Nucleic Acids Research, Vol 26, Issue 16 3640-3644, Copyright © 1998 by Oxford University Press
JP Rife, CS Cheng, PB Moore and SA Strobel
Modified nucleotides are resource-intensive alternatives to the four
nucleotides that constitute the bulk of natural RNAs. Yet, even in cases
where modifications are highly conserved, their functions are difficult to
identify. One possible function might be to modulate the stability of RNA
structures. To investigate this possibility for N 2- methylguanosine (m2G),
which is present in a wide variety of RNAs, we have determined the
thermodynamic consequences of substituting m2G for G in G-C Watson-Crick
pairs and G@U wobble pairs within RNA duplexes. The m2G substitution is
iso-energetic with G in all cases, except for aninternal m2G@U pair, where
it has a modest (0.3 kcal/mol) stabilizing effect. We have also examined
theconsequences of replacing G by m2G, and A by N 6, N 6-dimethyladenosine
(m26A) in the helix 45 tetraloop of 16S rRNA, which would otherwise be a
standard GNRA tetraloop. This loop is a conserved, hypermethylated region
of the ribosome where methylation appears to modulate activity. m26A
substitution destabilizes the tetraloop, presumably because it prevents the
formation of the G@A sheared pair it would otherwise contain. m2G
substitution has no effect on tetraloop stability. Together, these results
suggest that m2G is equally stable as either the s-cis or s- trans rotamer.
The lack of a significant effect on secondary structural stability in these
systems suggests that m2G is introduced into naturally occurring RNAs for
reasons other than modulation of duplex stability.
ARTICLES
N 2-methylguanosine is iso-energetic with guanosine in RNA duplexes and GNRA tetraloops
Department of Chemistry and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
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