Determinants of cyclization–decyclization kinetics of short DNA with sticky ends
Abstract Cyclization of DNA with sticky ends is commonly used to measure DNA bendability as a function of length and sequence, but how its kinetics depend on the rotational positioning of the sticky ends around the helical axis is less clear. Here, we measured cyclization (looping) and decyclization...
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| Veröffentlicht in: | Nucleic acids research 2020-05, Vol.48 (9), p.5147-5156 |
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| creator | Jeong, Jiyoun Kim, Harold D |
| description | Abstract
Cyclization of DNA with sticky ends is commonly used to measure DNA bendability as a function of length and sequence, but how its kinetics depend on the rotational positioning of the sticky ends around the helical axis is less clear. Here, we measured cyclization (looping) and decyclization (unlooping) rates (kloop and kunloop) of DNA with sticky ends over three helical periods (100-130 bp) using single-molecule fluorescence resonance energy transfer (FRET). kloop showed a nontrivial undulation as a function of DNA length whereas kunloop showed a clear oscillation with a period close to the helical turn of DNA (∼10.5 bp). The oscillation of kunloop was almost completely suppressed in the presence of gaps around the sticky ends. We explain these findings by modeling double-helical DNA as a twisted wormlike chain with a finite width, intrinsic curvature, and stacking interaction between the end base pairs. We also discuss technical issues for converting the FRET-based cyclization/decyclization rates to an equilibrium quantity known as the J factor that is widely used to characterize DNA bending mechanics. |
| doi_str_mv | 10.1093/nar/gkaa207 |
| format | Article |
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Cyclization of DNA with sticky ends is commonly used to measure DNA bendability as a function of length and sequence, but how its kinetics depend on the rotational positioning of the sticky ends around the helical axis is less clear. Here, we measured cyclization (looping) and decyclization (unlooping) rates (kloop and kunloop) of DNA with sticky ends over three helical periods (100-130 bp) using single-molecule fluorescence resonance energy transfer (FRET). kloop showed a nontrivial undulation as a function of DNA length whereas kunloop showed a clear oscillation with a period close to the helical turn of DNA (∼10.5 bp). The oscillation of kunloop was almost completely suppressed in the presence of gaps around the sticky ends. We explain these findings by modeling double-helical DNA as a twisted wormlike chain with a finite width, intrinsic curvature, and stacking interaction between the end base pairs. We also discuss technical issues for converting the FRET-based cyclization/decyclization rates to an equilibrium quantity known as the J factor that is widely used to characterize DNA bending mechanics.</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gkaa207</identifier><identifier>PMID: 32282905</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Cyclization ; DNA - chemistry ; Fluorescence Resonance Energy Transfer ; Kinetics ; Models, Molecular ; Nucleic Acid Conformation ; Structural Biology</subject><ispartof>Nucleic acids research, 2020-05, Vol.48 (9), p.5147-5156</ispartof><rights>The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. 2020</rights><rights>The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c412t-29a943146f571e56b0a2065cf5c3f471ea88215e10abe021140eb9affda122633</citedby><cites>FETCH-LOGICAL-c412t-29a943146f571e56b0a2065cf5c3f471ea88215e10abe021140eb9affda122633</cites><orcidid>0000-0003-0878-2169</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7229855/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7229855/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,1604,27923,27924,53790,53792</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32282905$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Jeong, Jiyoun</creatorcontrib><creatorcontrib>Kim, Harold D</creatorcontrib><title>Determinants of cyclization–decyclization kinetics of short DNA with sticky ends</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>Abstract
Cyclization of DNA with sticky ends is commonly used to measure DNA bendability as a function of length and sequence, but how its kinetics depend on the rotational positioning of the sticky ends around the helical axis is less clear. Here, we measured cyclization (looping) and decyclization (unlooping) rates (kloop and kunloop) of DNA with sticky ends over three helical periods (100-130 bp) using single-molecule fluorescence resonance energy transfer (FRET). kloop showed a nontrivial undulation as a function of DNA length whereas kunloop showed a clear oscillation with a period close to the helical turn of DNA (∼10.5 bp). The oscillation of kunloop was almost completely suppressed in the presence of gaps around the sticky ends. We explain these findings by modeling double-helical DNA as a twisted wormlike chain with a finite width, intrinsic curvature, and stacking interaction between the end base pairs. We also discuss technical issues for converting the FRET-based cyclization/decyclization rates to an equilibrium quantity known as the J factor that is widely used to characterize DNA bending mechanics.</description><subject>Cyclization</subject><subject>DNA - chemistry</subject><subject>Fluorescence Resonance Energy Transfer</subject><subject>Kinetics</subject><subject>Models, Molecular</subject><subject>Nucleic Acid Conformation</subject><subject>Structural Biology</subject><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNp9kctKAzEUhoMotlZX7mVWIsjYXKeTjVBab1AURNchTTNt7DSpSUapK9_BN_RJHG0tdePqcM75-M_lB-AQwTMEOWlb6dvjqZQYdrZAE5EMp5RneBs0IYEsRZDmDbAXwhOEiCJGd0GDYJxjDlkT3Pd11H5mrLQxJK5I1EKV5k1G4-zn-8dIb-TJ1FgdjfrhwsT5mPRvu8mriZMk1PXpItF2FPbBTiHLoA9WsQUeLy8eetfp4O7qptcdpIoiHFPMJacE0axgHaRZNoT1BRlTBVOkoHVJ5jlGTCMohxpihCjUQy6LYiQRxhkhLXC-1J1Xw5keKW2jl6WYezOTfiGcNOJvx5qJGLsX0cGY54zVAicrAe-eKx2imJmgdFlKq10VBCY570DOcl6jp0tUeReC18V6DILi2wVRuyBWLtT00eZma_b37TVwvARcNf9X6QtB85Oc</recordid><startdate>20200521</startdate><enddate>20200521</enddate><creator>Jeong, Jiyoun</creator><creator>Kim, Harold D</creator><general>Oxford University Press</general><scope>TOX</scope><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><scope>5PM</scope><orcidid>https://orcid.org/0000-0003-0878-2169</orcidid></search><sort><creationdate>20200521</creationdate><title>Determinants of cyclization–decyclization kinetics of short DNA with sticky ends</title><author>Jeong, Jiyoun ; Kim, Harold D</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c412t-29a943146f571e56b0a2065cf5c3f471ea88215e10abe021140eb9affda122633</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Cyclization</topic><topic>DNA - chemistry</topic><topic>Fluorescence Resonance Energy Transfer</topic><topic>Kinetics</topic><topic>Models, Molecular</topic><topic>Nucleic Acid Conformation</topic><topic>Structural Biology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Jeong, Jiyoun</creatorcontrib><creatorcontrib>Kim, Harold D</creatorcontrib><collection>Oxford Journals Open Access Collection</collection><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><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nucleic acids research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Jeong, Jiyoun</au><au>Kim, Harold D</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Determinants of cyclization–decyclization kinetics of short DNA with sticky ends</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2020-05-21</date><risdate>2020</risdate><volume>48</volume><issue>9</issue><spage>5147</spage><epage>5156</epage><pages>5147-5156</pages><issn>0305-1048</issn><eissn>1362-4962</eissn><abstract>Abstract
Cyclization of DNA with sticky ends is commonly used to measure DNA bendability as a function of length and sequence, but how its kinetics depend on the rotational positioning of the sticky ends around the helical axis is less clear. Here, we measured cyclization (looping) and decyclization (unlooping) rates (kloop and kunloop) of DNA with sticky ends over three helical periods (100-130 bp) using single-molecule fluorescence resonance energy transfer (FRET). kloop showed a nontrivial undulation as a function of DNA length whereas kunloop showed a clear oscillation with a period close to the helical turn of DNA (∼10.5 bp). The oscillation of kunloop was almost completely suppressed in the presence of gaps around the sticky ends. We explain these findings by modeling double-helical DNA as a twisted wormlike chain with a finite width, intrinsic curvature, and stacking interaction between the end base pairs. We also discuss technical issues for converting the FRET-based cyclization/decyclization rates to an equilibrium quantity known as the J factor that is widely used to characterize DNA bending mechanics.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>32282905</pmid><doi>10.1093/nar/gkaa207</doi><tpages>10</tpages><orcidid>https://orcid.org/0000-0003-0878-2169</orcidid><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Oxford Journals Open Access Collection; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Cyclization DNA - chemistry Fluorescence Resonance Energy Transfer Kinetics Models, Molecular Nucleic Acid Conformation Structural Biology |
| title | Determinants of cyclization–decyclization kinetics of short DNA with sticky ends |
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