TITLE:
Sequence and structure of naturally-occurring tRNA transcripts and site-directed variants are significant barriers to forming oligomers beyond dimers
AUTHORS:
Harold S. Bernhardt, Warren P. Tate
KEYWORDS:
Transfer RNA; TRNA; Dimerization; Oligomerization; Kissing-Loop Interaction
JOURNAL NAME:
Advances in Bioscience and Biotechnology,
Vol.4 No.5A,
May
27,
2013
ABSTRACT: Dimers of tRNAs can form through quasi self-complementary
anticodon-anticodon interactions, for example at neutral pH in yeast tRNAAsp(GUC) and at pH4.5 inEscherichia coli tRNAGly(GCC) through a partially protonated interaction. The requirements for tRNA
oligomerization, and the factors that prevented higher orders of structures
forming were examined with unmodified wild-type and variant E. coli tRNAsGly(GCC). Non-denaturing
agarose gel electrophoresis was used as a rapid screening method. A number of
tRNAGly(GCC) variants with nucleotide substitutions in the loop
regions formed dimers, but surprisingly there was no evidence that distinct
higher oligomers formed in any of the variants tested. The dimer interfaces of
two of the variants were delineated by competitive inhibition with complementary
DNA oligonucleotides. Components of an oligomerization facilitating buffer,
containing monovalent, divalent and multivalent cations (magnesium and sodium
ions and spermine), were tested separately and in combination, to optimize
oligomerization and its detection using agarose gel electrophoresis. A rationale
for the requirement for magnesium for dimerization is suggested from its role
in RNA loop-loop interactions. Sequence specific variant tRNAs that can
rapidly form heterodimers with damaging infectious RNA are potential
therapeutic agents against viral mechanisms by acting as base pairing
inhibitors.