Synthesis and pairing properties of alpha-tricyclo-DNA.
Identifieur interne : 002C87 ( Main/Exploration ); précédent : 002C86; suivant : 002C88Synthesis and pairing properties of alpha-tricyclo-DNA.
Auteurs : Simon P. Scheidegger [Suisse] ; Christian J. LeumannSource :
- Chemistry (Weinheim an der Bergstrasse, Germany) [ 0947-6539 ] ; 2006.
Descripteurs français
- KwdFr :
- ADN (), ADN (effets des radiations), ADN (synthèse chimique), ARN (), Appariement de bases, Composés organiques du phosphore (), Conformation d'acide nucléique, Dichroïsme circulaire, Oligonucléotides (), Oligonucléotides (effets des radiations), Oligonucléotides (synthèse chimique), Rayons ultraviolets, Séquence nucléotidique.
- MESH :
- effets des radiations : ADN, Oligonucléotides.
- synthèse chimique : ADN, Oligonucléotides.
- ADN, ARN, Appariement de bases, Composés organiques du phosphore, Conformation d'acide nucléique, Dichroïsme circulaire, Oligonucléotides, Rayons ultraviolets, Séquence nucléotidique.
English descriptors
- KwdEn :
- Base Pairing, Base Sequence, Circular Dichroism, DNA (chemical synthesis), DNA (chemistry), DNA (radiation effects), Nucleic Acid Conformation, Oligonucleotides (chemical synthesis), Oligonucleotides (chemistry), Oligonucleotides (radiation effects), Organophosphorus Compounds (chemistry), RNA (chemistry), Ultraviolet Rays.
- MESH :
- chemical , chemical synthesis : DNA, Oligonucleotides.
- chemical , chemistry : DNA, Oligonucleotides, Organophosphorus Compounds, RNA.
- chemical , radiation effects : DNA, Oligonucleotides.
- Base Pairing, Base Sequence, Circular Dichroism, Nucleic Acid Conformation, Ultraviolet Rays.
Abstract
We describe the synthesis of the phosphoramidite building blocks of alpha-tricyclo-DNA (alpha-tc-DNA) covering all four natural bases, starting from the already known corresponding alpha-tc-nucleosides. These building blocks were used for the preparation of three alpha-tc-oligonucleotide 10-mers representing a homopurine, a homopyrimidine, and a mixed purine/pyrimidine base sequence. The base-pairing properties with complementary parallel and antiparallel oriented DNA and RNA were studied by UV-melting analysis and CD spectroscopy. We found that alpha-tc-DNA binds preferentially to parallel nucleic acid complements through Watson-Crick duplex formation, with a preference for RNA over DNA. In comparison with natural DNA, alpha-tc-DNA shows equal to enhanced affinity to RNA and also pairs to antiparallel DNA or RNA complements, although with much lower affinity. In the mixed-base sequence these antiparallel duplexes are of the reversed Watson-Crick type, while in the homopurine/homopyrimidine sequences Hoogsteen and/or reversed Hoogsteen pairing is observed. Antiparallel duplex formation of two alpha-tc-oligonucleotides was also observed, although the thermal stability of this duplex was surprisingly low. The base-pairing properties of alpha-tc-DNA are discussed in the context of alpha-DNA, alpha-RNA, and alpha-LNA.
DOI: 10.1002/chem.200600597
PubMed: 16915595
Affiliations:
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Scheidegger</name><affiliation wicri:level="4"><nlm:affiliation>Department of Chemistry & Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.</nlm:affiliation><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Chemistry & Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern</wicri:regionArea><placeName><settlement type="city">Berne</settlement><region type="région" nuts="3">Canton de Berne</region></placeName><orgName type="university">Université de Berne</orgName><placeName><settlement type="city">Berne</settlement><region nuts="3" type="region">Canton de Berne</region></placeName></affiliation></author><author><name sortKey="Leumann, Christian J" sort="Leumann, Christian J" uniqKey="Leumann C" first="Christian J" last="Leumann">Christian J. 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Scheidegger</name><affiliation wicri:level="4"><nlm:affiliation>Department of Chemistry & Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.</nlm:affiliation><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Chemistry & Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern</wicri:regionArea><placeName><settlement type="city">Berne</settlement><region type="région" nuts="3">Canton de Berne</region></placeName><orgName type="university">Université de Berne</orgName><placeName><settlement type="city">Berne</settlement><region nuts="3" type="region">Canton de Berne</region></placeName></affiliation></author><author><name sortKey="Leumann, Christian J" sort="Leumann, Christian J" uniqKey="Leumann C" first="Christian J" last="Leumann">Christian J. Leumann</name></author></analytic><series><title level="j">Chemistry (Weinheim an der Bergstrasse, Germany)</title><idno type="ISSN">0947-6539</idno><imprint><date when="2006" type="published">2006</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Pairing</term><term>Base Sequence</term><term>Circular Dichroism</term><term>DNA (chemical synthesis)</term><term>DNA (chemistry)</term><term>DNA (radiation effects)</term><term>Nucleic Acid Conformation</term><term>Oligonucleotides (chemical synthesis)</term><term>Oligonucleotides (chemistry)</term><term>Oligonucleotides (radiation effects)</term><term>Organophosphorus Compounds (chemistry)</term><term>RNA (chemistry)</term><term>Ultraviolet Rays</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN ()</term><term>ADN (effets des radiations)</term><term>ADN (synthèse chimique)</term><term>ARN ()</term><term>Appariement de bases</term><term>Composés organiques du phosphore ()</term><term>Conformation d'acide nucléique</term><term>Dichroïsme circulaire</term><term>Oligonucléotides ()</term><term>Oligonucléotides (effets des radiations)</term><term>Oligonucléotides (synthèse chimique)</term><term>Rayons ultraviolets</term><term>Séquence nucléotidique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemical synthesis" xml:lang="en"><term>DNA</term><term>Oligonucleotides</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA</term><term>Oligonucleotides</term><term>Organophosphorus Compounds</term><term>RNA</term></keywords><keywords scheme="MESH" type="chemical" qualifier="radiation effects" xml:lang="en"><term>DNA</term><term>Oligonucleotides</term></keywords><keywords scheme="MESH" qualifier="effets des radiations" xml:lang="fr"><term>ADN</term><term>Oligonucléotides</term></keywords><keywords scheme="MESH" qualifier="synthèse chimique" xml:lang="fr"><term>ADN</term><term>Oligonucléotides</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Pairing</term><term>Base Sequence</term><term>Circular Dichroism</term><term>Nucleic Acid Conformation</term><term>Ultraviolet Rays</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN</term><term>ARN</term><term>Appariement de bases</term><term>Composés organiques du phosphore</term><term>Conformation d'acide nucléique</term><term>Dichroïsme circulaire</term><term>Oligonucléotides</term><term>Rayons ultraviolets</term><term>Séquence nucléotidique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">We describe the synthesis of the phosphoramidite building blocks of alpha-tricyclo-DNA (alpha-tc-DNA) covering all four natural bases, starting from the already known corresponding alpha-tc-nucleosides. These building blocks were used for the preparation of three alpha-tc-oligonucleotide 10-mers representing a homopurine, a homopyrimidine, and a mixed purine/pyrimidine base sequence. The base-pairing properties with complementary parallel and antiparallel oriented DNA and RNA were studied by UV-melting analysis and CD spectroscopy. We found that alpha-tc-DNA binds preferentially to parallel nucleic acid complements through Watson-Crick duplex formation, with a preference for RNA over DNA. In comparison with natural DNA, alpha-tc-DNA shows equal to enhanced affinity to RNA and also pairs to antiparallel DNA or RNA complements, although with much lower affinity. In the mixed-base sequence these antiparallel duplexes are of the reversed Watson-Crick type, while in the homopurine/homopyrimidine sequences Hoogsteen and/or reversed Hoogsteen pairing is observed. Antiparallel duplex formation of two alpha-tc-oligonucleotides was also observed, although the thermal stability of this duplex was surprisingly low. The base-pairing properties of alpha-tc-DNA are discussed in the context of alpha-DNA, alpha-RNA, and alpha-LNA.</div></front></TEI><affiliations><list><country><li>Suisse</li></country><region><li>Canton de Berne</li></region><settlement><li>Berne</li></settlement><orgName><li>Université de Berne</li></orgName></list><tree><noCountry><name sortKey="Leumann, Christian J" sort="Leumann, Christian J" uniqKey="Leumann C" first="Christian J" last="Leumann">Christian J. Leumann</name></noCountry><country name="Suisse"><region name="Canton de Berne"><name sortKey="Scheidegger, Simon P" sort="Scheidegger, Simon P" uniqKey="Scheidegger S" first="Simon P" last="Scheidegger">Simon P. Scheidegger</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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