Cited by 697DNA and Nucleic Acid ChemistryRNA and protein synthesis mechanismsAdvanced biosensing and bioanalysis techniques

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Thermodynamic Parameters To Predict Stability of RNA/DNA Hybrid Duplexes

Sugimoto, Naoki, Nakano, Shu-ichi, Katoh, Misa, Matsumura, Akiko, Nakamuta, Hiroyuki, Ohmichi, Tatsuo, Yoneyama, Mari, Sasaki, Muneo·1995·Biochemistry

DOI 10.1021/bi00035a029

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Abstract

The thermodynamic parameters (delta H degree, delta S degree, and delta G degree 37) for 16 nearest-neighbor sets and one initiation factor are presented here in order to predict stability of RNA/DNA hybrid duplexes. To determine the nearest-neighbor parameters, thermodynamics for 68 different hybrid sequences (136 single-stranded oligonucleotides) with 5-13 nucleotide length including several duplexes with identical nearest-neighbors were measured by UV melting procedure. These sequences were selected to have many different combinations of nearest-neighbor pairs, and so that the number of the 16 nearest-neighbor sequences in the oligomers were as equal as possible. The structures of the hybrids were also investigated by measuring circular dichroism spectra. Comparing delta G degree 37 values of the hybrids with DNA/DNA and RNA/RNA parameters reported previously (Breslauer, K.J., Frank, R., Blöcker, H., & Marky, L.A. (1986) Proc. Natl. Acad. Sci. U.S.A. 83, 3746-3750; Freier, S.M., Kierzek, R., Jaeger, J.A., Sugimoto, N., Caruthers, M.H., Neilson, T., & Turner, D.H. (1986) Proc. Natl. Acad. Sci. U.S.A. 83, 9373-9377), RNA/RNA double helix is the most stable of the three kinds of helixes with the same nearest-neighbor sequences. Which is more stable between DNA/DNA and RNA/DNA hybrid duplexes depends on its sequence. Calculated thermodynamic values of hybrid formation with the present parameters reproduce the experimental values within reasonable errors.

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Authors: Sugimoto, N., Nakano, S.-I., Katoh, M., Matsumura, A., Nakamuta, H., Ohmichi, T., Yoneyama, M., & Sasaki, M.
Affiliations: Konan University (JP)
ORCID: Sugimoto, Naoki
Nakano, Shu-ichi
Venue: Biochemistry
Publisher: American Chemical Society (ACS)
Published: 1995-09-05
Volume: 34
Issue: 35
Pages: 11211-11216
ISSN: 0006-2960 (ISSN-L)
1520-4995
DOI: 10.1021/bi00035a029
OpenAlex: W2010759469
Semantic Scholar: 5a5921b07eda10a7cfa0f9410e5f8048ae2d9247
Cited by: 697
References: 23
Citations by year: 2026: 23 · 2025: 21 · 2024: 35 · 2023: 19 · 2022: 23 · 2021: 23 · 2020: 25 · 2019: 27 · 2018: 17 · 2017: 23 · 2016: 23 · 2015: 23 · 2014: 27 · 2013: 30 · 2012: 26
FWCI: 2.85
Type: journal article
Language: en
Open access: closed
Locations: Biochemistry (publishedVersion)
PubMed (publishedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced biosensing and bioanalysis techniques
Keywords: hybrid stability, oligonucleotide duplexes, UV melting, circular dichroism, initiation factors
MeSH terms: Base Sequence, Circular Dichroism, DNA, Drug Stability, Molecular Sequence Data, Nucleic Acid Conformation, Nucleic Acid Hybridization, Oligodeoxyribonucleotides, Oligoribonucleotides, RNA, Thermodynamics, Molecular Structure

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Thermodynamic Parameters To Predict Stability of RNA/DNA Hybrid Duplexes

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