MersV1, PubMed, Corpus, bibRecord, 002553

Stabilization factors affecting duplex formation of peptide nucleic acid with DNA.

Identifieur interne : 002553 ( PubMed/Corpus ); précédent : 002552; suivant : 002554

Stabilization factors affecting duplex formation of peptide nucleic acid with DNA.

Auteurs : N. Sugimoto ; N. Satoh ; K. Yasuda ; S. Nakano

Source :

Biochemistry [ 0006-2960 ] ; 2001.

RBID : pubmed:11456481

English descriptors

KwdEn :
- Base Composition, Base Pairing, Circular Dichroism, DNA (chemistry), Hot Temperature, Nucleic Acid Heteroduplexes (chemistry), Oligodeoxyribonucleotides (chemistry), Peptide Nucleic Acids (chemistry), Spectrophotometry, Ultraviolet, Thermodynamics.
MESH :
- chemical , chemistry : DNA, Nucleic Acid Heteroduplexes, Oligodeoxyribonucleotides, Peptide Nucleic Acids.
- Base Composition, Base Pairing, Circular Dichroism, Hot Temperature, Spectrophotometry, Ultraviolet, Thermodynamics.

Abstract

Peptide nucleic acid (PNA) is an oligonucleotide analogue in which the sugar-phosphate backbone is replaced by an N-(2-aminoethyl)glycine unit to which the nucleobases are attached. We investigated the thermodynamic behavior of PNA/DNA hybrid duplexes with identical nearest neighbors but with different sequences and chain lengths (5, 6, 7, 8, 10, 12, and 16 mers) to reveal whether the nearest-neighbor model is valid for the PNA/DNA duplex stability. CD spectra of 6, 7, and 8 mer PNA/DNA duplexes showed similar signal, while 10, 12, and 16 mer duplexes did not. The average difference in Delta G degrees (37) for short PNA/DNA duplexes with identical nearest-neighbor pairs was only 3.5%, whereas that of longer duplexes (10, 12, and 16 mers) was 16.4%. Therefore, the nearest-neighbor model seems to be useful at least for the short PNA/DNA duplexes. Thermodynamics of PNA/DNA duplexes containing 1--3 bulge residues were also studied. While the stability of the 12 mer DNA/DNA duplex decreased as the number of bulge bases increases, the number of bulge bases in PNA/DNA unchanged the duplex stability. Thus, the influence of bulge insertion in the PNA/DNA duplexes is different from that of a DNA/DNA duplex. This might be due to the different base geometry in a helix which may potentially make hydrogen bonds in a base pair and stacking interaction unfavorable compared with DNA/DNA duplexes.

DOI: 10.1021/bi010480m
PubMed: 11456481

Links to Exploration step

pubmed:11456481

Le document en format XML

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<author><name sortKey="Sugimoto, N" sort="Sugimoto, N" uniqKey="Sugimoto N" first="N" last="Sugimoto">N. Sugimoto</name>
<affiliation><nlm:affiliation>Department of Chemistry, Faculty of Science and Engineering, Konan University, 8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan. sugimoto@konan-u.ac.jp</nlm:affiliation>
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<author><name sortKey="Satoh, N" sort="Satoh, N" uniqKey="Satoh N" first="N" last="Satoh">N. Satoh</name>
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<author><name sortKey="Yasuda, K" sort="Yasuda, K" uniqKey="Yasuda K" first="K" last="Yasuda">K. Yasuda</name>
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<author><name sortKey="Nakano, S" sort="Nakano, S" uniqKey="Nakano S" first="S" last="Nakano">S. Nakano</name>
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<term>Hot Temperature</term>
<term>Nucleic Acid Heteroduplexes (chemistry)</term>
<term>Oligodeoxyribonucleotides (chemistry)</term>
<term>Peptide Nucleic Acids (chemistry)</term>
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<front><div type="abstract" xml:lang="en">Peptide nucleic acid (PNA) is an oligonucleotide analogue in which the sugar-phosphate backbone is replaced by an N-(2-aminoethyl)glycine unit to which the nucleobases are attached. We investigated the thermodynamic behavior of PNA/DNA hybrid duplexes with identical nearest neighbors but with different sequences and chain lengths (5, 6, 7, 8, 10, 12, and 16 mers) to reveal whether the nearest-neighbor model is valid for the PNA/DNA duplex stability. CD spectra of 6, 7, and 8 mer PNA/DNA duplexes showed similar signal, while 10, 12, and 16 mer duplexes did not. The average difference in Delta G degrees (37) for short PNA/DNA duplexes with identical nearest-neighbor pairs was only 3.5%, whereas that of longer duplexes (10, 12, and 16 mers) was 16.4%. Therefore, the nearest-neighbor model seems to be useful at least for the short PNA/DNA duplexes. Thermodynamics of PNA/DNA duplexes containing 1--3 bulge residues were also studied. While the stability of the 12 mer DNA/DNA duplex decreased as the number of bulge bases increases, the number of bulge bases in PNA/DNA unchanged the duplex stability. Thus, the influence of bulge insertion in the PNA/DNA duplexes is different from that of a DNA/DNA duplex. This might be due to the different base geometry in a helix which may potentially make hydrogen bonds in a base pair and stacking interaction unfavorable compared with DNA/DNA duplexes.</div>
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<Title>Biochemistry</Title>
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<Abstract><AbstractText>Peptide nucleic acid (PNA) is an oligonucleotide analogue in which the sugar-phosphate backbone is replaced by an N-(2-aminoethyl)glycine unit to which the nucleobases are attached. We investigated the thermodynamic behavior of PNA/DNA hybrid duplexes with identical nearest neighbors but with different sequences and chain lengths (5, 6, 7, 8, 10, 12, and 16 mers) to reveal whether the nearest-neighbor model is valid for the PNA/DNA duplex stability. CD spectra of 6, 7, and 8 mer PNA/DNA duplexes showed similar signal, while 10, 12, and 16 mer duplexes did not. The average difference in Delta G degrees (37) for short PNA/DNA duplexes with identical nearest-neighbor pairs was only 3.5%, whereas that of longer duplexes (10, 12, and 16 mers) was 16.4%. Therefore, the nearest-neighbor model seems to be useful at least for the short PNA/DNA duplexes. Thermodynamics of PNA/DNA duplexes containing 1--3 bulge residues were also studied. While the stability of the 12 mer DNA/DNA duplex decreased as the number of bulge bases increases, the number of bulge bases in PNA/DNA unchanged the duplex stability. Thus, the influence of bulge insertion in the PNA/DNA duplexes is different from that of a DNA/DNA duplex. This might be due to the different base geometry in a helix which may potentially make hydrogen bonds in a base pair and stacking interaction unfavorable compared with DNA/DNA duplexes.</AbstractText>
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Stabilization factors affecting duplex formation of peptide nucleic acid with DNA.

Stabilization factors affecting duplex formation of peptide nucleic acid with DNA.

Source :

English descriptors

Abstract

Links to Exploration step

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