Flexible synthetic methodology has been developed for site-specifically modifying both DNA and RNA with structurally non-perturbing disulfide cross-links. This chemistry circumvents many of the problems commonly associated with other cross-linking protocols, and in preliminary experiments has been used to prepare cross-linked hairpins, duplexes, triplexes, non-ground-state DNA conformations, and RNA secondary structures. Because this modification removes the initiation site(s) for thermal denaturation, the cross-lined nucleic acids possess extraordinary long range stability. Most importantly, preliminary evidence clearly indicates that these disulfide cross-links do not appear to alter native conformation. Furthermore, in the reduced form the free thiol groups that form the cross-links do not compromise the thermodynamic stability or alter the denaturation pathway of the modified DNA/RNA relateive to the corresponding wild-type sequences. While these experiments have provided insights into both DNA and RNA that were not otherwise possible, routine application of this chemistry to many different problems necessitates a comprehensive understanding of the conformational, dynamic, and thermodynamic consequences of incorporating these cross-links. To meet this need three coordinated subprojects have been designed. First, using NMR spectroscopy we propose to elucidate the solution conformations and measure the base-pair opening kinetics for (bis)- and (mono)-cross-linked analogs of d(CGCGAATTCGCG)2. The thermodynamic stability of these duplexes in their reduced (free thiol) and oxidized (disulfide cross-linked) forms will be determined by UV thermal denaturation experiments and differential scanning calorimetry (DSC). The data from these experiments will be compared with those obtained using the parent duplex to judge the effects of the disulfide modifications. Second, the structural, dynamic, and thermodynamic properties of cross-linked triplexes based on the pyrimidine.purine-pyrimidine sequence motif will be examined under physiologically relevant conditions using NMR and CD spectroscopies and DSC. These studies will demonstrate the utility of disulfide cross-links in stabilizing conformationally-labile DNA structures, and the proposed experiments are not possible with the unmodified sequences. Lastly, in analogy to recent protein folding experiments, disulfide cross-links will be used to elucidate the fold pathway of small RNA's using tRNA (Phe as a model system. Specifically, four tRNA (Phe) molecules that each contain a single disulfide cross-link bridging two structural domains will be chemically synthesized. The solution conformation of these tRNA's (oxidized and reduced) will be probed by chemical modification experiments to verify that the thiol/disulfides do not alter RNA geometry. The free energy of folding and the kinetics of unfolding will then be studied by UV thermal denaturation and stopped-flow spectrophotometry, respectively. The free energies of these transitions will be interpreted in the context of a folding pathway for tRNA(Phe).

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
1R01GM052168-01
Application #
2191088
Study Section
Bio-Organic and Natural Products Chemistry Study Section (BNP)
Project Start
1995-01-01
Project End
1998-12-31
Budget Start
1995-01-01
Budget End
1995-12-31
Support Year
1
Fiscal Year
1995
Total Cost
Indirect Cost
Name
University of Michigan Ann Arbor
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
791277940
City
Ann Arbor
State
MI
Country
United States
Zip Code
48109
Pinard, R; Lambert, D; Heckman, J E et al. (2001) The hairpin ribozyme substrate binding-domain: a highly constrained D-shaped conformation. J Mol Biol 307:51-65
Maglott, E J; Deo, S S; Przykorska, A et al. (1998) Conformational transitions of an unmodified tRNA: implications for RNA folding. Biochemistry 37:16349-59