Capillary electrophoretic analysis of synthetic short-chain oligoribonucleotides

Thirty synthetic oligoribonucleotides, 3 to 18 nucleotides (nt) long, were analyzed by capillary electrophoresis, under nondenaturing conditions, usin g a commercial kit. The migration time t(m) was dependent on nt length and composition, capillary length, operating temperature, and type of sieving p olymer. Under fixed experimental conditions, the t(m) proved predictable by the equation: t(m) = [0.22(n-1) + 6.14A/n + 6.86G/n + 3.61 (C+U)/n] min, f or n>3, where A/n, G/n, C/n, U/n is the frequency of each type of nt within the oligonucleotide (ONT). The equation accounts for the influence of char ge-to-mass ratio on t(m), but not for structural effects, if present. This approximation is acceptable for short ONTs. The possibility of detecting n1, n-1, n-2 impurities, having predicted the t(m), is of crucial importance in assessing the purity of synthetic ONTs dedicated to structural studies. This appears to be feasible. High resolution was shown among homologous se ries of ONTs of increasing length, and in some cases, even within groups of ONTs of the same length but different composition. The addition of 7 M ure a to the buffer, as denaturing agent, accelerates the t(m) and significantl y lowers the resolution for the shortest ONTs. It was also possible to moni tor the state of association of mixtures of RNA and DNA sequence-complement ary strands.