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Nucleic Acids Research, 1990, Vol. 18, No. 14 4111-4122
© 1990

MOLECULAR BIOLOGY

CD evidence that the alternating purine-pyrimidine sequence poly[d(A-C)•d(G-T)], but not poly[d(A-T).d(A-T)], undergoes an acid-induced transition to a modified secondary conformation§

Vincent P. Antao+, Robert L. Ratliff1 and Donald M. Gray*

Program in Molecular and Cell Biology, Mail Station 3.1, University of Texas at Dallas Box 830688, Richardson, TX 75083-0688 1Life Sciences Division, Mail Stop 886, Los Alamos National Laboratory Box 1663, Los Alamos, NM 87545, USA

* To whom correspondence should be addressed

Received January 17, 1990. Revised June 19, 1990. Accepted June 19, 1990.

Circular dichroism and UV absorption data showed that poly[d(A-C)-•(G-T)] (at 0.01 M Na+ (phosphate), 20°C) underwent two reversible conformational transitions upon lowering of the pH. The first transition was complete at about pH 3.9 and resulted in an acid form of the polymer that was most likely a modified, protonated duplex. The second transition occurred between pH 3.9 and 3.4 and consisted of the denaturation of this protonated duplex to the single strands. UV absorption and CD data also showed that the separated poly[d(A-C)] strand formed two acid-induced self-complexes with pKa values of 6.1 and 4.7 (at 0.01 M Na+). However, neither one of these poly[d(A-C)] self-complexes was part of the acid-induced rearrangements of the duplex poly[d(A-C)•d(G-T)]. Acid titration of the separated polyfd(G-T)] strand, under similar conditions, did not show the formation of any protonated poly[d(G-T)] self-complexes. In contrast to poly[d(A-C)-d(G-T)], poly[d(A-T)-d(A-T)] underwent only one acid-induced transition, which consisted of the denaturation of the duplex to the single strands, as the pH was lowered from 7 to 3.

+Present address: Department of Chemistry and Laboratory of Chemical Biodynamics, University of California, Berkeley, CA 94720, USA

§This paper on the investigation of the acid-induced transitions of poly[d(A-C)-d(G-T)] and poly[d(A-T)d(A-T)/} is the third in a series of three papers on CD and UV absorption studies of the acid transitions of DNA sequences that have a simple dinucleotide repeat. The papers on the acid-induced transitions of poly[d(G-C)-d(G-C)] and poly[d(A-G)-d(C-T)] have been published.5, 6


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C Gaillard and F Strauss
Association of poly(CA).poly(TG) DNA fragments into four-stranded complexes bound by HMG1 and 2
Science, April 15, 1994; 264(5157): 433 - 436.
[Abstract] [PDF]


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