ArticleMethods in molecular biology (Clifton, N.J.)2012
Fluorescence methods to study DNA translocation and unwinding kinetics by nucleic acid motors.
Article in Methods in molecular biology (Clifton, N.J.), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 24 citations in OpenAlex.
- Subunit Communication within Dimeric SF1 DNA Helicases.Journal of molecular biology · 2024Article
- A new twist on PIFE: photoisomerisation-related fluorescence enhancement.Methods and applications in fluorescence · 2023Review
- Article
- CUREing biochemistry lab monotony.Journal of chemical education · 2022Article
- Determining translocation orientations of nucleic acid helicases.Methods (San Diego, Calif.) · 2022Review
- The Cellular Functions and Molecular Mechanisms of G-Quadruplex Unwinding Helicases in Humans.Frontiers in molecular biosciences · 2021Review
- Protein Environment and DNA Orientation Affect Protein-Induced Cy3 Fluorescence Enhancement.Biophysical journal · 2019Article
- Modulation of Escherichia coli UvrD Single-Stranded DNA Translocation by DNA Base Composition.Biophysical journal · 2017Article
- Monitoring Replication Protein A (RPA) dynamics in homologous recombination through site-specific incorporation of non-canonical amino acids.Nucleic acids research · 2017Article
- A rapid method for detecting protein-nucleic acid interactions by protein induced fluorescence enhancement.Scientific reports · 2016Article
- Methods to study the coupling between replicative helicase and leading-strand DNA polymerase at the replication fork.Methods (San Diego, Calif.) · 2016Review
- Processive DNA Unwinding by RecBCD Helicase in the Absence of Canonical Motor Translocation.Journal of molecular biology · 2016Article
- A Monomer of Pif1 Unwinds Double-Stranded DNA and It Is Regulated by the Nature of the Non-Translocating Strand at the 3'-End.Journal of molecular biology · 2016Article
- Diffusion of human replication protein A along single-stranded DNA.Journal of molecular biology · 2014Article
- Real-time fluorescence assays to monitor duplex unwinding and ATPase activities of helicases.Nature protocols · 2014Article
- Protein induced fluorescence enhancement (PIFE) for probing protein-nucleic acid interactions.Chemical Society reviews · 2014Review
- Translocation of Saccharomyces cerevisiae Pif1 helicase monomers on single-stranded DNA.Nucleic acids research · 2013Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Translocation of nucleic acid motor proteins (translocases) along linear nucleic acids can be studied by monitoring either the time course of the arrival of the motor protein at one end of the nucleic acid or the kinetics of ATP hydrolysis by the motor protein during translocation using pre-steady state ensemble kinetic methods in a stopped-flow instrument. Similarly, the unwinding of double-stranded DNA or RNA by helicases can be studied in ensemble experiments by monitoring either the kinetics of the conversion of the double-stranded nucleic acid into its complementary single strands by the helicase or the kinetics of ATP hydrolysis by the helicase during unwinding. Such experiments monitor translocation of the enzyme along or unwinding of a series of nucleic acids labeled at one position (usually the end) with a fluorophore or a pair of fluorophores that undergo changes in fluorescence intensity or efficiency of fluorescence resonance energy transfer (FRET). We discuss how the pre-steady state kinetic data collected in these ensemble experiments can be analyzed by simultaneous global nonlinear least squares (NLLS) analysis using simple sequential "n-step" mechanisms to obtain estimates of the macroscopic rates and processivities of translocation and/or unwinding, the rate-limiting step(s) in these mechanisms, the average "kinetic step-size," and the stoichiometry of coupling ATP binding and hydrolysis to movement along the nucleic acid.
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Registered trials
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.