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Nucleic Acids Research, 1988, Vol. 16, No. 2 719-738
© 1988

Articles

CD of six different conformational rearrangements of poly[(d(A-G)·d(C-T)] induced by low pH

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

Program in Molecular and Cell Biology, Mail Station FO 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 September 11, 1987. Revised December 15, 1987. Accepted December 15, 1987.

On the basis of circular dichroism (CD) data, we have now identified six different conformational states (other than the duplex) of poly[d(A-G)·d(C-T)] at pH values between 8 and 2.5 (at 0.01M Na+; 20°C). Three of these structural rearrangements were observed as the pH was lowered from 8 to 2.5, and three additional rearrangements were observed as the pH was raised from 2.5 back to neutral pH. The major components of the six conformatlonal states were defined using appropriate combinations of the CD spectra of the duplex, triplex, and denatured forms of this polymer, as well as the CD spectra of the individual single strands and their respective acid-induced self-complexes. Our results show that the acid-induced rearrangements of poly[d(A-G)·d(C-T)] include not only the poly[d(C+-T)·d(A-G)·d(C-T)] triplex, but also include the poly[d(C-T)] loop-out structure and a self-complexed form of the poly[d(A-G)] strand that is pH-dependent.


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