Before revision:  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 .
After revision:  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 I show here that direct recognition between homologous dsDNA is possible through formation of short quadruplexes by complementary hydrogen bonding of the major grooves .