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Nucleic Acids Research, 1983, Vol. 11, No. 7 2121-2134
© 1983

MOLECULAR BIOLOGY

Proton exchange rates in transfer RNA as a function of spermidine and magnesium

James S. Tropp* and Alfred G. Redfield+

Department of Biochemistry, Brandeis University, Waltham MA 02254, USA

+To whom correspondence should be addressed. Also at the physics Department and the Rosenstiel Basic Medical Sciences Research Center, Brandeis University

Received November 18, 1982. Revised February 18, 1983. Accepted February 18, 1983.

Solvent exchange rates of selected protons were measured by NMR saturation recovery for E. coli tRNAval, E. colifMet and yeast tRNAPhe, at temperatures from 20 to 40°C, in the presence of 0.12M Na+ and various levels of added spermidine. tRNAVal was also studied with added Mg++. The exchange rates in zero spermidine and Mg++ indicate early melting of the U8 A14 interaction, in accord with thermodynamic melting studies. Exchange rates for secondary protons suggest early melting of the T stem in tRNAfMet and the acceptor stem in tRNAPhe, in contradiction with melting transition assignments from thermo-dynamic work. Addition of 10 spermidines per tRNA stabilizes the secondary and tertiary interactions more effectively than added Na+, but less so than Mg++. Added spermidine has the curious effect of increasing the exchange rate of the Y55 Nl proton, while protecting the Y55 N3 proton from exchange in all three tRNA's. Added Mg++ has the same effect on tRNAVal.

*Present address: Nicolet Magnetics Corporation, 255 Fourier Avenue, Fremont CA 94539


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