A systematic study of nearest neighbor context effects on local base pair structure will be continued by completing the NMR-based solution structures of the 2 remaining structures in the CGNATNCG series and the three remaining structures in the CGNTANCG series. These 5 proposed sequences are the restriction sites for Bam H1, Sph I, Nhe I, Eco RV and Kpn I restriction endonucleases. The question of the critical size required to nucleate B-DNA in a B'-DNA environment will be elucidated by studying a series of duplexes of the type A5NnT5 (where n is varied from 1-4) in order to interpret gel retardation bending assays in oligomerized N5-iAiTiN5-i sequences. The structure of the bend at B-B' junctions and B'-B junctions will be studied in non-symmetrical dodecamers and in symmetrical hexadecamers in order to better define the helical axis of the flanking B-DNA segments. The structure and extent of bending will also be studied as a function of the flanking context sequence and the structural effects of G residues inserted into the B'oligo-A tract will be investigated. The structure of covalent junctions between DNA duplexes and hybrid DNA:RNA duplexes will be studied by NMR, especially retroviral junction sequences, and the ds DNA sequence at the right long-terminal-repeat of HIV-I will be investigated in an attempt to elucidate the structural basis for the ability of this LTR to integrate into the human genome. In addition to these goals, collaborative work on particular sequences of interest to other program laboratories will be carried out, and isotopic solid-state (DRAMA) atomic distance measurements will be undertaken with the Drobny lab to document structural peculiarities observed in our high-resolution structural studies.
| Edfeldt, N B Fredrik; Harwood, Eric A; Sigurdsson, Snorri Th et al. (2004) Sequence context effect on the structure of nitrous acid induced DNA interstrand cross-links. Nucleic Acids Res 32:2795-801 |
| Edfeldt, N B Fredrik; Harwood, Eric A; Sigurdsson, Snorri Th et al. (2004) Solution structure of a nitrous acid induced DNA interstrand cross-link. Nucleic Acids Res 32:2785-94 |
| Okonogi, T M; Alley, S C; Reese, A W et al. (2002) Sequence-dependent dynamics of duplex DNA: the applicability of a dinucleotide model. Biophys J 83:3446-59 |
| Okonogi, Tamara M; Alley, Stephen C; Harwood, Eric A et al. (2002) Phosphate backbone neutralization increases duplex DNA flexibility: a model for protein binding. Proc Natl Acad Sci U S A 99:4156-60 |
| Hatcher, M E; LeTrong, I; Stenkamp, R et al. (2001) Local dynamics of the CpG step in a DNA crystal. J Am Chem Soc 123:8874-5 |
| Meints, G A; Karlsson, T; Drobny, G P (2001) Modeling furanose ring dynamics in DNA. J Am Chem Soc 123:10030-8 |
| Meints, G A; Drobny, G P (2001) Dynamic impact of methylation at the M. Hhai target site: a solid-state deuterium NMR study. Biochemistry 40:12436-43 |
| Okonogi, T M; Alley, S C; Reese, A W et al. (2000) Sequence-dependent dynamics in duplex DNA. Biophys J 78:2560-71 |
| Harwood, E A; Hopkins, P B; Sigurdsson, S T (2000) Chemical synthesis of cross-link lesions found in nitrous acid treated DNA: a general method for the preparation of N2-substituted 2'-deoxyguanosines. J Org Chem 65:2959-64 |
| Geahigan, K B; Meints, G A; Hatcher, M E et al. (2000) The dynamic impact of CpG methylation in DNA. Biochemistry 39:4939-46 |
Showing the most recent 10 out of 102 publications
