Single-molecule probing the duplex and G4 unwinding patterns of a RecD family helicase

Xue, Zhen-Yong; Wu, Wen-Qiang; Zhao, Xiaocong; Kumar, Arvind; Ran, Xia; Zhang, Yueyue; Guo, Lijun

doi:10.1016/j.ijbiomac.2020.07.158

Cited by 10 publications

(8 citation statements)

References 62 publications

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“…One additional point to be noted here is that DrRecD2 can resolve the secondary structure of the 5!" platform in order to bind, this observation is in agreement with previous studies [14].…”

Section: Resultssupporting

confidence: 94%

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Probing the molecular mechanism of the action of Deinococcus radiodurans RecD2 at single-molecule resolution

Purkait

Islam

Mishra

2021

Preprint

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Helicases are ATP-driven molecular machines that directionally remodel nucleic acid polymers in all three domains of life. Helicases are responsible for resolving double-stranded DNA (dsDNA) into separate single-strands and this activity is essential for DNA replication, nucleotide excision repair, and homologous recombination. RecD2 from Deinococcus radiodurans (DrRecD2) has important contributions towards its unusually high tolerance to gamma radiation and hydrogen peroxide. Although previous X-ray Crystallography studies have revealed the structural characteristics of the protein, the direct experimental evidence regarding the dynamics of the DNA unwinding process by DrRecD2 in the context of other accessory proteins is yet to be found. In this study, we have probed the exact binding event and processivity of DrRecD2 at single-molecule resolution using Protein-induced fluorescence enhancement (smPIFE) and Forster resonance energy transfer (smFRET). We have found that the protein prefers to bind at the 5 prime terminal end of the single-stranded DNA (ssDNA) by Drift and has helicase activity even in absence of ATP. However, a faster and iterative mode of DNA unwinding was evident in presence of ATP. The rate of translocation of the protein was found to be slower on dsDNA compared to ssDNA. We also showed that DrRecD2 is recruited at the binding site by the single-strand binding protein (SSB) and during the unwinding, it can displace RecA from ssDNA.

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Section: Resultssupporting

confidence: 94%

“…All the previous studies have mentioned that a 10 to 15 nucleotides long ssDNA is required as the binding substrate for DrRecD2 (molecular weight of approximately 76.4 kDa) [12][13][14], hence we designed a 12 nucleotides long ssDNA sequence (5!TACAGCTACCTA3!) as the binding platform of DrRecD2 (afterwards referred as 5' platform).…”

Section: Resultsmentioning

confidence: 99%

Probing the molecular mechanism of the action of Deinococcus radiodurans RecD2 at single-molecule resolution

Purkait

Islam

Mishra

2021

Preprint

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“…To compare the activity levels of the three KH domains, the unwinding fractions of the Py25′ i-motifs calculated based on the peak areas of FRET ∼0.9 at certain times were fitted using single-exponential decays ( Fig. 9 D ) ( 33 , 35 ). Their unwinding parameters are shown in Table S3 .…”

Section: Resultsmentioning

confidence: 99%

Mechanistic insights into poly(C)-binding protein hnRNP K resolving i-motif DNA secondary structures

Wu¹,

Zhang²,

Bai

et al. 2022

Journal of Biological Chemistry

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“…Petite integration factor 1 (PIF1) helicases are 5′-3′ DNA helicases, which are widely present in prokaryotic to eukaryotic organisms, and are outstanding for their potent G4 unwinding activity ( Ribeyre et al, 2009 ; Paeschke et al, 2013 ; Liu et al, 2015 ; Xue et al, 2020 ). For eukaryotes, the cellular functions of PIF1 have been elucidated through yeast studies.…”

Section: G-quadruplex Unwinding Helicases and Their Functionsmentioning

confidence: 99%

The Cellular Functions and Molecular Mechanisms of G-Quadruplex Unwinding Helicases in Humans

Liu

Zhu

Wang

et al. 2021

Front. Mol. Biosci.

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G-quadruplexes (G4s) are stable non-canonical secondary structures formed by G-rich DNA or RNA sequences. They play various regulatory roles in many biological processes. It is commonly agreed that G4 unwinding helicases play key roles in G4 metabolism and function, and these processes are closely related to physiological and pathological processes. In recent years, more and more functional and mechanistic details of G4 helicases have been discovered; therefore, it is necessary to carefully sort out the current research efforts. Here, we provide a systematic summary of G4 unwinding helicases from the perspective of functions and molecular mechanisms. First, we provide a general introduction about helicases and G4s. Next, we comprehensively summarize G4 unfolding helicases in humans and their proposed cellular functions. Then, we review their study methods and molecular mechanisms. Finally, we share our perspective on further prospects. We believe this review will provide opportunities for researchers to reach the frontiers in the functions and molecular mechanisms of human G4 unwinding helicases.

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Single-molecule probing the duplex and G4 unwinding patterns of a RecD family helicase

Cited by 10 publications

References 62 publications

Probing the molecular mechanism of the action of Deinococcus radiodurans RecD2 at single-molecule resolution

Probing the molecular mechanism of the action of Deinococcus radiodurans RecD2 at single-molecule resolution

Mechanistic insights into poly(C)-binding protein hnRNP K resolving i-motif DNA secondary structures

The Cellular Functions and Molecular Mechanisms of G-Quadruplex Unwinding Helicases in Humans

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