The DOI matches its Crossref record; 22 of the 22 references it cites were found in a registry or an index.
Nearest-Neighbor Thermodynamics of Internal A·C Mismatches in DNA: Sequence Dependence and pH Effects
Abstract
Thermodynamics of 27 oligonucleotides with internal A.C mismatches at two different pHs were determined from UV absorbance versus temperature melting profiles. The data were combined with four literature values and used to derive nearest-neighbor parameters for all 16 trimer sequences with internal A.C mismatches at pH 7.0 and 5. 0. The results indicate that the contribution of single A.C mismatches to duplex stability is strongly dependent on the solution pH and the nearest-neighbor context. On average, the protonation of an internal A.C mismatch stabilizes the duplex by 1.39 kcal/mol for DeltaG degrees37 and 7.0 degreesC for the TM. The nearest-neighbor parameters predict DeltaG degrees37, DeltaH degrees, DeltaS degrees, and TM of oligonucleotides presented in this study with average deviations of 6.3%, 11.0%, 12.2%, and 1.8 degreesC, respectively, at pH 7.0 and 4.7%, 5.9%, 6.1%, and 1.3 degreesC, respectively, at pH 5. 0. At pH 7.0, the contribution of single A.C mismatches to helix stability ranges from 2.25 kcal/mol for TCA/AAT to 1.22 kcal/mol for GCG/CAC. At pH 5.0, however, the contribution of A+.C mismatches ranges from 1.09 kcal/mol for TCT/AAA to -0.43 kcal/mol for GCC/CAG. Implications of the results for replication fidelity and mismatch repair are discussed.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
An Introduction to the Bootstrap
Efron, B., & Tibshirani, R. J. (1994) · doi:10.1201/9780429246593 · Cited by 40,500
An Introduction to the Bootstrap
Efron, B., & Tibshirani, R. J. (1993) · doi:10.1007/978-1-4899-4541-9 · Cited by 21,230
Savitzky-Golay Smoothing Filters
Press, W. H., & Teukolsky, S. A. (1990) · Computers in Physics · doi:10.1063/1.4822961 · Cited by 11,670
Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions
Piotto, M., Saudek, V., & Sklenář, V. (1992) · Journal of Biomolecular NMR · doi:10.1007/bf02192855 · Cited by 3,712
On Finding All Suboptimal Foldings of an RNA Molecule
Zuker, M. (1989) · Science · doi:10.1126/science.2468181 · Cited by 2,005
MISMATCH REPAIR IN REPLICATION FIDELITY, GENETIC RECOMBINATION, AND CANCER BIOLOGY
Modrich, P., & Lahue, R. (1996) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.65.070196.000533 · Cited by 1,526
Stability of ribonucleic acid double-stranded helices
Borer, P. N., Dengler, B., Tinoco, I., & Uhlenbeck, O. C. (1974) · Journal of Molecular Biology · doi:10.1016/0022-2836(74)90357-x · Cited by 762
FIDELITY MECHANISMS IN DNA REPLICATION
Echols, H., & Goodman, M. F. (1991) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.60.070191.002401 · Cited by 712
Antisense Research and Applications
Agrawal, S., & Crooke, S. T. (1993) · Medical Entomology and Zoology · Cited by 610
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
Kramer, B., Kramer, W., & Fritz, H.-J. (1984) · Cell · doi:10.1016/0092-8674(84)90283-6 · Cited by 461
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
Modrich, P. (1987) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.56.070187.002251 · Cited by 425
Handbook of biochemistry and molecular biology. Nucleic acids - v. 1 - 3. ed.
Fasman, G. D., & Co., C. C. R. (1975) · Cited by 421
Cebula, T. A., Payne, W. L., & Feng, P. (1995) · Journal of Clinical Microbiology · doi:10.1128/jcm.33.1.248-250.1995 · Cited by 380
MISMATCH REPAIR IN ESCHERICHIA COLI
Radman, M., & Wagner, R. (1986) · Annual Review of Genetics · doi:10.1146/annurev.ge.20.120186.002515 · Cited by 256
Nearest Neighbor Influences on DNA Polymerase Insertion Fidelity
Mendelman, L. V., Boosalis, M. S., Petruska, J., & Goodman, M. F. (1989) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)71695-5 · Cited by 242
Use of a water flip-back pulse in the homonuclear NOESY experiment
Lippens, G., Dhalluin, C., & Wieruszeski, J. M. (1995) · Journal of Biomolecular NMR · doi:10.1007/bf00211762 · Cited by 167
TIBANYENDA, N., BRUIN, S. H. D., HAASNOOT, C. A. G., van der MAREL, G. A., BOOM, J. H. V., & Hilbers, C. W. (1984) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1984.tb07970.x · Cited by 129
Influence of pH on the conformation and stability of mismatch base-pairs in DNA
Brown, T. P., Leonard, G. A., Booth, E. D., & Kneale, G. G. (1990) · Journal of Molecular Biology · doi:10.1016/0022-2836(90)90320-l · Cited by 110
Bhattacharyya, A., & Lilley, D. M. J. (1989) · Journal of Molecular Biology · doi:10.1016/0022-2836(89)90596-2 · Cited by 66
Boulard, Y., Cognet, J. A. H., Gabarro‐Arpa, J., Bret, M. L., Carbonnaux, C., & Fazakerley, G. V. (1995) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.0076 · Cited by 55
Cited by
Mfold web server for nucleic acid folding and hybridization prediction
Zuker, M. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg595 · Cited by 13,404
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
LncTar: a tool for predicting the RNA targets of long noncoding RNAs
Li, J., Ma, W., Zeng, P., Wang, J., Geng, B., Yang, J., & Cui, Q. (2015) · Briefings in Bioinformatics · doi:10.1093/bib/bbu048 · Cited by 454
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
Metadata
- Authors
- Allawi, H. T., & SantaLucia, J.
- Venue
- Biochemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 1998-06-01
- Volume
- 37
- Issue
- 26
- Pages
- 9435-9444
- ISSN
- 0006-2960 (ISSN-L)
- 1520-4995
- OpenAlex
- W2125181285
- Cited by
- 255
- References
- 22
- FWCI
- 2.48
- Type
- journal article
- Language
- en
- Open access
- closed
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
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.
