Base-Pair Dynamics in an Antiparallel DNA Triplex Measured by Catalyzed Imino Proton Exchange Monitored via super(1)H NMR Spectroscopy

Using super(1)H NMR spectroscopy, the base-pair opening dynamics of an antiparallel foldback DNA triplex and the corresponding duplex has been characterized via catalyzed imino proton exchange. The triplex system was found to be in an equilibrium between a duplex and a triplex form. The exchange rat...

Full description

Saved in:
Bibliographic Details
Published in:Biochemistry (Easton) 2003-11, Vol.42 (43), p.12589-12595
Main Authors: Waermlaender, S, Sandstroem, K, Leijon, M, Graeslund, A
Format: Article
Language:English
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
cited_by
cites
container_end_page 12595
container_issue 43
container_start_page 12589
container_title Biochemistry (Easton)
container_volume 42
creator Waermlaender, S
Sandstroem, K
Leijon, M
Graeslund, A
description Using super(1)H NMR spectroscopy, the base-pair opening dynamics of an antiparallel foldback DNA triplex and the corresponding duplex has been characterized via catalyzed imino proton exchange. The triplex system was found to be in an equilibrium between a duplex and a triplex form. The exchange rate between the two forms (i.e., the on/off-rate of the third strand) was measured to be 5 s super(-1) at 1 degree C, and the base-pair dynamics of both forms were investigated separately. Both Watson-Crick and reverse Hoogsteen base pairs were found to have base-pair lifetimes in the order of milliseconds. The stability of the Watson-Crick base pairs was, however, substantially increased in the presence of the third strand. In the DNA triplex, the opening dynamics of the reverse Hoogsteen base pairs was significantly faster than the dynamics of the Watson-Crick pairs. We were able to conclude that, for both Watson-Crick and reverse Hoogsteen base pairs, spontaneous and individual opening from within the closed base triplet is the dominating opening pathway.
doi_str_mv 10.1021/bi034479u
format article
fullrecord <record><control><sourceid>proquest</sourceid><recordid>TN_cdi_proquest_miscellaneous_17963971</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>17963971</sourcerecordid><originalsourceid>FETCH-proquest_miscellaneous_179639713</originalsourceid><addsrcrecordid>eNqNyk1OwzAQQGEvQKL8LLjBrBAsAnYTJcqytEVlkaqC7qupGcDIsY3HRg0H6LkpEgdg9fRJT4hLJW-VHKu7rZFlVTVtPhIjKWVdjNtanohT5o8DK9lUI7G_R6ZihSbCbHDYG81gHKCDiUsmYERrycJsOYF1NMHSDjpCzpFeYDvAFBPa4fuAx944D6vok3cw3-l3dG8EnXcm-d_5yyBwDhSv1c0Clt0TPAfSKXrWPgzn4vgVLdPFX8_E1cN8PV0UIfrPTJw2vWFN1qIjn3mjmrYu20aV_x5_AOiOWB0</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>17963971</pqid></control><display><type>article</type><title>Base-Pair Dynamics in an Antiparallel DNA Triplex Measured by Catalyzed Imino Proton Exchange Monitored via super(1)H NMR Spectroscopy</title><source>American Chemical Society:Jisc Collections:American Chemical Society Read &amp; Publish Agreement 2022-2024 (Reading list)</source><creator>Waermlaender, S ; Sandstroem, K ; Leijon, M ; Graeslund, A</creator><creatorcontrib>Waermlaender, S ; Sandstroem, K ; Leijon, M ; Graeslund, A</creatorcontrib><description>Using super(1)H NMR spectroscopy, the base-pair opening dynamics of an antiparallel foldback DNA triplex and the corresponding duplex has been characterized via catalyzed imino proton exchange. The triplex system was found to be in an equilibrium between a duplex and a triplex form. The exchange rate between the two forms (i.e., the on/off-rate of the third strand) was measured to be 5 s super(-1) at 1 degree C, and the base-pair dynamics of both forms were investigated separately. Both Watson-Crick and reverse Hoogsteen base pairs were found to have base-pair lifetimes in the order of milliseconds. The stability of the Watson-Crick base pairs was, however, substantially increased in the presence of the third strand. In the DNA triplex, the opening dynamics of the reverse Hoogsteen base pairs was significantly faster than the dynamics of the Watson-Crick pairs. We were able to conclude that, for both Watson-Crick and reverse Hoogsteen base pairs, spontaneous and individual opening from within the closed base triplet is the dominating opening pathway.</description><identifier>ISSN: 0006-2960</identifier><identifier>DOI: 10.1021/bi034479u</identifier><language>eng</language><ispartof>Biochemistry (Easton), 2003-11, Vol.42 (43), p.12589-12595</ispartof><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,27924,27925</link.rule.ids></links><search><creatorcontrib>Waermlaender, S</creatorcontrib><creatorcontrib>Sandstroem, K</creatorcontrib><creatorcontrib>Leijon, M</creatorcontrib><creatorcontrib>Graeslund, A</creatorcontrib><title>Base-Pair Dynamics in an Antiparallel DNA Triplex Measured by Catalyzed Imino Proton Exchange Monitored via super(1)H NMR Spectroscopy</title><title>Biochemistry (Easton)</title><description>Using super(1)H NMR spectroscopy, the base-pair opening dynamics of an antiparallel foldback DNA triplex and the corresponding duplex has been characterized via catalyzed imino proton exchange. The triplex system was found to be in an equilibrium between a duplex and a triplex form. The exchange rate between the two forms (i.e., the on/off-rate of the third strand) was measured to be 5 s super(-1) at 1 degree C, and the base-pair dynamics of both forms were investigated separately. Both Watson-Crick and reverse Hoogsteen base pairs were found to have base-pair lifetimes in the order of milliseconds. The stability of the Watson-Crick base pairs was, however, substantially increased in the presence of the third strand. In the DNA triplex, the opening dynamics of the reverse Hoogsteen base pairs was significantly faster than the dynamics of the Watson-Crick pairs. We were able to conclude that, for both Watson-Crick and reverse Hoogsteen base pairs, spontaneous and individual opening from within the closed base triplet is the dominating opening pathway.</description><issn>0006-2960</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2003</creationdate><recordtype>article</recordtype><recordid>eNqNyk1OwzAQQGEvQKL8LLjBrBAsAnYTJcqytEVlkaqC7qupGcDIsY3HRg0H6LkpEgdg9fRJT4hLJW-VHKu7rZFlVTVtPhIjKWVdjNtanohT5o8DK9lUI7G_R6ZihSbCbHDYG81gHKCDiUsmYERrycJsOYF1NMHSDjpCzpFeYDvAFBPa4fuAx944D6vok3cw3-l3dG8EnXcm-d_5yyBwDhSv1c0Clt0TPAfSKXrWPgzn4vgVLdPFX8_E1cN8PV0UIfrPTJw2vWFN1qIjn3mjmrYu20aV_x5_AOiOWB0</recordid><startdate>20031104</startdate><enddate>20031104</enddate><creator>Waermlaender, S</creator><creator>Sandstroem, K</creator><creator>Leijon, M</creator><creator>Graeslund, A</creator><scope>7TM</scope></search><sort><creationdate>20031104</creationdate><title>Base-Pair Dynamics in an Antiparallel DNA Triplex Measured by Catalyzed Imino Proton Exchange Monitored via super(1)H NMR Spectroscopy</title><author>Waermlaender, S ; Sandstroem, K ; Leijon, M ; Graeslund, A</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-proquest_miscellaneous_179639713</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2003</creationdate><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Waermlaender, S</creatorcontrib><creatorcontrib>Sandstroem, K</creatorcontrib><creatorcontrib>Leijon, M</creatorcontrib><creatorcontrib>Graeslund, A</creatorcontrib><collection>Nucleic Acids Abstracts</collection><jtitle>Biochemistry (Easton)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Waermlaender, S</au><au>Sandstroem, K</au><au>Leijon, M</au><au>Graeslund, A</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Base-Pair Dynamics in an Antiparallel DNA Triplex Measured by Catalyzed Imino Proton Exchange Monitored via super(1)H NMR Spectroscopy</atitle><jtitle>Biochemistry (Easton)</jtitle><date>2003-11-04</date><risdate>2003</risdate><volume>42</volume><issue>43</issue><spage>12589</spage><epage>12595</epage><pages>12589-12595</pages><issn>0006-2960</issn><abstract>Using super(1)H NMR spectroscopy, the base-pair opening dynamics of an antiparallel foldback DNA triplex and the corresponding duplex has been characterized via catalyzed imino proton exchange. The triplex system was found to be in an equilibrium between a duplex and a triplex form. The exchange rate between the two forms (i.e., the on/off-rate of the third strand) was measured to be 5 s super(-1) at 1 degree C, and the base-pair dynamics of both forms were investigated separately. Both Watson-Crick and reverse Hoogsteen base pairs were found to have base-pair lifetimes in the order of milliseconds. The stability of the Watson-Crick base pairs was, however, substantially increased in the presence of the third strand. In the DNA triplex, the opening dynamics of the reverse Hoogsteen base pairs was significantly faster than the dynamics of the Watson-Crick pairs. We were able to conclude that, for both Watson-Crick and reverse Hoogsteen base pairs, spontaneous and individual opening from within the closed base triplet is the dominating opening pathway.</abstract><doi>10.1021/bi034479u</doi></addata></record>
fulltext fulltext
identifier ISSN: 0006-2960
ispartof Biochemistry (Easton), 2003-11, Vol.42 (43), p.12589-12595
issn 0006-2960
language eng
recordid cdi_proquest_miscellaneous_17963971
source American Chemical Society:Jisc Collections:American Chemical Society Read & Publish Agreement 2022-2024 (Reading list)
title Base-Pair Dynamics in an Antiparallel DNA Triplex Measured by Catalyzed Imino Proton Exchange Monitored via super(1)H NMR Spectroscopy
url http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-28T18%3A31%3A41IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Base-Pair%20Dynamics%20in%20an%20Antiparallel%20DNA%20Triplex%20Measured%20by%20Catalyzed%20Imino%20Proton%20Exchange%20Monitored%20via%20super(1)H%20NMR%20Spectroscopy&rft.jtitle=Biochemistry%20(Easton)&rft.au=Waermlaender,%20S&rft.date=2003-11-04&rft.volume=42&rft.issue=43&rft.spage=12589&rft.epage=12595&rft.pages=12589-12595&rft.issn=0006-2960&rft_id=info:doi/10.1021/bi034479u&rft_dat=%3Cproquest%3E17963971%3C/proquest%3E%3Cgrp_id%3Ecdi_FETCH-proquest_miscellaneous_179639713%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=17963971&rft_id=info:pmid/&rfr_iscdi=true