The possible recognition between double stranded (ds) DNA with homologous sequences was many times invoked to explain different biological observations. Direct pairing was considered among other possibilities, but it seems hardly compatible with the DNA structure . Using quantum chemistry, molecular mechanics, and hints from recent genetics experiments (Nat.Commun.5,3509,2014) here it is shown that direct recognition between homologous dsDNA is possible through formation of short quadruplexes by complementary hydrogen bonding of the major grooves . The constraints imposed by the predicted structures of the recognition units determine the mechanism of complexation between long dsDNA. This mechanism agrees with experimental data and explains several puzzling observations on the sequence dependence and the involvement of topoisomerases in the recognition.
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.
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The possible recognition between
Molecular recognition between two
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was many times invoked to explain different biological observations. Direct pairing was considered among other possibilities, but it seems hardly
may not seem
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DNA structure .
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.
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(Nat.Commun.5,3509,2014) here it is shown
I show here
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by
due to direct
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the major grooves
major groove surfaces in parallel alignment
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agrees with
and concomitant predictions agree with available
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explains several puzzling observations on the sequence dependence and the involvement of topoisomerases
shed light upon the sequence effects and the possible involvement of topoisomerase II