Modelling DNA stretching for physics and biology.
We have used internal coordinate molecular mechanics calculations to study how the DNA double helix deforms upon stretching. Results obtained for polymeric DNA under helical symmetry constraints suggest that two distinct forms, an unwound ribbon and a narrow fibre, can be formed as a function of which ends of the duplex are pulled. Similar results are also obtained with DNA oligomers. These experiments lead to force curves which exhibit a plateau as the conformational transition occurs. This behaviour is confirmed by applying an increasing force to DNA and observing a sudden length increase at a critical force value. It is finally shown some DNA binding proteins can also stretch DNA locally, to conformations related to those created by nanomanipulation.
Lavery
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R
Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Paris, France.
Lebrun
A
A
D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism; D051821:Lymphoid Enhancer-Binding Factor 1; D009682:Magnetic Resonance Spectroscopy; D019563:Mechanics; D008958:Models, Molecular; D009687:Nuclear Proteins; D009690:Nucleic Acid Conformation; D012097:Repressor Proteins / Q000737:chemistry / Q000378:metabolism; D051876:Sex-Determining Region Y Protein; D013314:Stress, Mechanical; D035181:TATA-Box Binding Protein; D014157:Transcription Factors / Q000737:chemistry / Q000378:metabolism
D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D051821:Lymphoid Enhancer-Binding Factor 1; D009687:Nuclear Proteins; C065825:PurR protein, Bacteria; D012097:Repressor Proteins; D051876:Sex-Determining Region Y Protein; D035181:TATA-Box Binding Protein; D014157:Transcription Factors; D004247:DNA