S. Ebel et al., THERMODYNAMIC STABILITY AND SOLUTION CONFORMATION OF TANDEM G-CENTER-DOT-A MISMATCHES IN RNA AND RNA-CENTER-DOT-DNA HYBRID DUPLEXES, European journal of biochemistry, 220(3), 1994, pp. 703-715
G.A mismatches form a variety of hydrogen-bonded structures in DNA, mo
st of which destabilise the duplex. Tandem G A mismatches in the conte
xt YGAR (Y = pyrimidine, R = purine), however, form base pairs using t
he amino group of the guanine residue [Li, Y., Zon, G. and Wilson, W D
. (1991) Proc. Natl Acad. Sci. USA 88, 26-30], which permits extensive
base-base stacking, leading to a slight stabilisation of the helix [E
bel, S., Lane, A. N. and Brown, T. (1992) Biochemistry 31, 12083-12086
]. We have measured the thermodynamic stability of several RNA and RNA
DNA hybrid duplexes containing tandem G A mismatches. The RNA duplexe
s are intrinsically much more stable than the corresponding DNA duplex
es and the mutations are destabilising in all cases. NOE and coupling-
constant data show that all of the sugars are in the C3'-endo range of
conformations, and glycosidic torsion angles are in the range -160 de
grees to -180 degrees in r(CCACGAGUGG) r(CCACGAGUGG). Both sequential
NOE intensities and circular-dichroism measurements indicate that the
global conformation of the mismatched RNA is A-like. The N1H group of
the mismatched guanine residue is not involved in hydrogen bonding wit
h the adenine residue, indicating the presence of the amino-pairing sc
heme. Determination of the structure using 'loose' NMR-derived constra
ints shows that the potential energies of the imino-paired and amino-p
aired forms are similar, but substantially higher than energy-minimise
d RNA. Using tighter constraints derived from more extensive analysis
of one-dimensional and two-dimensional NOE data showed that the amino-
paired structure agrees with the constraint data better than the imino
-paired structure, and also accounts for unusual chemical shifts and t
he lack of hydrogen bonding of the guanine N1H group. Resulting molecu
lar models show that the amino-paired mismatches are not as extensivel
y stacked on the neighbouring part of the duplex as in the B-DNA analo
gues, largely accounting for the lower thermodynamic stability in the
RNA duplexes.