DNA-DNA sequence homology recognition: physical mechanisms and open questions

First, we summarize recent experimental facts on homologous DNA pairing in vitro and discuss possible mechanisms of DNA-DNA sequence recognition. Then, we overview the mechanism of DNA-DNA recognition based on complementarity of DNA charge patterns. The theory predicts the recognition energy up to 10 k(B) T for close parallel homologous DNA fragments of gene-relevant lengths. We argue why this estimate cannot be directly applied to pairing of homologous DNA loci in experiments on yeast chromosomes. Namely, DNA-DNA distances assessed from experiments are much larger than those typically used in theory. Finally, we suggest some experiments that could help to judge whether short-range electrostatic forces indeed govern DNA pairing. This viewpoint paper introduces recently developed theoretical concepts to molecular biologists, with a hope to generate a junction between theory and future experiments on DNA recognition.