S. White et al., ON THE PAIRING RULES FOR RECOGNITION IN THE MINOR-GROOVE OF DNA BY PYRROLE-IMIDAZOLE POLYAMIDES, Chemistry & biology, 4(8), 1997, pp. 569-578
Background: Cell-permeable small molecules that target predetermined D
NA sequences with high affinity and specificity have the potential to
control gene expression, A binary code has been developed to correlate
DNA sequence with side-by-side pairings between N-methylpyrrole (Py)
and N-methylimidazole (Im) carboxamides in the DNA minor groove, We se
t out to determine the relative energetics of pairings of Im/Py, Py/Im
, Im/Im, and Py/Py for targeting G.C and A.T base pairs. A key specifi
city issue, which has not been previously addressed, is whether an Im/
Im pair is energetically equivalent to an Im/Py pair for targeting G.C
base pairs. Results: Equilibrium association constants were determine
d at two five-basepair sites for a series of four six-ring hairpin pol
yamides, in order to test the relative energetics of the four aromatic
amino-acid pairings opposite G.C and A.T base pairs in the central po
sition, We observed that a G.C base pair was effectively targeted with
Im/Py but not Py/Im, Py/Py, or Im/Im. The A.T base pair was effective
ly targeted with Py/Py but not Im/Py, Py/Im, or Im/Im. Conclusions: An
Im/Im pairing is energetically disfavored for the recognition of both
A.T and G.C. This specificity will create important limitations on un
desirable slipped motifs that are available for unlinked dimers in the
minor groove. Baseline energetic parameters will thus be created whic
h, using the predictability of the current pairing rules for specific
molecular recognition of double-helical DNA, will guide further second
-generation polyamide design for DNA recognition.