Abstract

The secondary structure of nucleic acids is probed by the psoralen photoreaction. Techniques have recently been developed in this laboratory for mapping such secondary structure. The objective of this proposal is to improve these techniques so that they can be used as a high resolution probe for secondary structure. When this objective is realized, the nucleotides in a defined sequence which are base-paired in a helical structure will be identifiable. The goals for the current year were: 1) A sequence resolution map of the hydroxymethyltrioxsalen (HMT) adducts and cross-links in Drosophila melanogaster 5S ribosomal RNA. 2) A sequence resolution map of hydroxymethyltrioxsalen adducts in E. coli phe tRNA. 3) The structure determination of all monoadducts of HMT formed in DNA utilizing mass spectrometry and high resolution NMR. 4) The dynamics of two-pulse laser excitation in promoting chemical cross-linkage of DNA.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM011180-23
Application #
3268242
Study Section
Biophysics and Biophysical Chemistry A Study Section (BBCA)
Project Start
1979-07-01
Project End
1988-06-30
Budget Start
1986-07-01
Budget End
1988-06-30
Support Year
23
Fiscal Year
1986
Total Cost
Indirect Cost

  Institution

Name
University of California Berkeley
Department
Type
Schools of Arts and Sciences
DUNS #
094878337
City
Berkeley
State
CA
Country
United States
Zip Code
94704

  Publications

Kao, J P; Isaacs, S T; Hearst, J E (1990) The molecular and stereochemical structures of photoproducts generated by UV-irradiation of 4'-hydroxymethyl-4,5',8'-trimethylpsoralen in aqueous solution. Photochem Photobiol 51:273-83
Piette, J; Gamper, H B; van de Vorst, A et al. (1988) Mutagenesis induced by site specifically placed 4'-hydroxymethyl-4,5',8-trimethylpsoralen adducts. Nucleic Acids Res 16:9961-77
Shi, Y B; Griffith, J; Gamper, H et al. (1988) Evidence for structural deformation of the DNA helix by a psoralen diadduct but not by a monoadduct. Nucleic Acids Res 16:8945-52
Lipson, S E; Cimino, G D; Hearst, J E (1988) Structure of M1 RNA as determined by psoralen cross-linking. Biochemistry 27:570-5
Shi, Y B; Gamper, H; Hearst, J E (1988) Interaction of T7 RNA polymerase with DNA in an elongation complex arrested at a specific psoralen adduct site. J Biol Chem 263:527-34
Cheng, S; Van Houten, B; Gamper, H B et al. (1988) Use of psoralen-modified oligonucleotides to trap three-stranded RecA-DNA complexes and repair of these cross-linked complexes by ABC excinuclease. J Biol Chem 263:15110-7
Van Houten, B; Gamper, H; Hearst, J E et al. (1988) Analysis of sequential steps of nucleotide excision repair in Escherichia coli using synthetic substrates containing single psoralen adducts. J Biol Chem 263:16553-60
Shi, Y B; Gamper, H; Van Houten, B et al. (1988) Interaction of Escherichia coli RNA polymerase with DNA in an elongation complex arrested at a specific psoralen crosslink site. J Mol Biol 199:277-93
Shi, Y B; Spielmann, H P; Hearst, J E (1988) Base-catalyzed reversal of a psoralen-DNA cross-link. Biochemistry 27:5174-8
Gamper, H B; Cimino, G D; Hearst, J E (1987) Solution hybridization of crosslinkable DNA oligonucleotides to bacteriophage M13 DNA. Effect of secondary structure on hybridization kinetics and equilibria. J Mol Biol 197:349-62

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