demonstrate that the dimer has a higher inhibitory potency on the enzymatic activity compared to the monomer in accord with the observed DNA binding differences. A scheme of a possible side-by-side alignment of the C7 dimer in the minor groove is proposed.

Günther Burckhardt1
Ingo Förtsch1
Hannelore Simon1
Eckhard Birch-Hirschfeld2
Leonhard Kittler3
Holger Schütz1
Sanjay K. Sharma4
J. William Lown4
and Christoph Zimmer1

1Institut für Molekularbiologie der Friedrich-Schiller-Universität (FSU) Jena
Winzerlaer Str. 10
D-07745 Jena, Germany
2Institut für Virologie des Klinikums der FSU Jena
Winzerlaer Str. 10
D-07745 Jena, Germany
3Institut für Molekulare Biotechnologie e.V.
Beutenbergstraße 11
D-07745 Jena, Germany
4Department of Chemistry
University of Alberta
Edmonton, Canada T6G2G2

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