Absorption and Optical Rotatory Dispersion of Seven Trinucleoside Diphosphates

Abstract

ApApC† ApApU, GpGpC, GpApU, ApGpU and GpGpU were prepared by pancreatic ribonuclease digestion of yeast BNA and subsequent chromatographic separations. The optical rotatory dispersion and hypochromism‡ of these six trinucleoside diphosphates and ApApA have been studied at pH 1, 7 and 11·5. In addition, the OBD and hypochromism have been calculated from corresponding dinucleoside phosphate properties, assuming that only nearest-neighbor interaction between nucleoside bases is important. The calculations agree very well with experiment, suggesting that neighboring bases in dinucleoside phosphates and trinucleoside diphosphates have similar conformations. The results indicate that ApApA, ApApC, ApGpU, GpApU and ApApU have stacked bases at pH 7. GpGpC is the only compound to show much stacking at pH 1, and ApApC and ApApU are stacked at pH 11·5. Both the calculated and experimental OBD of GpApU and ApGpU are very different at pH 7. This means that nucleotide sequence can be determined by optical measurements alone.