Modelling single-molecule kinetics of helicase translocation using high-resolution nanopore tweezers (SPRNT).
Helicases
enzymology
kinetics
nanopores
single-molecule
Journal
Essays in biochemistry
ISSN: 1744-1358
Titre abrégé: Essays Biochem
Pays: England
ID NLM: 0043306
Informations de publication
Date de publication:
16 04 2021
16 04 2021
Historique:
received:
30
09
2020
revised:
23
11
2020
accepted:
30
11
2020
pubmed:
26
1
2021
medline:
7
4
2022
entrez:
25
1
2021
Statut:
ppublish
Résumé
Single-molecule picometer resolution nanopore tweezers (SPRNT) is a technique for monitoring the motion of individual enzymes along a nucleic acid template at unprecedented spatiotemporal resolution. We review the development of SPRNT and the application of single-molecule kinetics theory to SPRNT data to develop a detailed model of helicase motion along a single-stranded DNA substrate. In this review, we present three examples of questions SPRNT can answer in the context of the Superfamily 2 helicase Hel308. With Hel308, SPRNT's spatiotemporal resolution enables resolution of two distinct enzymatic substates, one which is dependent upon ATP concentration and one which is ATP independent. By analyzing dwell-time distributions and helicase back-stepping, we show, in detail, how SPRNT can be used to determine the nature of these observed steps. We use dwell-time distributions to discern between three different possible models of helicase backstepping. We conclude by using SPRNT's ability to discern an enzyme's nucleotide-specific location along a DNA strand to understand the nature of sequence-specific enzyme kinetics and show that the sequence within the helicase itself affects both step dwell-time and backstepping probability while translocating on single-stranded DNA.
Identifiants
pubmed: 33491732
pii: 227668
doi: 10.1042/EBC20200027
pmc: PMC8722770
mid: NIHMS1764190
doi:
Substances chimiques
DNA, Single-Stranded
0
Nucleotides
0
DNA Helicases
EC 3.6.4.-
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
109-127Subventions
Organisme : NHGRI NIH HHS
ID : R01 HG005115
Pays : United States
Informations de copyright
© 2021 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.
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