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Nucleic Acids Research, 1987, Vol. 15, No. 21 9011-9025
© 1987

Articles

Base pair opening dynamics of a 2-aminopurine substituted Eco RI restricion sequence and its unsubstituted counterpart in oligonucleotides

P.-O. Lycksell, A. Gräslund, F. Claesens1, L.W. McLaughlin2, U. Larsson1 and R. Rigler1

Department of Biophysics, University of Stockholm, Arrhenius Laboratory S-106 91 Stockholm 1Department of Medical Biophysics, Karolinska Institute Box 60400, S-104 01 Stockholm, Sweden 2Department of Chemistry, Boston College Chestnut Hill, MA 02167, USA

Received July 27, 1987. Revised October 7, 1987. Accepted October 7, 1987.

Studies of 1H NMR selective saturation recovery were performed to determine the imino proton exchange with solvent water of the base pairs in the Eco RI endonuclease recognition sequence GAATTC. placed at the center of selfcomplementary decamer and dodecamer oligonucleotides. In one oligonucleotide the innermost adenine ras replaced by the fluorescent base analogue 2-aminopurine (2AP). From the measurements at different concentrations of TRIS buffer acting as proton exchange catalyst. base pair lifetimes were evaluated. The results at 25° show that the AT base pairs have lifetimes of the order of a few ms. whereas the surrounding GC base pairs in a dodecamer have lifetimes of about 100 ms. The (2AP)T base pair has a shorter lifetime than the corresponding AT base pair. The temperature dependent optical absorption. and for the 2AP containing oligonucleotide fluorescence, were used to study the single strand-duplex equilibrium of the decamers. The results indicate that NMR and the optical techniques. although applied at very different concentrations. monitor the same conformational transition of the oligonucleotide.


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