Determination of the base pairing content of ribonucleic acids by infrared spectroscopy

A method is described for determining the fractions of adenine-uracil and guanine-cytosine base pairs of partly double-helical ribonucleic acids in aqueous solution. The method is based upon the ability to distinguish between paired and unpaired bases by means of infrared spectroscopy of their deuterium oxide solutions in the 1500–1800 cm^?1 frequency region of the infrared spectrum. An application of the method to yeast ribosomal RNA is described. At 30°C, ribosomal RNA is 64± 6% paired (35% GC, 29% AU). The method can be applied to determine the fractions of Watson-Crick base pairs at a given temperature in any RNA containing the four common bases in known ratios.