Logo - springer
Slogan - springer

Physics - Biophysics & Biological Physics | Journal of Biological Physics - incl. option to publish open access (Press)

Journal of Biological Physics

Journal of Biological Physics

Editors-in-Chief: S. Bahar; R. Podgornik

ISSN: 0092-0606 (print version)
ISSN: 1573-0689 (electronic version)

Journal no. 10867

$99.00 Personal Rate e-only for the Americas
Get Subscription

Online subscription, valid from January through December of current calendar year

Immediate access to this year's issues via SpringerLink

1 Volume(-s) with 4 issue(-s) per annual subscription

Automatic annual renewal

More information: >> FAQs // >> Policy

New York / Heidelberg, 5 December 2013

DNA helicity and elasticity explained on the nanoscale

Korean researchers propose simple model to explain DNA helicity and elasticity on a nanometer scale

10867
A simple mechanical model to effectively implement the well-known double-stranded structure and the elasticity of DNA on a nano-meter scale has been developed by Jae-Hyung Jeon and Wokyung Sung of Pohang University of Science and Technology in the Republic of Korea, in an effort to more comprehensively explore the nucleic acid containing genetic material of cells. The model was published in Springer’s Journal of Biological Physics.
Ever since Watson and Crick first described the basic structure of DNA in 1953, a number of quantum chemical calculations to describe it on an atomistic scale or small molecule level have been developed. So far, however, these have proved too computationally demanding or analytically unfeasible to adequately describe the nanoscale DNA conformation and mechanics probed by modern single molecule experiments. At micron scales, on the other hand, the wormlike chain model has been instrumental to analytically describe DNA mechanics and elasticity. It however lacks certain molecular details which are essential to describe the hybridization, nanoscale confinement, and local denaturation or structural changes in DNA caused by extreme conditions.
To fill this fundamental gap, the Korean researchers set about to develop a workable and predictive mesoscopic model of double-stranded DNA, where the nucleotides beads constitute the basic degrees of freedom.
Using the model, the Korean researchers studied how a DNA duplex self-assembles into the helix structure due to the stacking interaction modelled by interaction between diagonally opposed bases, and also how the helix is deformed against the stretching force in comparison with related single molecule experiments. They found that an overstretching transition with the force plateau, as shown in typical force-extension experiments, can be induced by the coexistence of helix and ladder structures at a critical force close to the experimental value. This plateau occurs due to the transition between the helical state and ladderlike state of DNA.
The research duo also showed analytically how a wormlike-chainlike elastic model, frequently used in DNA mechanics, can be derived by using their new model. It is used to explain the bending and twist stiffness in terms of basic interactions in their model and DNA geometrical constants, in reasonable agreement with corresponding experimental values.
“This basic model and its extension, used together with further analytical calculations and numerical simulations, provides new possibilities with which to study a variety of single DNA phenomena from nano to micron length scales,” writes Jeon and Sung. “It can, for instance, be used to study the effects of sequence heterogeneity, ionic solutions, and torsional constraints on mechanics and, furthermore, various phenomena such as DNA local denaturation and protein-DNA interaction.”
Reference:
Jeon, J-H. & Sung, W. (2013). An effective mesoscopic model of double-stranded DNA, Journal of Biological Physics. DOI 10.1007/s10867-013-9333-9
The full-text article is available to journalists on request.

Contact: 

For authors and editors


  • Journal Citation Reports®
    2016 Impact Factor
  • 1.241
  • Aims and Scope

    Aims and Scope

    Close

    Many physicists are turning their attention to domains that were not traditionally part of physics and are applying the sophisticated tools of theoretical, computational and experimental physics to investigate biological processes, systems and materials.

    The Journal of Biological Physics provides a medium where this growing community of scientists can publish its results and discuss its aims and methods. It welcomes papers which use the tools of physics in an innovative way to study biological problems, as well as research aimed at providing a better understanding of the physical principles underlying biological processes.

    All areas of biological physics can be addressed, from the molecular level, through the mesoscale of membranes and cells, up to the macroscopic level of a population of living organisms, the main criteria of acceptance being the physical content of the research and its relevance to biological systems. In order to increase the links between physics and biology and among the various fields of biological physics, authors are advised to include a first section that introduces the basic issues addressed and the primary achievements to a non-specialist reader.

    In addition to original peer-reviewed research papers, the Journal of Biological Physics publishes Short Notes, Perspectives and Review Papers. Book reviews are also welcome.

  • Submit Online
  • Open Choice - Your Way to Open Access
  • Instructions for Authors
  • Author Tools (LaTex)

    Author tools to prepare your article

    Close

  • Author Academy: Training for Authors
  • English Language Editing

    English Language Editing

    Close

  • Copyright Information

    Copyright Information

    Close

    Copyright Information

    For Authors

    Submission of a manuscript implies: that the work described has not been published before (except in form of an abstract or as part of a published lecture, review or thesis); that it is not under consideration for publication elsewhere; that its publication has been approved by all co-authors, if any, as well as – tacitly or explicitly – by the responsible authorities at the institution where the work was carried out.

    Author warrants (i) that he/she is the sole owner or has been authorized by any additional copyright owner to assign the right, (ii) that the article does not infringe any third party rights and no license from or payments to a third party is required to publish the article and (iii) that the article has not been previously published or licensed. The author signs for and accepts responsibility for releasing this material on behalf of any and all co-authors. Transfer of copyright to Springer (respective to owner if other than Springer) becomes effective if and when a Copyright Transfer Statement is signed or transferred electronically by the corresponding author. After submission of the Copyright Transfer Statement signed by the corresponding author, changes of authorship or in the order of the authors listed will not be accepted by Springer.

    The copyright to this article, including any graphic elements therein (e.g. illustrations, charts, moving images), is assigned for good and valuable consideration to Springer effective if and when the article is accepted for publication and to the extent assignable if assignability is restricted for by applicable law or regulations (e.g. for U.S. government or crown employees).

    The copyright assignment includes without limitation the exclusive, assignable and sublicensable right, unlimited in time and territory, to reproduce, publish, distribute, transmit, make available and store the article, including abstracts thereof, in all forms of media of expression now known or developed in the future, including pre- and reprints, translations, photographic reproductions and microform. Springer may use the article in whole or in part in electronic form, such as use in databases or data networks for display, print or download to stationary or portable devices. This includes interactive and multimedia use and the right to alter the article to the extent necessary for such use.

    Authors may self-archive the Author's accepted manuscript of their articles on their own websites. Authors may also deposit this version of the article in any repository, provided it is only made publicly available 12 months after official publication or later. He/she may not use the publisher's version (the final article), which is posted on SpringerLink and other Springer websites, for the purpose of self-archiving or deposit. Furthermore, the Author may only post his/her version provided acknowledgement is given to the original source of publication and a link is inserted to the published article on Springer's website. The link must be accompanied by the following text: "The final publication is available at link.springer.com".

    Prior versions of the article published on non-commercial pre-print servers like arXiv.org can remain on these servers and/or can be updated with Author's accepted version. The final published version (in pdf or html/xml format) cannot be used for this purpose. Acknowledgement needs to be given to the final publication and a link must be inserted to the published article on Springer's website, accompanied by the text "The final publication is available at link.springer.com". Author retains the right to use his/her article for his/her further scientific career by including the final published journal article in other publications such as dissertations and postdoctoral qualifications provided acknowledgement is given to the original source of publication.

    Author is requested to use the appropriate DOI for the article. Articles disseminated via link.springer.com are indexed, abstracted and referenced by many abstracting and information services, bibliographic networks, subscription agencies, library networks, and consortia.

    For Readers

    While the advice and information in this journal is believed to be true and accurate at the date of its publication, neither the authors, the editors, nor the publisher can accept any legal responsibility for any errors or omissions that may have been made. The publisher makes no warranty, express or implied, with respect to the material contained herein.

    All articles published in this journal are protected by copyright, which covers the exclusive rights to reproduce and distribute the article (e.g., as offprints), as well as all translation rights. No material published in this journal may be reproduced photographically or stored on microfilm, in electronic data bases, video disks, etc., without first obtaining written permission from the publisher (respective the copyright owner if other than Springer). The use of general descriptive names, trade names, trademarks, etc., in this publication, even if not specifically identified, does not imply that these names are not protected by the relevant laws and regulations.

    Springer has partnered with Copyright Clearance Center's RightsLink service to offer a variety of options for reusing Springer content. For permission to reuse our content please locate the material that you wish to use on link.springer.com or on springerimages.com and click on the permissions link or go to copyright.com, then enter the title of the publication that you wish to use. For assistance in placing a permission request, Copyright Clearance Center can be connected directly via phone: +1-855-239-3415, fax: +1-978-646-8600, or e-mail: info@copyright.com.


    © Springer Science+Business Media Dordrecht

Alerts for this journal

 

Get the table of contents of every new issue published in Journal of Biological Physics.