Impediment of E. coli UvrD by DNA-destabilizing force reveals a strained-inchworm mechanism of DNA unwinding

• Published in: The EMBO journal 2008-12, Vol.27 (24), p.3279-3287
• Main Authors: Sun, Bo, Wei, Kong-Ji, Zhang, Bo, Zhang, Xing-Hua, Dou, Shuo-Xing, Li, Ming, Xi, Xu Guang
• Format: Article
• Language: English
• Subjects: Deoxyribonucleic acid; Dimerization; DNA; DNA Helicases - metabolism; DNA, Bacterial - metabolism; E coli; Enzymes; Escherichia coli; Escherichia coli - enzymology; Escherichia coli Proteins - metabolism; Genomics; helicase; Kinetics; Life Sciences; Models, Biological; Molecular biology; molecular motor; single molecule; Translocation; unwinding mechanism; UvrD
• ISSN: 0261-4189; 1460-2075
• DOI: 10.1038/emboj.2008.240

Escherichia coli UvrD is a non‐ring‐shaped model helicase, displaying a 3′—5′ polarity in DNA unwinding. Using a transverse magnetic tweezer and DNA hairpins, we measured the unwinding kinetics of UvrD at various DNA‐destabilizing forces. The multiform patterns of unwinding bursts and the distributions of the off‐times favour the mechanism that UvrD unwinds DNA as a dimer. The two subunits of the dimer coordinate to unwind DNA processively. They can jointly switch strands and translocate backwards on the other strand to allow slow (∼40 bp/s) rewinding, or unbind simultaneously to allow quick rehybridization. Partial dissociation of the dimer results in pauses in the middle of the unwinding or increases the translocation rate from ∼40 to ∼150 nt/s in the middle of the rewinding. Moreover, the unwinding rate was surprisingly found to decrease from ∼45 to ∼10 bp/s when the force is increased from 2 to 12 pN. The results lead to a strained‐inchworm mechanism in which a conformational change that bends and tenses the ssDNA is required to activate the dimer.