Thermodynamics and NMR of Internal G·T Mismatches in DNA
Abstract
Thermodynamics of 39 oligonucleotides with internal G.T mismatches dissolved in 1 M NaCl were determined from UV absorbance versus temperature profiles. These data were combined with literature values of six sequences to derive parameters for 10 linearly independent trimer and tetramer sequences with G.T mismatches and Watson-Crick base pairs. The G.T mismatch parameters predict DeltaG degrees 37, DeltaH degrees , DeltaS degrees , and TM with average deviations of 5.1%, 7.5%, 8.0%, and 1.4 degrees C, respectively. These predictions are within the limits of what can be expected for a nearest-neighbor model. The data show that the contribution of a single G.T mismatch to helix stability is context dependent and ranges from +1.05 kcal/mol for AGA/TTT to -1.05 kcal/mol for CGC/GTG. Several tests of the applicability of the nearest-neighbor model to G.T mismatches are described. Analysis of imino proton chemical shifts show that structural perturbations from the G.T mismatches are highly localized. One-dimensional NOE difference spectra demonstrate that G.T mismatches form stable hydrogen-bonded wobble pairs in diverse contexts. Refined nearest-neighbor parameters for Watson-Crick base pairs are also presented.
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For DNAs, duplex stabilities including effects of mismatches can be reliably estimated based on nearest neighbor interactions.
“for DNAs, duplex stabilities including effects of mismatches can be reliably estimated based on nearest neighbor interactions [40].”
From Thermodynamic Basis for the Emergence of Genomes during Prebiotic Evolution (2012) · cites this paper as [40]
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BackgroundMicroarray oligonucleotide probes.
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“…change of the nucleation reaction and is based on the sequence content of an oligonucleotide and its target region using the updated N-N parameter tables (Allawi and SantaLucia, 1997); R is the universal molar gas constant, R = 8.314472(15) J/M/K = 1.9872 kcal/mol/K, with the thermodynamic…”
BackgroundMethodInfluentialKunz, C., Saito, Y., & Schär, P. (2009) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-009-8739-9 · Cited by 101 · see citing works
Single nucleotide polymorphisms : methods and protocols
Kwok, P.-Y. (2002) · doi:10.1385/1592593275 · Cited by 73
MFEprimer: multiple factor evaluation of the specificity of PCR primers
Qu, W.-B., Shen, Z., Zhao, D.-S., Yang, Y., & Zhang, C.-G. (2009) · Bioinform. · doi:10.1093/bioinformatics/btn614 · Cited by 72
“The preferred range of Tm, 50–80˚C, is usually considered by popular primer design programs (Rozen and Skaletsky, 2000) and primer databases (Han and Kim, 2006; Wang and Seed, 2003).”
BackgroundPredicting crossover generation in DNA shuffling
Moore, G. L., Maranas, C., Lutz, S., & Benkovic, S. (2001) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.051631498 · Cited by 72
Sequence context effect for hMSH2-hMSH6 mismatch-dependent activation
Mazurek, A., Johnson, C. N., Germann, M., & Fishel, R. (2009) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.0808572106 · Cited by 67 · see citing works
“Nucleotide-stacking interactions serve an important role in stabilizing DNA helical structure (17) and have been used to account for the thermal stability of mismatched DNA (16, 18).”
BackgroundGordon, P. M. K. (2004) · Nucleic Acids Research · doi:10.1093/nar/gnh127 · Cited by 55 · see citing works
Wang, X.-Y., Zou, M., Huang, H.-D., Ren, Y., Li, L.-M., Yang, X.-D., & Li, N. (2013) · Biosensors & bioelectronics · doi:10.1016/j.bios.2012.09.023 · Cited by 66 · see citing works
Biomolecular detection with a thin membrane transducer.
Cha, M., Shin, J., Kim, J., Kim, I., Choi, J.-B., Lee, N., Kim, B.-G., & Lee, J. (2008) · Lab on a Chip · doi:10.1039/b719101d · Cited by 66
Multiplex pairwise assembly of array-derived DNA oligonucleotides
Klein, J. C., Lajoie, M. J., Schwartz, J. J., Strauch, E.-M., Nelson, J. W., Baker, D., & Shendure, J. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1177 · Cited by 65 · see citing works
“Briefly, we automated the following procedure using python: bases for the overlap region were dynamically added starting from the midpoint-7 position until the melting temperature was >56◦C (34).”
MethodLiew, M., Nelson, L., Margraf, R., Mitchell, S., Erali, M., Mao, R., Lyon, E., & Wittwer, C. (2006) · Journal of Molecular Diagnostics · doi:10.2353/jmoldx.2006.050053 · Cited by 65
Kumari, S., & Ware, D. (2013) · PLoS ONE · doi:10.1371/journal.pone.0079011 · Cited by 62 · see citing works
“It uses experimentally established dinucleotide free energy values in a sliding window of size 15bps as proposed by Allawai and Santalucia [142] and Santalucia [143].”
MethodAn analytical pipeline for genomic representations used for cytosine methylation studies
Thompson, R. F., Reimers, M., Khulan, B., Gissot, M., Richmond, T., Chen, Q., Zheng, X., Kim, K., & Greally, J. (2008) · Bioinform. · doi:10.1093/bioinformatics/btn096 · Cited by 59 · see citing works
Beltz, H., Piémont, É., Schaub, E., Ficheux, D., Roques, B., Darlix, J., & Mély, Y. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.03.019 · Cited by 59
- Authors
- Allawi, H. T., & SantaLucia, J.
- Affiliations
- Wayne State University (US)
- Corresponding author
- SantaLucia, John
- Venue
- Biochemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 1997-08-26
- Volume
- 36
- Issue
- 34
- Pages
- 10581-10594
- ISSN
- 0006-2960 (ISSN-L)
- 1520-4995
- OpenAlex
- W2125882871
- Cited by
- 623
- References
- 0
- Citations by year
- 2026: 14 · 2025: 19 · 2024: 22 · 2023: 15 · 2022: 32 · 2021: 22 · 2020: 11 · 2019: 19 · 2018: 17 · 2017: 15 · 2016: 10 · 2015: 28 · 2014: 15 · 2013: 20 · 2012: 22
- FWCI
- 3.88
- 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
- G-T mismatch, DNA thermodynamics, oligonucleotide stability, nearest-neighbor model, helix stability, melting point, enthalpy and entropy, Watson-Crick base pairing
- MeSH terms
- Base Composition, DNA, Hydrogen Bonding, Magnetic Resonance Spectroscopy, Nucleic Acid Conformation, Nucleic Acid Heteroduplexes, Oligodeoxyribonucleotides, Regression Analysis, RNA, Double-Stranded, Sodium Chloride, Spectrophotometry, Ultraviolet, Temperature, Thermodynamics
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