USE OF SHAPED PULSES FOR SEMI-SELECTIVE EXCITATION OF IMINO H-1 RESONANCES IN DUPLEX DNA AND RNA

The application of shaped pulses, e.g. TOPHAT and hyperbolic secant, for the semi-selective excitation of the imino H-1 resonances of duplex DNA and RNA in aqueous solution is explored. The excitation profiles for the shaped poises are calibrated on a sample containing a mixture of A:U base pairs in deuteriochloroform solution. The data obtained by performing a semi-selective inversion-recovery pulse sequence using a TOPHAT waveform for the 90 degrees pulse and a hyperbolic secant waveform for the 180 degrees pulse are fitted well by a single exponential function, are independent of transmitter offset over a 1 kHz bandwidth and are in good agreement with the value obtained with hard rectangular pulses. This approach for measuring T-1 values was applied to a 2 mM sample of a self-complementary oligoribonucleotide containing the nucleoside analogue 5-fluorouridine in 90% H2O. The T-1 values were calculated as a function of Tris concentration, a catalyst added to promote imino hydrogen exchange. The T-1 values were obtained by good fits of single exponential functions to the inversion-recovery data. The T-1 values depend on the concentration of added Tris. Shaped pulses provide a convenient alternative to long rectangular pulses and hard pulse trains for the semi-selective excitation of imino H-1 resonances.