The length of a junction between the B and Z conformations in DNA is three base pairs or less.
Recently it has been suggested that double-helical complexes formed between the DNA sequences (CG)n(A)m and their conjugates, (T)m(CG)n, would be candidates for the formation of a B-Z junction in aqueous solution at high salt concentrations [Peticolas et al. (1988) Proc. Natl. Acad. Sci. U.S.A. 85, 2579-2583]. The junction was predicted to occur between a B-type helix in the d(A)m.d(T)m section and a Z-type helix in the self-complementary (CG)n.(CG)n sequence. In this paper we report Raman experiments on the deoxyoligonucleotides d(CGCGCGCGCGCGAAAAA) and d(CGCGCGAAAAA) and their complements. It is found the latter compound cannot be induced into the Z form in saturated salt solution but that the former sequence goes into a B-Z junction at 5.5 M salt. From a comparison of the relative intensity of the Raman conformational marker bands for B and Z DNA for both the A-T and C-G base pairs, it is shown that in 5.5 M NaCl solution none of the A-T base pairs are in the Z form, but nine of the C-G base pairs are in the Z form. The remaining three C-G base pairs are either in the junction or in the B form. Thus, the junction is formed from three or less C-G base pairs. If the solution is made 95 microM with NiCl2, then the entire duplex goes into the Z form and the Raman bands of the adenine are completely changed into those of the Z form.(ABSTRACT TRUNCATED AT 250 WORDS)
Dai
Z Y
ZY
Department of Chemistry, University of Oregon, Eugene 97403.
Thomas
G A
GA
Evertsz
E
E
Peticolas
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D001482:Base Composition; D001483:Base Sequence; D002942:Circular Dichroism; D004247:DNA; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides; D009994:Osmolar Concentration; D012996:Solutions; D013059:Spectrum Analysis, Raman; D013329:Structure-Activity Relationship
D009838:Oligodeoxyribonucleotides; D012996:Solutions; D004247:DNA