Nuclear magnetic resonance study on the exchange behavior of the NH-N protons of a ribonucleic acid miniduplex

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Abstract
The exchange behavior of the guanine N(1) and uracil N(3) protons in the self-complementary hexanucleotide r(ApApGpCpUpU) was studied at 5.degree. C in 80% H2O 20% D2O by proton NMR. Under these conditions, the hexanucleotide forms a stable miniduplex. The exchange rate of all Watson-Crick NH protons is unaffected by addition of trifluoroethylamine up to 0.07 M. On the other hand, addition of phosphate buffer, pH 6.9, enhances the exchange rate of the uracil N(3) protons of both terminal and internal A.cntdot.U base pairs but does not influence the exchange rate of the guanine N(1) protons of the central G.cntdot.C base pairs. Catalysis by increased phosphate concentrations results in an open-limited rate of the internal A.cntdot.U base pairs with kex = 233 s-1, equivalent to a lifetime of 4.3 ms. The proton exchange of the central G.cntdot.C is regulated by the opening rate of the central core of the miniduplex. On the other hand, the sensitivity of the exchange rate of internal as well as of terminal A.cntdot.U base pairs can be explained by their reduced lifetime due to end fraying and a subsequent catalysis of the exchange process from the opened state. It may be possible to probe labilized parts of RNA such as tRNA by gradual addition of the exchange catalyst phosphate and to monitor their exchange rates by proton NMR.