The long term objectives of this research are conformational and ligand binding studies of DNA and their possible implications on the gene regulatory mechanism. The focus of this proposal will be on the physico-chemical studies of the remarkable conformational lability of poly(dG-m5dC):poly(dG-m5dC) under low salt conditions. In addition to studying ligand binding characteristics of the recently discovered low-salt form of Z DNA, we will concentrate on the elucidation of a striking """"""""metastable"""""""" Z conformation of poly(dG-m5dC):poly(dG-m5dC) which can be made to exist under B-form stabilizing solution condition.
Specific aims for the next three years will be: (1) To map out conformational phase diagram of poly(dG-m5dC):poly(dG-m5dC) under low salt conditions as functions of NaC1 concentration and acidity; (2) To carry out detailed spectroscopic characterization (absorbance, CD, NMR) of a """"""""metastable"""""""" state of Z form poly(dG-m5dC):poly(dG-m5dC) in solutions containing 2.5 to 30 mM NaC1; (3) To elucidate the various possible pathways in which this metastable state can be formed; (4) To investigate the thermal stability of poly(dG-m5dC):poly(dG-m5dC) under low salt conditions; (5) To study the binding characteristics of low-salt forms of Z- and the """"""""metastable"""""""" z-poly(dG-m5dC):poly(dG-m5dC) with ethidium bromide, actinomycin D, and benzo(a) pyrene metabolites; (6) To synthesize oligonucleotide (dG-m5dC) of various chain lengths and with varying end attachments so that their effects on the formation of the low-salt Z and """"""""metastable"""""""" Z forms can be ascertained; (7) To obtain detailed structural and dynamic information on the synthesized oligomers by NMR studies.
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