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Salt- and sequence-dependence of the secondary structure of DNA in Solution by 31P-nmr spectroscopy

✍ Scribed by Chi-wan Chen; Jack S. Cohen


Publisher
Wiley (John Wiley & Sons)
Year
1983
Tongue
English
Weight
810 KB
Volume
22
Category
Article
ISSN
0006-3525

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✦ Synopsis


We examined three sonicated, specific-sequence polydeoxynucleotides in solution over a wide range of concentrations of several salts by "P-nmr spectroscopy, and we found that the alternating copolymer poly(dAdT)-poly(dAdT) exhibits a dinucleotide repeat unit in all five salts and at all concentrations studied, as indicated by the presence of a doublet in its 31P-nmr spectra. The two components of the doublet show selective shift effects. The upfield component is assigned to dApdT in the gauche--gaucheconformation and shifts upfield in all four monovalent salts used, relative to a single-stranded oligonucleotide control. The downfield component is assigned to dTpdA in the trans-gaucheconformation and shifts downfield with increasing CsF concentration but remains essentially constant in LiC1, NaCl, and CsCl. These changes indicate a fast noncooperative transition for poly(dAdT)-poly-(dAdT) from a presumed right-handed dinucleotide-repeat B-form to another conformation with a dinucleotide-repeat structure, via a continuum of structures that may differ in the extent of the winding of the double helix. Ethanol causes the upfield component to collapse into the other component, indicating conversion to a structure with a mononucleotide repeat unit and a trans-gauche-Conformation. Up to 1M Mg2+ appears to have no significant effect on the phosphodiester conformations of poly(dAdT)-poly(dAdT). By contrast, poly-(dGdC)-poly(dGdC) gives a slow cooperative transition from what is considered to be a right-handed regular B-form to a left-handed Z-form on increasing MgC12 and NaCl concentrations, although we observed no changes in chemical shifts below the transition points. The homopolymer poly(dA)-poly(dT) exhibits no unusual shift effects or transitions upon the addition of salts when compared to the oligonucleotide control and is considered to be a regular B-form with a gauche--gauchephosphodiester backbone conformation. These differences emphasize the distinct secondary structures of DNAs of different sequences and their selective responses to changes in solution conditions.


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