dorsal/arxiv
View SchemaDNA as a programmable viscoelastic nanoelement
| Authors | Richard A. Neher, Ulrich Gerland |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0506026 |
| URL | https://arxiv.org/abs/q-bio/0506026 |
| DOI | 10.1529/biophysj.105.068866 |
| Journal | Biophysical Journal, 89, 3846-3855 (2005) |
Abstract
The two strands of a DNA molecule with a repetitive sequence can pair into many different basepairing patterns. For perfectly periodic sequences, early bulk experiments of Poerschke indicate the existence of a sliding process, permitting the rapid transition between different relative strand positions [Biophys. Chem. 2 (1974) 83]. Here, we use a detailed theoretical model to study the basepairing dynamics of periodic and nearly periodic DNA. As suggested by Poerschke, DNA sliding is mediated by basepairing defects (bulge loops), which can diffuse along the DNA. Moreover, a shear force f on opposite ends of the two strands yields a characteristic dynamic response: An outward average sliding velocity v~1/N is induced in a double strand of length N, provided f is larger than a threshold f_c. Conversely, if the strands are initially misaligned, they realign even against an external force less than f_c. These dynamics effectively result in a viscoelastic behavior of DNA under shear forces, with properties that are programmable through the choice of the DNA sequence. We find that a small number of mutations in periodic sequences does not prevent DNA sliding, but introduces a time delay in the dynamic response. We clarify the mechanism for the time delay and describe it quantitatively within a phenomenological model. Based on our findings, we suggest new dynamical roles for DNA in artificial nanoscale devices. The basepairing dynamics described here is also relevant for the extension of repetitive sequences inside genomic DNA.
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"abstract": "The two strands of a DNA molecule with a repetitive sequence can pair into\nmany different basepairing patterns. For perfectly periodic sequences, early\nbulk experiments of Poerschke indicate the existence of a sliding process,\npermitting the rapid transition between different relative strand positions\n[Biophys. Chem. 2 (1974) 83]. Here, we use a detailed theoretical model to\nstudy the basepairing dynamics of periodic and nearly periodic DNA. As\nsuggested by Poerschke, DNA sliding is mediated by basepairing defects (bulge\nloops), which can diffuse along the DNA. Moreover, a shear force f on opposite\nends of the two strands yields a characteristic dynamic response: An outward\naverage sliding velocity v~1/N is induced in a double strand of length N,\nprovided f is larger than a threshold f_c. Conversely, if the strands are\ninitially misaligned, they realign even against an external force less than\nf_c. These dynamics effectively result in a viscoelastic behavior of DNA under\nshear forces, with properties that are programmable through the choice of the\nDNA sequence. We find that a small number of mutations in periodic sequences\ndoes not prevent DNA sliding, but introduces a time delay in the dynamic\nresponse. We clarify the mechanism for the time delay and describe it\nquantitatively within a phenomenological model. Based on our findings, we\nsuggest new dynamical roles for DNA in artificial nanoscale devices. The\nbasepairing dynamics described here is also relevant for the extension of\nrepetitive sequences inside genomic DNA.",
"arxiv_id": "q-bio/0506026",
"authors": [
"Richard A. Neher",
"Ulrich Gerland"
],
"categories": [
"q-bio.BM",
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],
"doi": "10.1529/biophysj.105.068866",
"journal_ref": "Biophysical Journal, 89, 3846-3855 (2005)",
"title": "DNA as a programmable viscoelastic nanoelement",
"url": "https://arxiv.org/abs/q-bio/0506026"
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