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Nearest Neighbor Thermodynamic Parameters for Internal G·A Mismatches in DNA
Abstract
Thermodynamics of 22 oligonucleotides with internal single G.A mismatches dissolved in 1 M NaCl were determined from absorbance versus temperature melting curves. These data, combined with five literature sequences, were used to derive nearest-neighbor thermodynamic parameters for seven linearly independent trimer sequences with internal G.A mismatches and Watson-Crick flanking base pairs. The G.A mismatch parameters predict DeltaG degrees 37, DeltaH degrees, DeltaS degrees, and TM with average deviations of 4.4%, 7.4%, 8.0%, and 1.5 degrees C, respectively. The nearest-neighbor parameters show that G.A mismatch stability is strongly context dependent, and DeltaG degrees 37 ranges from +1.16 kcal/mol for TGA/AAT to -0.78 kcal/mol for GGC/CAG. In addition, one-dimensional 1H NMR spectra show that the G.A pairing geometry is pH and context dependent.
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Cites
CONFORMATIONAL COUPLING IN DNA POLYMERASE FIDELITY
Johnson, K. A. (1993) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.62.070193.003345 · Cited by 560
Biochemical Basis of DNA Replication Fidelity
Goodman, M. F., Creighton, S., Bloom, L. B., Petruska, J., & Kunkel, T. A. (1993) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.3109/10409239309086792 · Cited by 446
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The Thermodynamics of DNA Structural Motifs
SantaLucia, J., & Hicks, D. (2004) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.32.110601.141800 · Cited by 1,314
Self-citationPerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR
Marshall, O. J. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth254 · Cited by 677
Applications of DNA tiling arrays for whole-genome analysis
Mockler, T. C., & Ecker, J. R. (2005) · Genomics · doi:10.1016/j.ygeno.2004.10.005 · Cited by 400
Sequencing-by-hybridization revisited: the analog-spectrum proposal
Preparata, F. P. (2004) · IEEE/ACM Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2004.12 · Cited by 320
Metadata
- Authors
- Allawi, H. T., & SantaLucia, J.
- Venue
- Biochemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 1998-02-01
- Volume
- 37
- Issue
- 8
- Pages
- 2170-2179
- ISSN
- 0006-2960 (ISSN-L)
- 1520-4995
- OpenAlex
- W2077433900
- Cited by
- 240
- References
- 2
- FWCI
- 2.93
- Type
- journal article
- Language
- en
- Open access
- closed
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- Allawi, H. T., & SantaLucia, J. (1998). Nearest Neighbor Thermodynamic Parameters for Internal G·A Mismatches in DNA. Biochemistry. https://doi.org/10.1021/bi9724873
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
