Modeling of the mechanism of interactions of oligonucleotides with 3'-end of the yeast tRNA (Phe)
Vorob'ev, I.N.
Molekuliarnaia Biologiia 39(5): 887-895
2005
ISSN/ISBN: 0026-8984 PMID: 16240722 Document Number: 594690
Three dimensional atomic models of complexes between 10-, 15-mer long oligonucleotides and east tRNAPhe have been calculated. It has been found that the fast-forming primary complexes are the major groove complexes with the coaxial acceptor- and T-steams of the tRNA(Phe). Oligonucleotide forms a triplex of the recombinant R-triplex type. The long steams allow to make a "strong complexes" whith oligonucleotide, which delivers its 3'-end nucleotides to the vicinity of the T-loop, adjacent to the steam. These nucleotides destabilize the loop structure and initiate conformational rearrangement with a local destruction of the tRNA(Phe) and formation of the final tRNA(Phe)-oligonucleotide complementary complex. The primary complex formation and following destruction of the tRNA(Phe) constitutes the mechanism of the 'molecular wedge'. The effective anticense oligonucleotide should consist of the three segments: 1--complex initiator, 2--complex formative, 3--loop destructor an have to be complementary to the tRNA structure element of [(free end)/loop-steam-loop].