The DOI matches its Crossref record; 47 of the 47 references it cites were found in a registry or an index.
Direct observation of processive exoribonuclease motion using optical tweezers
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Significance: Bacteria regulate the synthesis and degradation of RNA molecules to ensure timely and robust responses to an ever-changing environment. The transcript’s lifetime can be influenced profoundly by a secondary structure that can form in the RNA and that may inhibit or promote its digestion by RNases. The molecular mechanisms by which RNases interact with structured RNAs therefore are of great interest. In this study we used optical tweezers to investigate the mechanistic properties of two such enzymes from Escherichia coli , polynucleotide phosphorylase and RNase R. Our results offer new insights into the functional characteristics of these two enzymes, including the sequence-dependent behavior of RNase R and the presence of discrete steps of six or seven nucleotides taken by polynucleotide phosphorylase.
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The degradation speed of an mRNA polymer chain was taken to be 88 nt / s.
“with the speed taken to be 88 nt / s.”
From Bringing the genetically minimal cell to life on a computer in 4D (2026) · cites this paper as [96]
The Results report an average RNase R velocity of 88 ± 8 nt/s, supporting the speed used in the citing sentence. That measurement was made on a dsRNA construct held at 20 pN; the paper does not establish 88 nt/s as the degradation speed of an mRNA polymer chain generally. (LLM, conf=0.84)
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“The rate of degradation is then determined by a velocity of 88 nt/s measured for the exoribonuclease RNase R using optical tweezers (Fazal et al., 2015) divided by the length of the mRNA.”
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“Notable examples include the development of far-off resonance traps (FORTs) for confining atoms [6, 7], the use of optical tweezers to generate three-dimensional optical crystals [8, 9], and the application of ODF traps for the manipulation of biological molecules [10, 11], measurements of bond strengths [12], and pro…”
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“0 ( , ) exp( ) ( ), z r E r z A ik z J k r (1)”
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“More recently, nanowires and nanotubes [4], flat particles [5], DNA [6], bacteria [7], and exonucleases and helicases [8] have all been successfully trapped and studied using optical tweezers.”
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“As for the other enzymes, we add a capacity constraint for the RNase to account for its cost, where we use k deg RNase ¼ 88 NT s (cid:2) 1 of an enzyme called RNase R 30 .”
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“Investigating mechanical changes in cancer cells [2], examining enzyme activity [3], and stretching single molecules [4] are just a few of the studies that have been enabled by optical tweezers.”
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“This selectivity has allowed researchers to directly observe enzyme behaviour in highly controlled conditions [20].”
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Metadata
- Authors
- Fazal, F. M., Koslover, D. J., Luisi, B. F., & Block, S. M.
- Affiliations
- Stanford University (US)
- University of Cambridge (GB)
- Corresponding author
- Block, Steven M.
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2015-11-23
- Volume
- 112
- Issue
- 49
- Pages
- 15101-15106
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC4679025
- OpenAlex
- W2261670798
- Cited by
- 29
- References
- 47
- Citations by year
- 2026: 2 · 2024: 1 · 2023: 4 · 2022: 4 · 2021: 1 · 2020: 3 · 2019: 3 · 2018: 6 · 2017: 3 · 2016: 2
- FWCI
- 1.59
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- HHS | NIH | National Institute of General Medical Sciences (GM057035)
- Wellcome Trust (none)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Force Microscopy Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Keywords
- RNase R, polynucleotide phosphorylase, RNA degradation, inchworm mechanism, RNA-binding domain, KH domain, S1 domain, Escherichia coli, helicase
- MeSH terms
- DNA, Exoribonucleases, RNA, Optical Tweezers
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