Sequence-dependent base pair stepping dynamics in XPD helicase unwinding

Zhi Qi; Robert A Pugh; Maria Spies; Yann R Chemla

doi:10.7554/eLife.00334

Helicases couple the chemical energy of ATP hydrolysis to directional translocation along nucleic acids and transient duplex separation. Understanding helicase mechanism requires that the basic physicochemical process of base pair separation be understood. This necessitates monitoring helicase activity directly, at high spatio-temporal resolution. Using optical tweezers with single base pair (bp) resolution, we analyzed DNA unwinding by XPD helicase, a Superfamily 2 (SF2) DNA helicase involved in DNA repair and transcription initiation. We show that monomeric XPD unwinds duplex DNA in 1-bp steps, yet exhibits frequent backsteps and undergoes conformational transitions manifested in 5-bp backward and forward steps. Quantifying the sequence dependence of XPD stepping dynamics with near base pair resolution, we provide the strongest and most direct evidence thus far that forward, single-base pair stepping of a helicase utilizes the spontaneous opening of the duplex. The proposed unwinding mechanism may be a universal feature of DNA helicases that move along DNA phosphodiester backbones. DOI: http://dx.doi.org/10.7554/eLife.00334.001 During many cellular processes, the double helix must be transiently unwound so that the enzymes responsible for maintaining the genome can access the two strands. During DNA synthesis, for instance, the two strands of DNA are first separated and then used as templates for the production of new strands. The role of destabilizing, separating and unwinding the double helix falls to enzymes known as DNA helicases. Helicases are also involved in separating strands of nucleic acids during myriad other cellular processes, including DNA repair, transcription and translation. While the functions of helicases are clear, the precise mechanisms by which they unwind DNA are not. Here, Qi et al. have investigated the mechanism of a helicase called XPD, which is involved in DNA repair and the initiation of transcription of DNA into RNA. Using optical tweezers—in which a laser beam is used to exert extremely small forces on a single DNA molecule—they followed the activity of individual molecules of XPD as they unwound DNA with base pair resolution. Qi et al. observed that the helicase unwinds DNA strands 1 base pair at a time, but that it sometimes moves backwards by 1 base pair and at other times makes 5 base pair backward and forward steps. The frequency of these backwards steps depends on the availability of ATP, and the sequence of the DNA. Due to the high resolution of the data, Qi et al. were able to correlate these stepping dynamics with the DNA sequence with base pair level accuracy. While some helicases actively separate the strands, using energy derived from ATP to break the hydrogen bonds between pairs of bases, Qi et al. showed that XPD appears to take advantage of momentary separations that arise spontaneously between base pairs. As well as providing insights into the role of XPD in DNA repair and transcription, the work of Qi et al. presents a method that could be used to explore the mechanisms of other helicases. Given that the unwinding mechanism described here is likely to be a universal feature of enzymes related to XPD, the current work could shed light on a number of other cellular processes involving XPD-like helicases, such as homologous DNA recombination, inter-strand cross-link repair, and accurate chromosome segregation. DOI: http://dx.doi.org/10.7554/eLife.00334.002

Sequence-dependent base pair stepping dynamics in XPD helicase unwinding

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