dorsal/arxiv
View SchemaDNA entropic elasticity for short molecules attached to beads
| Authors | Jinyu Li, Philip C. Nelson, M. D. Betterton |
|---|---|
| Categories | |
| ArXiv ID | physics/0601185 |
| URL | https://arxiv.org/abs/physics/0601185 |
Abstract
Single-molecule experiments in which force is applied to DNA or RNA molecules have enabled important discoveries of nucleic acid properties and nucleic acid-enzyme interactions. These experiments rely on a model of the polymer force-extension behavior to calibrate the experiments; typically the experiments use the worm-like chain (WLC) theory for double-stranded DNA and RNA. This theory agrees well with experiments for long molecules. Recent single-molecule experiments have used shorter molecules, with contour lengths in the range of 1-10 persistence lengths. Most WLC theory calculations to date have assumed infinite molecule lengths, and do not agree well with experiments on shorter chains. Key physical effects that become important when shorter molecules are used include (i) boundary conditions which constrain the allowed fluctuations at the ends of the molecule and (ii) rotational fluctuations of the bead to which the polymer is attached, which change the apparent extension of the molecule. We describe the finite worm-like chain (FWLC) theory, which takes into account these effects. We show the FWLC predictions diverge from the classic WLC solution for molecules with contour lengths a few times the persistence length. Thus the FWLC will allow more accurate experimental calibration for relatively short molecules, facilitating future discoveries in single-molecule force microscopy.
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"abstract": "Single-molecule experiments in which force is applied to DNA or RNA molecules\nhave enabled important discoveries of nucleic acid properties and nucleic\nacid-enzyme interactions. These experiments rely on a model of the polymer\nforce-extension behavior to calibrate the experiments; typically the\nexperiments use the worm-like chain (WLC) theory for double-stranded DNA and\nRNA. This theory agrees well with experiments for long molecules. Recent\nsingle-molecule experiments have used shorter molecules, with contour lengths\nin the range of 1-10 persistence lengths. Most WLC theory calculations to date\nhave assumed infinite molecule lengths, and do not agree well with experiments\non shorter chains. Key physical effects that become important when shorter\nmolecules are used include (i) boundary conditions which constrain the allowed\nfluctuations at the ends of the molecule and (ii) rotational fluctuations of\nthe bead to which the polymer is attached, which change the apparent extension\nof the molecule. We describe the finite worm-like chain (FWLC) theory, which\ntakes into account these effects. We show the FWLC predictions diverge from the\nclassic WLC solution for molecules with contour lengths a few times the\npersistence length. Thus the FWLC will allow more accurate experimental\ncalibration for relatively short molecules, facilitating future discoveries in\nsingle-molecule force microscopy.",
"arxiv_id": "physics/0601185",
"authors": [
"Jinyu Li",
"Philip C. Nelson",
"M. D. Betterton"
],
"categories": [
"physics.bio-ph",
"cond-mat.soft",
"q-bio.BM"
],
"title": "DNA entropic elasticity for short molecules attached to beads",
"url": "https://arxiv.org/abs/physics/0601185"
},
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