The detection of B-form/A-form junction in a deoxyribonucleotide duplex
Identifieur interne : 003F20 ( Main/Exploration ); précédent : 003F19; suivant : 003F21The detection of B-form/A-form junction in a deoxyribonucleotide duplex
Auteurs : V. I. Ivanov [Russie] ; L. E. Minchenkova [Russie] ; G. Burckhardt [Russie] ; E. Birch-Hirschfeld [Russie] ; H. Fritzsche [Russie] ; C. Zimmer [Russie]Source :
- Biophysical Journal [ 0006-3495 ] ; 1996.
English descriptors
- Teeft :
- Base pairs, Binding ligands, Biol, Christoph zimmer, Circular dichroism, Decimal code, Deoxyoligonucleotide duplex, Dichroism, Double helix, Duplex, Free duplex, Free energy, Free energy change, Free energy difference, Horizontal axis, Ivanov, Junction, Krylov, Ligand, Minchenkova, Minyat, Molecular biology, Nucleic, Nucleic acids, Open circles, Possible contacts, Relative change, Relative humidity, Second duplex, Stable junction, Terminal base pair, Transition curves, Transition point, Transition profile, Transition profiles, Water content, Zimmer.
Abstract
The transition of the 14-meric deoxyoligonucleotide duplex d-(ACCCCCTTTTTTTG).d-(CAAAAAAAGGGGGT) from the B- to the A-conformation in water/trifluorethanol (TFE) solution was studied with the use of circular dichroism. An increase in the fraction of TFE induces a two-step B-A transition. In the first step, up to 73% TFE, the A-form is generated from the GC-rich part; in the second step, 73–82% TFE, the AT-rich part shifts to the A-form. By this we suggest the existence of a B/A junction near 73% TFE. Emergence of the B/A junction has been directly confirmed with the use of distamycin A and netropsin, ligands known to selectively bind to AT stretches of B-DNA. It can be shown that both ligands suppress formation of the A-form in the B-philic part. The free energy value for the B/A junction was estimated to be 2.1 kcal/mol, which agrees well with known data for polymeric DNAs. The obtained results may have biological relevance in connection with recently published x-ray data about the occurrence of the B/A junction in the complex of DNA with reverse transcriptase of HIV.
Url:
DOI: 10.1016/S0006-3495(96)79527-9
Affiliations:
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Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow</wicri:regionArea><placeName><settlement type="city">Moscou</settlement><region>District fédéral central</region></placeName></affiliation></author></analytic><monogr></monogr><series><title level="j">Biophysical Journal</title><title level="j" type="abbrev">BPJ</title><idno type="ISSN">0006-3495</idno><imprint><publisher>ELSEVIER</publisher><date type="published" when="1996">1996</date><biblScope unit="volume">71</biblScope><biblScope unit="issue">6</biblScope><biblScope unit="page" from="3344">3344</biblScope><biblScope unit="page" to="3349">3349</biblScope></imprint><idno type="ISSN">0006-3495</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0006-3495</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="Teeft" xml:lang="en"><term>Base pairs</term><term>Binding ligands</term><term>Biol</term><term>Christoph zimmer</term><term>Circular dichroism</term><term>Decimal code</term><term>Deoxyoligonucleotide duplex</term><term>Dichroism</term><term>Double helix</term><term>Duplex</term><term>Free duplex</term><term>Free energy</term><term>Free energy change</term><term>Free energy difference</term><term>Horizontal axis</term><term>Ivanov</term><term>Junction</term><term>Krylov</term><term>Ligand</term><term>Minchenkova</term><term>Minyat</term><term>Molecular biology</term><term>Nucleic</term><term>Nucleic acids</term><term>Open circles</term><term>Possible contacts</term><term>Relative change</term><term>Relative humidity</term><term>Second duplex</term><term>Stable junction</term><term>Terminal base pair</term><term>Transition curves</term><term>Transition point</term><term>Transition profile</term><term>Transition profiles</term><term>Water content</term><term>Zimmer</term></keywords></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract">The transition of the 14-meric deoxyoligonucleotide duplex d-(ACCCCCTTTTTTTG).d-(CAAAAAAAGGGGGT) from the B- to the A-conformation in water/trifluorethanol (TFE) solution was studied with the use of circular dichroism. An increase in the fraction of TFE induces a two-step B-A transition. In the first step, up to 73% TFE, the A-form is generated from the GC-rich part; in the second step, 73–82% TFE, the AT-rich part shifts to the A-form. By this we suggest the existence of a B/A junction near 73% TFE. Emergence of the B/A junction has been directly confirmed with the use of distamycin A and netropsin, ligands known to selectively bind to AT stretches of B-DNA. It can be shown that both ligands suppress formation of the A-form in the B-philic part. The free energy value for the B/A junction was estimated to be 2.1 kcal/mol, which agrees well with known data for polymeric DNAs. The obtained results may have biological relevance in connection with recently published x-ray data about the occurrence of the B/A junction in the complex of DNA with reverse transcriptase of HIV.</div></front></TEI><affiliations><list><country><li>Russie</li></country><region><li>District fédéral central</li></region><settlement><li>Moscou</li></settlement></list><tree><country name="Russie"><region name="District fédéral central"><name sortKey="Ivanov, V I" sort="Ivanov, V I" uniqKey="Ivanov V" first="V. I." last="Ivanov">V. I. Ivanov</name></region><name sortKey="Birch Hirschfeld, E" sort="Birch Hirschfeld, E" uniqKey="Birch Hirschfeld E" first="E." last="Birch-Hirschfeld">E. Birch-Hirschfeld</name><name sortKey="Burckhardt, G" sort="Burckhardt, G" uniqKey="Burckhardt G" first="G." last="Burckhardt">G. Burckhardt</name><name sortKey="Fritzsche, H" sort="Fritzsche, H" uniqKey="Fritzsche H" first="H." last="Fritzsche">H. Fritzsche</name><name sortKey="Minchenkova, L E" sort="Minchenkova, L E" uniqKey="Minchenkova L" first="L. E." last="Minchenkova">L. E. Minchenkova</name><name sortKey="Zimmer, C" sort="Zimmer, C" uniqKey="Zimmer C" first="C." last="Zimmer">C. Zimmer</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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