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Improved Nearest-Neighbor Parameters for Predicting DNA Duplex Stability
Abstract
Thermodynamic data were determined from UV absorbance vs temperature profiles of 23 oligonucleotides. These data were combined with data from the literature for 21 sequences to derive improved parameters for the 10 Watson-Crick nearest neighbors. The observed trend in nearest-neighbor stabilities at 37 degrees C is GC > CG > GG > GA approximately GT approximately CA > CT > AA > AT > TA (where only the top strand is shown for each nearest neighbor). This trend suggests that both sequence and base composition are important determinants of DNA duplex stability. On average, the improved parameters predict deltaG degrees(37), deltaH degrees, deltaS degrees, and T(m) within 4%, 7%, 8%, and 2 degrees C, respectively. The parameters are optimized for the prediction of oligonucleotides dissolved in 1 M NaC1.
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Citations
Cited by
Design and self-assembly of two-dimensional DNA crystals
Winfree, E., Liu, F., Wenzler, L. A., & Seeman, N. C. (1998) · Nature · doi:10.1038/28998 · Cited by 2,857
Xia, 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
Self-citationTouchdown PCR for increased specificity and sensitivity in PCR amplification
Korbie, D. J., & Mattick, J. S. (2008) · Nature Protocols · doi:10.1038/nprot.2008.133 · Cited by 624
Reliability and reproducibility issues in DNA microarray measurements
DRAGHICI, S., KHATRI, P., EKLUND, A., & SZALLASI, Z. (2006) · Trends in Genetics · doi:10.1016/j.tig.2005.12.005 · Cited by 590
Li, Y., & Breaker, R. R. (1999) · Journal of the American Chemical Society · doi:10.1021/ja990592p · Cited by 587
Metadata
- Authors
- SantaLucia, Allawi, H. T., & Seneviratne, P. A.
- Venue
- Biochemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 1996-01-01
- Volume
- 35
- Issue
- 11
- Pages
- 3555-3562
- ISSN
- 0006-2960 (ISSN-L)
- 1520-4995
- OpenAlex
- W1970663985
- Cited by
- 831
- References
- 0
- FWCI
- 8.78
- Type
- journal article
- Language
- en
- Open access
- closed
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- SantaLucia, Allawi, H. T., & Seneviratne, P. A. (1996). Improved Nearest-Neighbor Parameters for Predicting DNA Duplex Stability. Biochemistry. https://doi.org/10.1021/bi951907q
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