INTERACTIONS OF PSORALEN-DERIVATIZED OLIGODEOXYRIBONUCLEOSIDE METHYLPHOSPHONATES WITH VESICULAR STOMATITIS-VIRUS MESSENGER-RNA

The ability of oligonucleotides to interact selectively with their tar gets is an important consideration in the design of antisense oligonuc leotides. This is especially important in the case of antisense oligom ers, such as psoralen-derivatized oligomers, which can irreversibly bi nd to their targets. We have studied the interactions of a series of p soralen-derivatized antisense oligonucleoside methylphosphonates with the mRNAs of vesicular stomatitis virus (VSV), mRNAs that have a high degree of sequence homology. Cross-linking reactions were carried out under conditions of low ionic strength in order to reduce mRNA seconda ry structure. A 12-mer, whose sequence was complementary to VSV M-mRNA and partially complementary to sequences found in N, NS, and G mRNA c ross-linked extensively to N-message. On the other hand, 16-mers whose sequences were uniquely complementary to binding sites on N- or M-mRN A specifically and efficiently cross-linked to their targeted mRNAs ov er the temperature range 0 degrees to 37 degrees C. A reverse transcri ptase-catalyzed primer extension assay was used to show that one of th e N-specific oligomers cross-linked at the expected site on N-mRNA and to estimate the extent of cross-linking. The results demonstrate that psoralen-derivatized oligonucleoside methylphosphonates can cross-lin k in a sequence-specific manner if the sequences of these oligomers ar e chosen carefully so as to avoid extensive partial complementarity wi th other mRNA sequences.