ArticleNucleic acids research2019
Determining the effects of DNA sequence on Hel308 helicase translocation along single-stranded DNA using nanopore tweezers.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 47 citations in OpenAlex.
- HELQ & Hel308: ancient enzymes of DNA repair and recombination.Biochemical Society transactions · 2026Review
- An information theory approach to quantifying the sequence-dependent response of nucleic acid motors with applications to nanopore DNA sequencing.Nature communications · 2026Article
- Review
- Structural and functional insights into acidophilic helicases as DNA-unwinding motors.Applied and environmental microbiology · 2025Article
- Sequencing a DNA analog composed of artificial bases.Nature communications · 2025Article
- Unwinding process of DNA/RNA quadruplexes by proteins under label-free nanopore monitoring.Nucleic acids research · 2025Article
- Redesign of Translocon EXP2 Nanopore for Detecting Peptide Fragments.Small methods · 2025Article
- Helicase HELQ: Molecular Characters Fit for DSB Repair Function.International journal of molecular sciences · 2024Review
- Nanopores map the acid-base properties of a single site in a single DNA molecule.Nucleic acids research · 2024Article
- Nanopore tweezers show fractional-nucleotide translocation in sequence-dependent pausing by RNA polymerase.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Detection of phosphorylation post-translational modifications along single peptides with nanopores.Nature biotechnology · 2024Article
- Observing inhibition of the SARS-CoV-2 helicase at single-nucleotide resolution.Nucleic acids research · 2023Article
- Archaeal Hel308 suppresses recombination through a catalytic switch that controls DNA annealing.Nucleic acids research · 2023Article
- Assessing Readability of an 8-Letter Expanded Deoxyribonucleic Acid Alphabet with Nanopores.Journal of the American Chemical Society · 2023Article
- Mesoscience in cell biology and cancer research.Cancer innovation · 2022Review
- Nanopore tweezers measurements of RecQ conformational changes reveal the energy landscape of helicase motion.Nucleic acids research · 2022Article
- Inhibition of the SARS-CoV-2 helicase at single-nucleotide resolution.bioRxiv : the preprint server for biology · 2022Article
- Sequence-dependent mechanochemical coupling of helicase translocation and unwinding at single-nucleotide resolution.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Epigenetic tumor heterogeneity in the era of single-cell profiling with nanopore sequencing.Clinical epigenetics · 2022Review
- Direct detection of RNA modifications and structure using single-molecule nanopore sequencing.Cell genomics · 2022Article
Corrections and comments
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Authors and funding
10 authors at 1 institution in 1 country.
Funding
Abstract
Motor enzymes that process nucleic-acid substrates play vital roles in all aspects of genome replication, expression, and repair. The DNA and RNA nucleobases are known to affect the kinetics of these systems in biologically meaningful ways. Recently, it was shown that DNA bases control the translocation speed of helicases on single-stranded DNA, however the cause of these effects remains unclear. We use single-molecule picometer-resolution nanopore tweezers (SPRNT) to measure the kinetics of translocation along single-stranded DNA by the helicase Hel308 from Thermococcus gammatolerans. SPRNT can measure enzyme steps with subangstrom resolution on millisecond timescales while simultaneously measuring the absolute position of the enzyme along the DNA substrate. Previous experiments with SPRNT revealed the presence of two distinct substates within the Hel308 ATP hydrolysis cycle, one [ATP]-dependent and the other [ATP]-independent. Here, we analyze in-depth the apparent sequence dependent behavior of the [ATP]-independent step. We find that DNA bases at two sites within Hel308 control sequence-specific kinetics of the [ATP]-independent step. We suggest mechanisms for the observed sequence-specific translocation kinetics. Similar SPRNT measurements and methods can be applied to other nucleic-acid-processing motor enzymes.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.