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  1. Article ; Online: Tracking Native

    Potratz, Jeffrey P / Russell, Rick

    Biochemistry

    2023  Volume 62, Issue 22, Page(s) 3173–3180

    Abstract: Folding of ... ...

    Abstract Folding of the
    MeSH term(s) Nucleic Acid Conformation ; RNA, Catalytic/metabolism ; Tetrahymena/genetics ; Fluorescence ; Introns ; Kinetics
    Chemical Substances RNA, Catalytic
    Language English
    Publishing date 2023-11-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021/acs.biochem.3c00363
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 217: Show issues Location:
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  2. Article ; Online: A tweak and a peek: How Cas9 pries open double-stranded DNA to check its sequence.

    Sinan, Selma / Russell, Rick

    Nature structural & molecular biology

    2022  Volume 29, Issue 4, Page(s) 286–288

    MeSH term(s) CRISPR-Cas Systems ; DNA
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2022-04-14
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2126708-X
    ISSN 1545-9985 ; 1545-9993
    ISSN (online) 1545-9985
    ISSN 1545-9993
    DOI 10.1038/s41594-022-00763-1
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  3. Article: Kinetic dissection of pre-crRNA binding and processing by CRISPR-Cas12a.

    Sinan, Selma / Appleby, Nathan M / Russell, Rick

    bioRxiv : the preprint server for biology

    2023  

    Abstract: CRISPR-Cas12a binds and processes a single pre-crRNA during maturation, providing a simple tool for genome editing applications. Here, we constructed a kinetic and thermodynamic framework for pre-crRNA processing by ... ...

    Abstract CRISPR-Cas12a binds and processes a single pre-crRNA during maturation, providing a simple tool for genome editing applications. Here, we constructed a kinetic and thermodynamic framework for pre-crRNA processing by Cas12a
    Language English
    Publishing date 2023-07-25
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.07.25.550589
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  4. Article ; Online: Impact of Ion-Mixing Entropy on Orientational Preferences of DNA Helices: FRET Measurements and Computer Simulations.

    Templeton, Clark / Hamilton, Ian / Russell, Rick / Elber, Ron

    The journal of physical chemistry. B

    2023  Volume 127, Issue 41, Page(s) 8796–8808

    Abstract: Biological processes require DNA and RNA helices to pack together in specific interhelical orientations. While electrostatic repulsion between backbone charges is expected to be maximized when helices are in parallel alignment, such orientations are ... ...

    Abstract Biological processes require DNA and RNA helices to pack together in specific interhelical orientations. While electrostatic repulsion between backbone charges is expected to be maximized when helices are in parallel alignment, such orientations are commonplace in nature. To better understand how the repulsion is overcome, we used experimental and computational approaches to investigate how the orientational preferences of DNA helices depend on the concentration and valence of mobile cations. We used Förster resonance energy transfer (FRET) to probe the relative orientations of two 24-bp helices held together via a freely rotating PEG linker. At low cation concentrations, the helices preferred more "cross"-like orientations over those closer to parallel, and this preference was reduced with increasing salt concentrations. The results were in good quantitative agreement with Poisson-Boltzmann (PB) calculations for monovalent salt (Na
    MeSH term(s) Fluorescence Resonance Energy Transfer ; Entropy ; Nucleic Acid Conformation ; DNA/metabolism ; Molecular Dynamics Simulation ; Cations ; Sodium ; Sodium Chloride ; Static Electricity
    Chemical Substances DNA (9007-49-2) ; Cations ; Sodium (9NEZ333N27) ; Sodium Chloride (451W47IQ8X)
    Language English
    Publishing date 2023-10-10
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.3c04354
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  5. Article ; Online: How to Kinetically Dissect an RNA Machine.

    Das, Rhiju / Russell, Rick

    Biochemistry

    2021  Volume 60, Issue 46, Page(s) 3485–3490

    Abstract: RNA-based machines are ubiquitous in Nature and increasingly important for medicines. They fold into complex, dynamic structures that process information and catalyze reactions, including reactions that generate new RNAs and proteins across biology. What ...

    Abstract RNA-based machines are ubiquitous in Nature and increasingly important for medicines. They fold into complex, dynamic structures that process information and catalyze reactions, including reactions that generate new RNAs and proteins across biology. What are the experimental strategies and steps that are necessary to understand how these complex machines work? Two 1990 papers from Herschlag and Cech on "Catalysis of RNA Cleavage by the
    MeSH term(s) Biocatalysis ; History, 20th Century ; Introns ; Kinetics ; RNA Precursors/metabolism ; RNA Splicing ; RNA, Catalytic/history ; RNA, Catalytic/metabolism ; Tetrahymena/genetics ; Tetrahymena/metabolism
    Chemical Substances RNA Precursors ; RNA, Catalytic
    Language English
    Publishing date 2021-09-07
    Publishing country United States
    Document type Historical Article ; Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021/acs.biochem.1c00392
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    Zs.A 217: Show issues Location:
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  6. Article ; Online: Reflections on 20 years of RNA folding, dynamics, and structure.

    Russell, Rick

    RNA (New York, N.Y.)

    2015  Volume 21, Issue 4, Page(s) 723–724

    MeSH term(s) Nucleic Acid Conformation ; RNA/chemistry
    Chemical Substances RNA (63231-63-0)
    Language English
    Publishing date 2015-03-16
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1241540-6
    ISSN 1469-9001 ; 1355-8382
    ISSN (online) 1469-9001
    ISSN 1355-8382
    DOI 10.1261/rna.050781.115
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    Zs.A 4777: Show issues Location:
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  7. Article ; Online: Direct Measurement of Interhelical DNA Repulsion and Attraction by Quantitative Cross-Linking.

    Hamilton, Ian / Gebala, Magdalena / Herschlag, Daniel / Russell, Rick

    Journal of the American Chemical Society

    2022  Volume 144, Issue 4, Page(s) 1718–1728

    Abstract: To better understand the forces that mediate nucleic acid compaction in biology, we developed the disulfide cross-linking approach xHEED (X-linking of Helices to measure Electrostatic Effects at Distance) to measure the distance-dependent encounter ... ...

    Abstract To better understand the forces that mediate nucleic acid compaction in biology, we developed the disulfide cross-linking approach xHEED (X-linking of Helices to measure Electrostatic Effects at Distance) to measure the distance-dependent encounter frequency of two DNA helices in solution. Using xHEED, we determined the distance that the electrostatic potential extends from DNA helices, the dependence of this distance on ionic conditions, and the magnitude of repulsion when two helices approach one another. Across all conditions tested, the potential falls to that of the bulk solution within 15 Å of the major groove surface. For separations of ∼30 Å, we measured a repulsion of 1.8 kcal/mol in low monovalent ion concentration (30 mM Na
    MeSH term(s) Cobalt/chemistry ; DNA/chemistry ; Disulfides/chemistry ; Kinetics ; Magnesium/chemistry ; Nucleic Acid Conformation ; Sodium/chemistry ; Static Electricity
    Chemical Substances Disulfides ; Cobalt (3G0H8C9362) ; DNA (9007-49-2) ; Sodium (9NEZ333N27) ; Magnesium (I38ZP9992A)
    Language English
    Publishing date 2022-01-24
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021/jacs.1c11122
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  8. Article ; Online: Measurement of ATP utilization in RNA unwinding and RNA chaperone activities by DEAD-box helicase proteins.

    Jarmoskaite, Inga / Helmers, Anna E / Russell, Rick

    Methods in enzymology

    2022  Volume 673, Page(s) 53–76

    Abstract: RNA helicase proteins perform coupled reactions in which cycles of ATP binding and hydrolysis are used to drive local unwinding of double-stranded RNA (dsRNA). For some helicases in the ubiquitous DEAD-box family, these local unwinding events are ... ...

    Abstract RNA helicase proteins perform coupled reactions in which cycles of ATP binding and hydrolysis are used to drive local unwinding of double-stranded RNA (dsRNA). For some helicases in the ubiquitous DEAD-box family, these local unwinding events are integral to folding transitions in structured RNAs, and thus these helicases function as RNA chaperones. An important measure of the efficiency of the helicase-catalyzed reaction is the ATP utilization value, which represents the average number of ATP molecules hydrolyzed during RNA unwinding or a chaperone-assisted RNA structural rearrangement. Here we outline procedures that can be used to measure the ATP utilization value in RNA unwinding or folding transitions. As an example of an RNA folding transition, we focus on the refolding of the Tetrahymena thermophila group I intron ribozyme from a long-lived misfolded structure to its native structure, and we outline strategies for adapting this assay to other RNA folding transitions. For a simple dsRNA unwinding event, the ATP utilization value provides a measure of the coupling between the ATPase and RNA unwinding activities, and for a complex RNA structural transition it can give insight into the scope of the rearrangement and the efficiency with which the helicase uses the energy from ATPase cycles to promote the rearrangement.
    MeSH term(s) Adenosine Triphosphatases/metabolism ; Adenosine Triphosphate/metabolism ; DEAD-box RNA Helicases/chemistry ; DEAD-box RNA Helicases/genetics ; DEAD-box RNA Helicases/metabolism ; DNA Helicases/metabolism ; Nucleic Acid Conformation ; RNA, Double-Stranded
    Chemical Substances RNA, Double-Stranded ; Adenosine Triphosphate (8L70Q75FXE) ; Adenosine Triphosphatases (EC 3.6.1.-) ; DNA Helicases (EC 3.6.4.-) ; DEAD-box RNA Helicases (EC 3.6.4.13)
    Language English
    Publishing date 2022-05-14
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ISSN 1557-7988
    ISSN (online) 1557-7988
    DOI 10.1016/bs.mie.2022.04.004
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  9. Article ; Online: Unwinding the mechanisms of a DEAD-box RNA helicase in cancer.

    Russell, Rick

    Journal of molecular biology

    2015  Volume 427, Issue 9, Page(s) 1797–1800

    MeSH term(s) Adenosine Triphosphate/metabolism ; DEAD-box RNA Helicases/genetics ; DEAD-box RNA Helicases/metabolism ; Humans ; Medulloblastoma/genetics ; Mutation/genetics ; RNA/genetics
    Chemical Substances RNA (63231-63-0) ; Adenosine Triphosphate (8L70Q75FXE) ; DEAD-box RNA Helicases (EC 3.6.4.13)
    Language English
    Publishing date 2015-05-08
    Publishing country England
    Document type Comment ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2015.03.009
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    Zs.A 867: Show issues Location:
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  10. Article ; Online: Kinetics measurements of G-quadruplex binding and unfolding by helicases.

    Chang-Gu, Bruce / Venkatesan, Sneha / Russell, Rick

    Methods (San Diego, Calif.)

    2022  Volume 204, Page(s) 1–13

    Abstract: G-quadruplex structures (G4s) form readily in DNA and RNA and play diverse roles in gene expression and other processes, and their inappropriate formation and stabilization are linked to human diseases. G4s are inherently long-lived, such that their ... ...

    Abstract G-quadruplex structures (G4s) form readily in DNA and RNA and play diverse roles in gene expression and other processes, and their inappropriate formation and stabilization are linked to human diseases. G4s are inherently long-lived, such that their timely unfolding depends on a suite of DNA and RNA helicase proteins. Biochemical analysis of G4 binding and unfolding by individual helicase proteins is important for establishing their levels of activity, affinity, and specificity for G4s, including individual G4s of varying sequence and structure. Here we describe a set of simple, accessible methods in which electrophoretic mobility shift assays (EMSA) are used to measure the kinetics of G4 binding, dissociation, and unfolding by helicase proteins. We focus on practical considerations and the pitfalls that are most likely to arise when these methods are used to study the activities of helicases on G4s.
    MeSH term(s) DEAD-box RNA Helicases/chemistry ; DNA/chemistry ; DNA Helicases/genetics ; DNA Helicases/metabolism ; G-Quadruplexes ; Humans ; Kinetics ; RNA/genetics
    Chemical Substances RNA (63231-63-0) ; DNA (9007-49-2) ; DNA Helicases (EC 3.6.4.-) ; DEAD-box RNA Helicases (EC 3.6.4.13)
    Language English
    Publishing date 2022-04-25
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1066584-5
    ISSN 1095-9130 ; 1046-2023
    ISSN (online) 1095-9130
    ISSN 1046-2023
    DOI 10.1016/j.ymeth.2022.04.012
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