MersV1, Main, Exploration, bibRecord, 001580

Sequence-dependent structural changes in a self-assembling DNA oligonucleotide.

Identifieur interne : 001580 ( Main/Exploration ); précédent : 001579; suivant : 001581

Sequence-dependent structural changes in a self-assembling DNA oligonucleotide.

Auteurs : Maithili Saoji [États-Unis] ; Paul J. Paukstelis [États-Unis]

Source :

Acta crystallographica. Section D, Biological crystallography [ 1399-0047 ] ; 2015.

RBID : pubmed:26627654

Descripteurs français

KwdFr :
- ADN (), Appariement de bases, Cations divalents, Conformation d'acide nucléique, Cristallographie aux rayons X, Données de séquences moléculaires, Liaison hydrogène, Magnésium (), Modèles moléculaires, Oligonucléotides (), Séquence nucléotidique, Thermodynamique.
MESH :
- ADN, Appariement de bases, Cations divalents, Conformation d'acide nucléique, Cristallographie aux rayons X, Données de séquences moléculaires, Liaison hydrogène, Magnésium, Modèles moléculaires, Oligonucléotides, Séquence nucléotidique, Thermodynamique.

English descriptors

KwdEn :
- Base Pairing, Base Sequence, Cations, Divalent, Crystallography, X-Ray, DNA (chemistry), Hydrogen Bonding, Magnesium (chemistry), Models, Molecular, Molecular Sequence Data, Nucleic Acid Conformation, Oligonucleotides (chemistry), Thermodynamics.
MESH :
- chemical , chemistry : DNA, Magnesium, Oligonucleotides.
- chemical : Cations, Divalent.
- Base Pairing, Base Sequence, Crystallography, X-Ray, Hydrogen Bonding, Models, Molecular, Molecular Sequence Data, Nucleic Acid Conformation, Thermodynamics.

Abstract

DNA has proved to be a remarkable molecule for the construction of sophisticated two-dimensional and three-dimensional architectures because of its programmability and structural predictability provided by complementary Watson-Crick base pairing. DNA oligonucleotides can, however, exhibit a great deal of local structural diversity. DNA conformation is strongly linked to both environmental conditions and the nucleobase identities inherent in the oligonucleotide sequence, but the exact relationship between sequence and local structure is not completely understood. This study examines how a single-nucleotide addition to a class of self-assembling DNA 13-mers leads to a significantly different overall structure under identical crystallization conditions. The DNA 13-mers self-assemble in the presence of Mg(2+) through a combination of Watson-Crick and noncanonical base-pairing interactions. The crystal structures described here show that all of the predicted Watson-Crick base pairs are present, with the major difference being a significant rearrangement of noncanonical base pairs. This includes the formation of a sheared A-G base pair, a junction of strands formed from base-triple interactions, and tertiary interactions that generate structural features similar to tandem sheared G-A base pairs. The adoption of this alternate noncanonical structure is dependent in part on the sequence in the Watson-Crick duplex region. These results provide important new insights into the sequence-structure relationship of short DNA oligonucleotides and demonstrate a unique interplay between Watson-Crick and noncanonical base pairs that is responsible for crystallization fate.

DOI: 10.1107/S1399004715019598
PubMed: 26627654

Affiliations:

Le document en format XML

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<term>Cristallographie aux rayons X</term>
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<term>Liaison hydrogène</term>
<term>Magnésium</term>
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<front><div type="abstract" xml:lang="en">DNA has proved to be a remarkable molecule for the construction of sophisticated two-dimensional and three-dimensional architectures because of its programmability and structural predictability provided by complementary Watson-Crick base pairing. DNA oligonucleotides can, however, exhibit a great deal of local structural diversity. DNA conformation is strongly linked to both environmental conditions and the nucleobase identities inherent in the oligonucleotide sequence, but the exact relationship between sequence and local structure is not completely understood. This study examines how a single-nucleotide addition to a class of self-assembling DNA 13-mers leads to a significantly different overall structure under identical crystallization conditions. The DNA 13-mers self-assemble in the presence of Mg(2+) through a combination of Watson-Crick and noncanonical base-pairing interactions. The crystal structures described here show that all of the predicted Watson-Crick base pairs are present, with the major difference being a significant rearrangement of noncanonical base pairs. This includes the formation of a sheared A-G base pair, a junction of strands formed from base-triple interactions, and tertiary interactions that generate structural features similar to tandem sheared G-A base pairs. The adoption of this alternate noncanonical structure is dependent in part on the sequence in the Watson-Crick duplex region. These results provide important new insights into the sequence-structure relationship of short DNA oligonucleotides and demonstrate a unique interplay between Watson-Crick and noncanonical base pairs that is responsible for crystallization fate.</div>
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Serveur d'exploration MERS

Sequence-dependent structural changes in a self-assembling DNA oligonucleotide.

Sequence-dependent structural changes in a self-assembling DNA oligonucleotide.

Source :

Descripteurs français

English descriptors

Abstract

Links toward previous steps (curation, corpus...)

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki

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