The DOI matches its Crossref record; 23 of the 23 references it cites were found in a registry or an index.
Thermodynamic Parameters To Predict Stability of RNA/DNA Hybrid Duplexes
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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“These energy terms have an error of around 5–10% (32,33,35).”
From The prebiotic evolutionary advantage of transferring genetic information from RNA to DNA (2011) · cites this paper as [35]
Citations
Cites
Predicting DNA duplex stability from the base sequence
Breslauer, K. J., Frank, R., Blöcker, H., & Marky, L. A. (1986) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.83.11.3746 · Cited by 1,837
Improved free-energy parameters for predictions of RNA duplex stability.
Freier, S. M., Kierzek, R., Jaeger, J. A., Sugimoto, N., Caruthers, M. H., Neilson, T., & Turner, D. H. (1986) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.83.24.9373 · Cited by 1,470
Self-citationAntisense Oligonucleotides as Therapeutic Agents—Is the Bullet Really Magical?
Stein, C., & Cheng, Y. C. (1993) · Science · doi:10.1126/science.8351515 · Cited by 1,300
Ivanov, V. I., Minchenkova, L. E., Schyolkina, A. K., et al. (1973) · Biopolymers · doi:10.1002/bip.1973.360120109 · Cited by 936
Form and Function of Retroviral Proviruses
VARMUS, H. E. (1982) · Science · doi:10.1126/science.6177038 · Cited by 577
Free energy of imperfect nucleic acid helices
Gralla, J. D., & Crothers, D. M. (1973) · Journal of Molecular Biology · doi:10.1016/0022-2836(73)90096-x · Cited by 503
Petersheim, M., & Turner, D. H. (1983) · Biochemistry · doi:10.1021/bi00271a004 · Cited by 497
Martin, F. H., & Tinoco, I. (1980) · Nucleic Acids Research · doi:10.1093/nar/8.10.2295 · Cited by 304
Ogawa, T., & Okazaki, T. (1980) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.49.070180.002225 · Cited by 223
A thermodynamic analysis of RNA transcript elongation and termination in Escherichia coli
Yager, T. D., & von Hippel, P. H. (1991) · Biochemistry · doi:10.1021/bi00218a032 · Cited by 193
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High-Frequency off-Target Mutagenesis Induced by CRISPR-Cas Nucleases in Human Cells
Fu, Y., Foden, J. A., Khayter, C., Maeder, M. L., Reyon, D., Joung, J. K., & Sander, J. D. (2013) · Nature Biotechnology · doi:10.1038/nbt.2623 · Cited by 3,292
RNAstructure: software for RNA secondary structure prediction and analysis
Reuter, J. S., & Mathews, D. H. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-129 · Cited by 2,018
“DNA-RNA hybridization parameters are also used by OligoWalk [93].”
MethodA general purpose RNA-cleaving DNA enzyme
Santoro, S. W., & Joyce, G. F. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.9.4262 · Cited by 1,546
The microRNAs of Caenorhabditis elegans
Lim, L. P., Lau, N. C., Weinstein, E. G., Abdelhakim, A., Yekta, S., Rhoades, M. W., Burge, C. B., & Bartel, D. P. (2003) · Genes & Development · doi:10.1101/gad.1074403 · Cited by 1,259
“To maintain hybridization specificity without varying hybridization or washing conditions, the length of probes for different sequences was adjusted so that the predicted melting temperatures of the miRNA-probe duplexes did not exceed 60°C (Sugimoto et al. 1995).”
BackgroundXia, T., SantaLucia, J., Burkard, M. E., Kierzek, R., Schroeder, S. J., Jiao, X., Cox, C., & Turner, D. H. (1998) · Biochemistry · doi:10.1021/bi9809425 · Cited by 1,140
Metadata
- Authors
- Sugimoto, N., Nakano, S.-I., Katoh, M., Matsumura, A., Nakamuta, H., Ohmichi, T., Yoneyama, M., & Sasaki, M.
- Affiliations
- Konan University (JP)
- 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
- 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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