DNA parameters, version 3.1, last updated May 2000
Please cite the articles indicated by §

• Watson-Crick pairs:
  § SantaLucia, J Jr. (1998) "A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics." Proc. Natl. Acad. Sci. USA 95, 1460-1465. (Abstract)

• Mismatches:
  
  • § Allawi, HT & SantaLucia, J Jr. (1997)
    "Thermodynamics and NMR of Internal G·T Mismatches in DNA"
    Biochemistry 36, 10581-10594.
  • Allawi, HT & SantaLucia, J Jr. (1998)
    "Nearest Neighbor Thermodynamic Parameters for internal G·A mismtaches in DNA"
    Biochemistry 37, 2170-2179.
  • Allawi, HT & SantaLucia, J Jr. (1998)
    "Thermodynamics of internal C·T mismatches in DNA"
    Nucleic Acids Research 26, 2694-2701.
  • Allawi, HT & SantaLucia, J Jr. (1998)
    "Nearest-neighbor thermodynamics of internal A·C mismatches in DNA: Sequence dependence and pH effects"
    Biochemistry 37, 9435-9444.
  • Peyret, N, Seneviratne, PA, Allawi, HT & SantaLucia, J Jr. (1999)
    "Nearest neighbor thermodynamics of DNA with A·A, C·C, G·G, and T·T mismatches"
    Biochemistry 38, 3468-3477.

• Dangling-ends and terminal mismatches:
  Bommarito S, Peyret N, & SantaLucia J Jr. (2000) "Thermodynamic parameters for DNA sequences with dangling ends."
  Nucleic Acids Res 28(9), 1929-1934.

• Loop parameters: (SantaLucia, J Jr., unpublished results)
  Loop parameters are based on an analysis of data from the literature data using the Watson-Crick parameters described above and salt dependence data from the SantaLucia lab. The following list contains the majority of data used to determine loop parameters (but is not exhaustive):

  • Hairpin data:
    Hilbers et al. (1985) Biochimie 67, 685-695.
    Blommers et al. (1989) Biochemistry 28, 7491-7498.
    Antao et al. (1991) Nucleic Acids Res. 19, 5901-5905.
    Antao et al. (1991) Nucleic Acids Res. 20, 819-824.
    Senior et al. (1988) Proc. Natl. Acad. Sci. USA 85, 6242-6246
    

  • Bulge data:
    LeBlanc and Morden (1991) Biochemistry 30, 4042-4047
    Zieba et al. (1991) Biochemistry 30, 8018-8026
    Ke et al. (1995) Biochemistry 34, 4593-4600.
    Turner, DH (1992) Curr. Opin. Struc. Biol. 2, 334-337.
    

  • Internal loops:
    unpublished data on internal loops from the SantaLucia lab.

  • Multi-branched loops:
    The parameters for multi-branched loops are from a best fit analysis of secondary structure predictions vs. experiments as done by Jaeger et al. for RNA (Jaeger et al. (1989) PNAS 86, 7706-7710). The current parameters for multi-branched loops neglect the sequence and complicated length dependence described by Leontis and coworkers (see below) and other groups in the literature, but approximate 4 way junctions fairly well. The implementation of more complicated rules will require modification of the mfold algorithm as well as the acquistion of a more complete thermodynamic data base in the future.

    Multi-loop references:
    Kadrmas et al. (1995) Nucleic Acids Res. 23, 2122
    Lilley and Hallam (1984) J. Mol. Biol. 180, 179-200
    Lu et al. (1991) J. Mol. Biol. 223, 781-789.
    Ladbury et al. (1994) Biochemistry 33, 6828-6833.
    Leontis et al. (1991) Nucleic Acids Res. 19, 759-766.
    

DNA Free Energies at arbitrary temperatures: (version 3.0)
Enter a temperature between 0 and 100 °
Ionic conditions: [Na+]     [Mg++]
Correction type: Oligomer     Polymer

DNA enthalpies: