  Molecular recognition between two double stranded (ds) DNA with homologous
sequences may not seem compatible with the B-DNA structure because the sequence
information is hidden when it is used for joining the two strands.
Nevertheless, it has to be invoked to account for various biological data.
Using quantum chemistry, molecular mechanics, and hints from recent genetics
experiments I show here that direct recognition between homologous dsDNA is
possible through formation of short quadruplexes due to direct complementary
hydrogen bonding of major groove surfaces in parallel alignment. The
constraints imposed by the predicted structures of the recognition units
determine the mechanism of complexation between long dsDNA. This mechanism and
concomitant predictions agree with available experimental data and shed light
upon the sequence effects and the possible involvement of topoisomerase II in
the recognition.
