Macroscopic loop formation in circular DNA denaturation

The statistical mechanics of DNA denaturation under fixed linking number is qualitatively different from that of unconstrained DNA. Quantitatively different melting scenarios are reached from two alternative assumptions, namely, that the denatured loops are formed at the expense of (i) overtwist or...

Ausführliche Beschreibung

Gespeichert in:
Bibliographische Detailangaben
Veröffentlicht in:Physical review. E, Statistical, nonlinear, and soft matter physics Statistical, nonlinear, and soft matter physics, 2012-05, Vol.85 (5 Pt 1), p.051919-051919, Article 051919
Hauptverfasser: Kabakçıoğlu, Alkan, Bar, Amir, Mukamel, David
Format: Artikel
Sprache:eng
Schlagworte:
Online-Zugang:Volltext
Tags: Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
container_end_page 051919
container_issue 5 Pt 1
container_start_page 051919
container_title Physical review. E, Statistical, nonlinear, and soft matter physics
container_volume 85
creator Kabakçıoğlu, Alkan
Bar, Amir
Mukamel, David
description The statistical mechanics of DNA denaturation under fixed linking number is qualitatively different from that of unconstrained DNA. Quantitatively different melting scenarios are reached from two alternative assumptions, namely, that the denatured loops are formed at the expense of (i) overtwist or (ii) supercoils. Recent work has shown that the supercoiling mechanism results in a picture similar to Bose-Einstein condensation where a macroscopic loop appears at T{c} and grows steadily with temperature, while the nature of the denatured phase for the overtwisting case has not been studied. By extending an earlier result, we show here that a macroscopic loop appears in the overtwisting scenario as well. We calculate its size as a function of temperature and show that the fraction of the total sum of microscopic loops decreases above T{c}, with a cusp at the critical point.
doi_str_mv 10.1103/PhysRevE.85.051919
format Article
fullrecord <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_1186918229</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>1186918229</sourcerecordid><originalsourceid>FETCH-LOGICAL-c303t-7c6d022d5f729b9bd5751d8f35fbb6a5d5416e419057d5db9edb686874799263</originalsourceid><addsrcrecordid>eNo9kElPwzAQhS0EoqXwBzigHLmkeIm3Y1XKIpVFqHfLW0RQEgc7Qeq_p6Etpxlp3nua9wFwjeAcIUju3j-36cP_rOaCziFFEskTMEWUwhwTzk7HnciccEon4CKlLwgJJqI4BxNMICy4lFPAX7SNIdnQVTarQ-iyMsRG91Vos6rNbBXtUOuY3b8uMudb3Q_x73gJzkpdJ391mDOweVhtlk_5-u3xeblY55ZA0ufcMgcxdrTkWBppHOUUOVESWhrDNHW0QMwXSELKHXVGemeYYIKP32FGZuB2H9vF8D341KumStbXtW59GJJCSDCJBMZyJ8V76dgnRV-qLlaNjluFoBp5qSMvJaja89qZbg75g2m8-7ccAZFfFYFnHA</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1186918229</pqid></control><display><type>article</type><title>Macroscopic loop formation in circular DNA denaturation</title><source>MEDLINE</source><source>American Physical Society Journals</source><creator>Kabakçıoğlu, Alkan ; Bar, Amir ; Mukamel, David</creator><creatorcontrib>Kabakçıoğlu, Alkan ; Bar, Amir ; Mukamel, David</creatorcontrib><description>The statistical mechanics of DNA denaturation under fixed linking number is qualitatively different from that of unconstrained DNA. Quantitatively different melting scenarios are reached from two alternative assumptions, namely, that the denatured loops are formed at the expense of (i) overtwist or (ii) supercoils. Recent work has shown that the supercoiling mechanism results in a picture similar to Bose-Einstein condensation where a macroscopic loop appears at T{c} and grows steadily with temperature, while the nature of the denatured phase for the overtwisting case has not been studied. By extending an earlier result, we show here that a macroscopic loop appears in the overtwisting scenario as well. We calculate its size as a function of temperature and show that the fraction of the total sum of microscopic loops decreases above T{c}, with a cusp at the critical point.</description><identifier>ISSN: 1539-3755</identifier><identifier>EISSN: 1550-2376</identifier><identifier>DOI: 10.1103/PhysRevE.85.051919</identifier><identifier>PMID: 23004799</identifier><language>eng</language><publisher>United States</publisher><subject>DNA, Circular - chemistry ; Models, Molecular ; Nucleic Acid Conformation ; Nucleic Acid Denaturation ; Temperature ; Thermodynamics</subject><ispartof>Physical review. E, Statistical, nonlinear, and soft matter physics, 2012-05, Vol.85 (5 Pt 1), p.051919-051919, Article 051919</ispartof><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c303t-7c6d022d5f729b9bd5751d8f35fbb6a5d5416e419057d5db9edb686874799263</citedby><cites>FETCH-LOGICAL-c303t-7c6d022d5f729b9bd5751d8f35fbb6a5d5416e419057d5db9edb686874799263</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,2876,2877,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23004799$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Kabakçıoğlu, Alkan</creatorcontrib><creatorcontrib>Bar, Amir</creatorcontrib><creatorcontrib>Mukamel, David</creatorcontrib><title>Macroscopic loop formation in circular DNA denaturation</title><title>Physical review. E, Statistical, nonlinear, and soft matter physics</title><addtitle>Phys Rev E Stat Nonlin Soft Matter Phys</addtitle><description>The statistical mechanics of DNA denaturation under fixed linking number is qualitatively different from that of unconstrained DNA. Quantitatively different melting scenarios are reached from two alternative assumptions, namely, that the denatured loops are formed at the expense of (i) overtwist or (ii) supercoils. Recent work has shown that the supercoiling mechanism results in a picture similar to Bose-Einstein condensation where a macroscopic loop appears at T{c} and grows steadily with temperature, while the nature of the denatured phase for the overtwisting case has not been studied. By extending an earlier result, we show here that a macroscopic loop appears in the overtwisting scenario as well. We calculate its size as a function of temperature and show that the fraction of the total sum of microscopic loops decreases above T{c}, with a cusp at the critical point.</description><subject>DNA, Circular - chemistry</subject><subject>Models, Molecular</subject><subject>Nucleic Acid Conformation</subject><subject>Nucleic Acid Denaturation</subject><subject>Temperature</subject><subject>Thermodynamics</subject><issn>1539-3755</issn><issn>1550-2376</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNo9kElPwzAQhS0EoqXwBzigHLmkeIm3Y1XKIpVFqHfLW0RQEgc7Qeq_p6Etpxlp3nua9wFwjeAcIUju3j-36cP_rOaCziFFEskTMEWUwhwTzk7HnciccEon4CKlLwgJJqI4BxNMICy4lFPAX7SNIdnQVTarQ-iyMsRG91Vos6rNbBXtUOuY3b8uMudb3Q_x73gJzkpdJ391mDOweVhtlk_5-u3xeblY55ZA0ufcMgcxdrTkWBppHOUUOVESWhrDNHW0QMwXSELKHXVGemeYYIKP32FGZuB2H9vF8D341KumStbXtW59GJJCSDCJBMZyJ8V76dgnRV-qLlaNjluFoBp5qSMvJaja89qZbg75g2m8-7ccAZFfFYFnHA</recordid><startdate>201205</startdate><enddate>201205</enddate><creator>Kabakçıoğlu, Alkan</creator><creator>Bar, Amir</creator><creator>Mukamel, David</creator><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope></search><sort><creationdate>201205</creationdate><title>Macroscopic loop formation in circular DNA denaturation</title><author>Kabakçıoğlu, Alkan ; Bar, Amir ; Mukamel, David</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c303t-7c6d022d5f729b9bd5751d8f35fbb6a5d5416e419057d5db9edb686874799263</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2012</creationdate><topic>DNA, Circular - chemistry</topic><topic>Models, Molecular</topic><topic>Nucleic Acid Conformation</topic><topic>Nucleic Acid Denaturation</topic><topic>Temperature</topic><topic>Thermodynamics</topic><toplevel>online_resources</toplevel><creatorcontrib>Kabakçıoğlu, Alkan</creatorcontrib><creatorcontrib>Bar, Amir</creatorcontrib><creatorcontrib>Mukamel, David</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Physical review. E, Statistical, nonlinear, and soft matter physics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kabakçıoğlu, Alkan</au><au>Bar, Amir</au><au>Mukamel, David</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Macroscopic loop formation in circular DNA denaturation</atitle><jtitle>Physical review. E, Statistical, nonlinear, and soft matter physics</jtitle><addtitle>Phys Rev E Stat Nonlin Soft Matter Phys</addtitle><date>2012-05</date><risdate>2012</risdate><volume>85</volume><issue>5 Pt 1</issue><spage>051919</spage><epage>051919</epage><pages>051919-051919</pages><artnum>051919</artnum><issn>1539-3755</issn><eissn>1550-2376</eissn><abstract>The statistical mechanics of DNA denaturation under fixed linking number is qualitatively different from that of unconstrained DNA. Quantitatively different melting scenarios are reached from two alternative assumptions, namely, that the denatured loops are formed at the expense of (i) overtwist or (ii) supercoils. Recent work has shown that the supercoiling mechanism results in a picture similar to Bose-Einstein condensation where a macroscopic loop appears at T{c} and grows steadily with temperature, while the nature of the denatured phase for the overtwisting case has not been studied. By extending an earlier result, we show here that a macroscopic loop appears in the overtwisting scenario as well. We calculate its size as a function of temperature and show that the fraction of the total sum of microscopic loops decreases above T{c}, with a cusp at the critical point.</abstract><cop>United States</cop><pmid>23004799</pmid><doi>10.1103/PhysRevE.85.051919</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record>
fulltext fulltext
identifier ISSN: 1539-3755
ispartof Physical review. E, Statistical, nonlinear, and soft matter physics, 2012-05, Vol.85 (5 Pt 1), p.051919-051919, Article 051919
issn 1539-3755
1550-2376
language eng
recordid cdi_proquest_miscellaneous_1186918229
source MEDLINE; American Physical Society Journals
subjects DNA, Circular - chemistry
Models, Molecular
Nucleic Acid Conformation
Nucleic Acid Denaturation
Temperature
Thermodynamics
title Macroscopic loop formation in circular DNA denaturation
url https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-22T20%3A22%3A10IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Macroscopic%20loop%20formation%20in%20circular%20DNA%20denaturation&rft.jtitle=Physical%20review.%20E,%20Statistical,%20nonlinear,%20and%20soft%20matter%20physics&rft.au=Kabak%C3%A7%C4%B1o%C4%9Flu,%20Alkan&rft.date=2012-05&rft.volume=85&rft.issue=5%20Pt%201&rft.spage=051919&rft.epage=051919&rft.pages=051919-051919&rft.artnum=051919&rft.issn=1539-3755&rft.eissn=1550-2376&rft_id=info:doi/10.1103/PhysRevE.85.051919&rft_dat=%3Cproquest_cross%3E1186918229%3C/proquest_cross%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1186918229&rft_id=info:pmid/23004799&rfr_iscdi=true