Nucleic Acids Research, 1987, Vol. 15, No. 10 4325-4335
© 1987
Articles |
The alternating conformation of analogues of poly[d(AT)]
1Department of Biochemistry, University of Saskatchewan Saskatoon, Saskatchewan S7N 0WO, Canada 2Department of Chemistry, University of Saskatchewan Saskatoon, Saskatchewan S7N 0WO, Canada 3Department of Veterinary Physiological Sciences, University of Saskatchewan Saskatoon, Saskatchewan S7N OWO, Canada
*To whom correspondence should be addressed
Received December 30, 1986. Revised April 27, 1987. Accepted April 27, 1987.
Synthetic DNAs were prepared containing 6-methyl adenine (m6 A)in place of adenine and 5-ethyl uracil (Et5 U) or 5-methoxymethyl uracil (Mm5 U) in place of thymine. All three modifications destabilized duplex DNAs to varying degrees. The binding of ethidiun was studied to analogues of poly[d(AT)]. There was no evidence of cooperative binding and the "neighbour exclusion rule" was obeyed in all cases although the binding constant to poly[d(m6 AT)] was approximately 6 fold higher than to poly[d(AT). P NMR spectra were recorded in increasing concentrations of CsF. Poly[d(AEt5U)] showed two well-resolved signals separated by 0.55 ppm in 1 M CsF compared to 0.32 ppm for poly[d(AT)] under identical conditions. In contrast, poly[d(AMm5 U) and poly[d(m6 AT)] showed two signals separated by 0.28 ppm and 0.15 ppm respectively, only when the concentration of CsF was raised to 2 M. The signals for poly[d(AT)] in 2 M CsF were better resolved and were separated by 0.41 ppm. These results suggest that ainor modifications to the bases may have conformational effects which could be recognized by DNA-binding proteins.