A New DNA Inversion Mechanism: Recombination of the DNA Foldback Intercoil Structure

Abstract

It is widely known that DNA inversion is performed by serine recombinases through site-specific recombination. In detail, the recombinases help recombination sites undergo exchange between inverted-repeat strands, resulting in the inversion of target sequences. However, the following questions still need to be clarified: (i) it is not clear how synaptic complex can be formed by recombinases, and (ii) the subunit rotation model for strand exchange is unexplained. To answer these questions, in this study, we propose a new DNA inversion mechanism based on the DNA foldback intercoil (FBI) structure. As a kind of four-stranded DNA structure, FBI is constructed by folding back a DNA duplex (loop part) and intertwining two inverted repeat sequences in the major groove (stem part). The stem part consists of four DNA strands sharing the same helical axis and its diameter is closely in agreement with that of a conventional B-DNA. We suggest that the recombination can be achieved within this stem part by flipping base pairs around their N-glycosidic bonds. It implies the recombination is performed by not only enzyme-DNA contact but also DNA-DNA interaction. Our hypothesis also suggests a spatially reliable pathway for strand exchange in consideration of geometrical features of the FBI structure. To verify the proposed DNA inversion pathway, we evaluate structural stability of intermediate conformations on the pathway in terms of conformational energy and robustness of new base pairing by using 3D computer modelling and molecular dynamics simulation. In conclusion, through this computational and theoretical approach, we demonstrate a new possibility of existence of more reasonable and effective DNA inversion mechanism in aid of the FBI structure.