How to determine local stretching and tension in a flow-stretched DNA molecule

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    Abstract

    We determine the nonuniform stretching of and tension in amega base pairs-long fragment of deoxyribonucleic acid (DNA) that is flow stretched in a nanofluidic chip. We use no markers, do not know the contour length of the DNA, and do not have the full DNA molecule inside our field of view. Instead, we analyze the transverse thermal motion of the DNA. Tension at the center of the DNA adds up to 16 pN, giving almost fully stretched DNA. This method was devised for optical mapping of DNA, specifically, DNA denaturation patterns. It may be useful also for other studies, e.g., DNA-protein interactions, specifically, their tension dependence. Generally, wherever long strands of DNA—e.g., native DNA extracted from human cells or bacteria—must be stretched with ease for inspection, this method applies.
    Original languageEnglish
    Article number042405
    JournalPhysical Review E
    Volume93
    Issue number4
    Number of pages17
    ISSN2470-0045
    DOIs
    Publication statusPublished - 2016

    Bibliographical note

    ©2016 American Physical Society

    Cite this

    @article{89784e0cdf994a57974795505971fb93,
    title = "How to determine local stretching and tension in a flow-stretched DNA molecule",
    abstract = "We determine the nonuniform stretching of and tension in amega base pairs-long fragment of deoxyribonucleic acid (DNA) that is flow stretched in a nanofluidic chip. We use no markers, do not know the contour length of the DNA, and do not have the full DNA molecule inside our field of view. Instead, we analyze the transverse thermal motion of the DNA. Tension at the center of the DNA adds up to 16 pN, giving almost fully stretched DNA. This method was devised for optical mapping of DNA, specifically, DNA denaturation patterns. It may be useful also for other studies, e.g., DNA-protein interactions, specifically, their tension dependence. Generally, wherever long strands of DNA—e.g., native DNA extracted from human cells or bacteria—must be stretched with ease for inspection, this method applies.",
    author = "Pedersen, {Jonas Nyvold} and Rodolphe Marie and Anders Kristensen and Henrik Flyvbjerg",
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    How to determine local stretching and tension in a flow-stretched DNA molecule. / Pedersen, Jonas Nyvold; Marie, Rodolphe ; Kristensen, Anders; Flyvbjerg, Henrik.

    In: Physical Review E, Vol. 93, No. 4, 042405, 2016.

    Research output: Contribution to journalJournal articleResearchpeer-review

    TY - JOUR

    T1 - How to determine local stretching and tension in a flow-stretched DNA molecule

    AU - Pedersen, Jonas Nyvold

    AU - Marie, Rodolphe

    AU - Kristensen, Anders

    AU - Flyvbjerg, Henrik

    N1 - ©2016 American Physical Society

    PY - 2016

    Y1 - 2016

    N2 - We determine the nonuniform stretching of and tension in amega base pairs-long fragment of deoxyribonucleic acid (DNA) that is flow stretched in a nanofluidic chip. We use no markers, do not know the contour length of the DNA, and do not have the full DNA molecule inside our field of view. Instead, we analyze the transverse thermal motion of the DNA. Tension at the center of the DNA adds up to 16 pN, giving almost fully stretched DNA. This method was devised for optical mapping of DNA, specifically, DNA denaturation patterns. It may be useful also for other studies, e.g., DNA-protein interactions, specifically, their tension dependence. Generally, wherever long strands of DNA—e.g., native DNA extracted from human cells or bacteria—must be stretched with ease for inspection, this method applies.

    AB - We determine the nonuniform stretching of and tension in amega base pairs-long fragment of deoxyribonucleic acid (DNA) that is flow stretched in a nanofluidic chip. We use no markers, do not know the contour length of the DNA, and do not have the full DNA molecule inside our field of view. Instead, we analyze the transverse thermal motion of the DNA. Tension at the center of the DNA adds up to 16 pN, giving almost fully stretched DNA. This method was devised for optical mapping of DNA, specifically, DNA denaturation patterns. It may be useful also for other studies, e.g., DNA-protein interactions, specifically, their tension dependence. Generally, wherever long strands of DNA—e.g., native DNA extracted from human cells or bacteria—must be stretched with ease for inspection, this method applies.

    U2 - 10.1103/PhysRevE.93.042405

    DO - 10.1103/PhysRevE.93.042405

    M3 - Journal article

    C2 - 27176327

    VL - 93

    JO - Physical Review E (Statistical, Nonlinear, and Soft Matter Physics)

    JF - Physical Review E (Statistical, Nonlinear, and Soft Matter Physics)

    SN - 2470-0045

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