Sequence-Dependent Persistence Length of Long DNA

Hui Min Chuang, Jeffrey G. Reifenberger, Han Cao, Kevin D. Dorfman

Research output: Contribution to journalArticlepeer-review

16 Scopus citations


Using a high-throughput genome-mapping approach, we obtained circa 50 million measurements of the extension of internal human DNA segments in a 41 nm×41 nm nanochannel. The underlying DNA sequences, obtained by mapping to the reference human genome, are 2.5-393 kilobase pairs long and contain percent GC contents between 32.5% and 60%. Using Odijk's theory for a channel-confined wormlike chain, these data reveal that the DNA persistence length increases by almost 20% as the percent GC content increases. The increased persistence length is rationalized by a model, containing no adjustable parameters, that treats the DNA as a statistical terpolymer with a sequence-dependent intrinsic persistence length and a sequence-independent electrostatic persistence length.

Original languageEnglish (US)
Article number227802
JournalPhysical review letters
Issue number22
StatePublished - Nov 29 2017

Bibliographical note

Funding Information:
This work was supported by NIH R01-HG006851. We thank Damini Gupta for assistance in the data analysis. J. G. R. and H. C. are employees of BioNano Genomics, which is commercializing nanochannel genome mapping.

Publisher Copyright:
© 2017 American Physical Society.

Copyright 2017 Elsevier B.V., All rights reserved.

PubMed: MeSH publication types

  • Journal Article

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