{"525321":{"#nid":"525321","#data":{"type":"news","title":"The Contrarian Dance of DNA","body":[{"value":"\u003Cp\u003EHave a close-up look at DNA; you\u2019ll see it wiggles in the oddest way.\u003C\/p\u003E\u003Cp\u003EPut more scientifically, a piece of DNA\u2019s movements are often counterintuitive to those of objects in our everyday grasp.\u0026nbsp; Take a rod of rubber, for example. Bend it until its ends meet, and you can count on the elastic tension to snap it back straight when you let go, said biological physicist Harold Kim.\u003C\/p\u003E\u003Cp\u003E\u201cThat doesn\u2019t always work that way with a piece of DNA. When you bend it into a loop, the elastic energy more often than not wants to bend the chain further in instead of pushing it back out,\u201d said Kim, an associate professor at the\u0026nbsp;Georgia Institute of Technology.\u003C\/p\u003E\u003Cp\u003EAt the School of Physics, Kim is fine-tuning the observation of how biopolymers behave, in particular DNA at short lengths. He published his latest results on \u003Ca href=\u0022http:\/\/link.aps.org\/doi\/10.1103\/PhysRevE.93.043315\u0022 target=\u0022_blank\u0022\u003E\u201cForce distribution in a semiflexible loop\u201d in the journal Physical Review E\u003C\/a\u003E on April 18, 2016.\u003Cstrong\u003E\u0026nbsp;\u0026nbsp;\u003C\/strong\u003EThe research is funded by National Institutes of Health. Georgia Tech\u2019s James T. Waters coauthored the research paper.\u003C\/p\u003E\u003Cp\u003EIn complex simulations, Kim studied the motions of DNA chains at lengths where they still have springy qualities, in order to understand their mechanochemical properties, or how they work as microscopic objects.\u0026nbsp;In particular, he has illuminated the forces acting upon DNA bound up in short\u0026nbsp;loops.\u003C\/p\u003E\u003Cp\u003EThat\u2019s a common and important shape that keeps DNA from expressing when it shouldn\u2019t and then possibly messing up cell functioning.\u003C\/p\u003E\u003Cp\u003EKim\u2019s most significant counterintuitive find could improve understanding of how DNA snaps free from the proteins that bind them into those loops. He has observed that looped DNA, though on average very gentle in its motions, is beset by moments of\u0026nbsp;unusually high force.\u0026nbsp;\u003C\/p\u003E\u003Cp\u003E\u201cIt would be a little like a\u0026nbsp;chaotic spring drawn up to a loop making pretty even jumbly movements\u0026nbsp;then\u0026nbsp;suddenly whipping out violently,\u201d Kim said.\u003C\/p\u003E\u003Cp\u003EThe range of observed forces on DNA loops breaks the bounds of what thermodynamics predicts. Even though the mean of the force distribution does indeed equal the thermodynamic force, the distribution of forces pushes past the anticipated norm, falling broadly outside a Gaussian distribution on both ends.\u003C\/p\u003E\u003Cp\u003EThat\u2019s a key determination.\u003C\/p\u003E\u003Cp\u003EIt could help scientists in various disciplines predict the lifespans of many DNA loops and understand the frequency and likelihood of their undoing.\u003C\/p\u003E\u003Cp\u003EThe forces contributing to those momentary jerks and snaps work on the whole contrary to one another. While that elastic energy works on DNA pieces in its ways, the forces of entropy push hard in their own ways.\u003C\/p\u003E\u003Cp\u003EReflective of the universe overall, in Kim\u2019s observations of springy DNA loops, entropy, here too, wins. Entropic forces slightly outdo the elastic forces.\u003C\/p\u003E\u003Cp\u003EAnd they, too, defy intuition.\u003C\/p\u003E\u003Cp\u003ETo understand how, let\u2019s take a look back at that rubber bar. When a short DNA chain is not looped but only bent, it acts more like the rubber bar. The elastic force dominates and mostly wants to push it back straight, while entropy mostly wants to keep it curvy.\u003C\/p\u003E\u003Cp\u003EThen, as the DNA chain lengthens a bit and loops: That relation starkly turns on its head.\u003C\/p\u003E\u003Cp\u003EThe elastic force then pulls inward with vehemence, and the entropic force then pushes the chain outward with even more vigor.\u003C\/p\u003E\u003Cp\u003EThe length of a DNA loop appears to contribute strongly to how likely these intermittent extreme forces are to destabilize its bond with the protein holding it shut.\u003C\/p\u003E\u003Cp\u003EThat, incidentally, plays right into many scientists\u2019 current discussions on other biopolymers.\u003C\/p\u003E\u003Cp\u003E\u201cThere\u2019s a lot of speculation right now that the kinds of force-peaks we observed actually regulate the length of some biopolymers, so, in an interesting way, our observations and methods may help colleagues explore this idea more closely,\u201d Kim said.\u003C\/p\u003E\u003Cp\u003EKim\u2019s group augmented thermodynamic calculations with a novel simulation method, \u201cphase-space sampling.\u201d It not only establishes the positon of molecular components in space but also their momentum at a given time.\u003C\/p\u003E\u003Cp\u003EThis took into account the constant bombardment by water molecules, i.e. the \u201cheat bath.\u201d\u003C\/p\u003E\u003Cp\u003EThis way, Kim was better able to access the fluctuating forces on looped DNA chains \u2013 and see more closely how they really wriggle.\u003C\/p\u003E\u003Cp\u003E\u003Cem\u003EThe work is funded by the National Institutes of Health, grant number R01GM112882. Any conclusions or opinions are those of the authors and do not necessarily represent the official views of the NIH.\u003C\/em\u003E\u003C\/p\u003E\u003Cp\u003E\u003Cstrong\u003EResearch News\u003C\/strong\u003E\u003C\/p\u003E\u003Cp\u003E\u003Cstrong\u003EGeorgia Insitute of Technology\u003C\/strong\u003E\u003C\/p\u003E\u003Cp\u003E\u003Cstrong\u003E177 North Avenue\u003C\/strong\u003E\u003C\/p\u003E\u003Cp\u003E\u003Cstrong\u003EAtlanta, Georgia 30032-0181\u003C\/strong\u003E\u003C\/p\u003E\u003Cp\u003E\u003Cstrong\u003EMedia Relations Contacts:\u003C\/strong\u003E Ben Brumfield (\u003Ca href=\u0022mailto:ben.brumfield@comm.gatech.edu\u0022\u003Eben.brumfield@comm.gatech.edu\u003C\/a\u003E) (404-385-1933)\u003C\/p\u003E\u003Cp\u003E\u003Cstrong\u003EWriter:\u003C\/strong\u003E Ben Brumfield\u003C\/p\u003E","summary":null,"format":"limited_html"}],"field_subtitle":"","field_summary":[{"value":"\u003Cp\u003EHarold Kim studies DNA and other biomolecules to fine-tune observations of their mechanochemical properties, that is, how they act as microscopic objects. At a length and formation often seen in gene non-expression, a short loop of DNA moves in a counterintuitive way with moments of extreme stress, as elastic forces and entropy act upon it.\u003C\/p\u003E","format":"limited_html"}],"field_summary_sentence":[{"value":"Short DNA loops play a role in gene non-expression, but how force acts on them defies expectations, creating moments of extreme stress."}],"uid":"31759","created_gmt":"2016-04-15 14:56:58","changed_gmt":"2016-10-08 03:21:21","author":"Ben Brumfield","boilerplate_text":"","field_publication":"","field_article_url":"","dateline":{"date":"2016-04-18T00:00:00-04:00","iso_date":"2016-04-18T00:00:00-04:00","tz":"America\/New_York"},"extras":[],"hg_media":{"525291":{"id":"525291","type":"image","title":"DNA double helix black background istock","body":null,"created":"1461074400","gmt_created":"2016-04-19 14:00:00","changed":"1475895296","gmt_changed":"2016-10-08 02:54:56","alt":"DNA double helix black background istock","file":{"fid":"205487","name":"small.istock_000054497160_medium.jpg","image_path":"\/sites\/default\/files\/images\/small.istock_000054497160_medium_0.jpg","image_full_path":"http:\/\/tlwarc.hg.gatech.edu\/\/sites\/default\/files\/images\/small.istock_000054497160_medium_0.jpg","mime":"image\/jpeg","size":174896,"path_740":"http:\/\/tlwarc.hg.gatech.edu\/sites\/default\/files\/styles\/740xx_scale\/public\/images\/small.istock_000054497160_medium_0.jpg?itok=BLJvinhg"}}},"media_ids":["525291"],"groups":[{"id":"1188","name":"Research Horizons"}],"categories":[{"id":"141","name":"Chemistry and Chemical Engineering"},{"id":"146","name":"Life Sciences and Biology"},{"id":"135","name":"Research"},{"id":"150","name":"Physics and Physical Sciences"}],"keywords":[{"id":"1041","name":"dna"},{"id":"12337","name":"DNA Elasticity"},{"id":"171924","name":"entropy"},{"id":"7092","name":"gene expression"},{"id":"15109","name":"harold kim"},{"id":"171925","name":"mechanochemistry"}],"core_research_areas":[{"id":"39441","name":"Bioengineering and Bioscience"},{"id":"39541","name":"Systems"}],"news_room_topics":[{"id":"71881","name":"Science and Technology"}],"event_categories":[],"invited_audience":[],"affiliations":[],"classification":[],"areas_of_expertise":[],"news_and_recent_appearances":[],"phone":[],"contact":[{"value":"\u003Cp\u003EBen Brumfield\u003C\/p\u003E\u003Cp\u003EResearch News\u003C\/p\u003E\u003Cp\u003E\u003Ca href=\u0022mailto:ben.brumfield@comm.gatech.edu\u0022\u003Eben.brumfield@comm.gatech.edu\u003C\/a\u003E\u003C\/p\u003E\u003Cp\u003E(404) 385-1933\u003C\/p\u003E","format":"limited_html"}],"email":["ben.brumfield@comm.gatech.edu"],"slides":[],"orientation":[],"userdata":""}}}