Use of shaped pulses for semi‐selective excitation of imino 1H resonances in duplex DNA and RNA

Abstract

AbstractThe application of shaped pulses, e.g. TOPHAT and hyperbolic secant, for the semi‐selective excitation of the imino 1H resonances of duplex DNA and RNA in aqueous solution is explored. The excitation profiles for the shaped pulses 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° pulse and a hyperbolic secant waveform for the 180° 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 T1 values was applied to a 2 mM sample of a self‐complementary oligoribonucleotide containing the nucleoside analogue 5‐fluorouridine in 90% H2O. The T1, values were calculated as a function of Tris concentration, a catalyst added to promote imino hydrogen exchange. The T1, values were obtained by good fits of single exponential functions to the inversion‐recovery data. The T1, 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 1H resonances.