free energy calculations???

Michael Schmitz MSchmitz at lbl.gov
Sat May 22 01:09:06 EST 1999


Helge Steen wrote:
> I am urgently looking for a formula/program to calculate the free energy of a
> oligonucleotide- DNA template duplex. The problem is that the oligonucleotide
> and the template are not completely complementary, but there are single base
> exchanges present in the oligo. This situation may f.e. turn up when dealing
> with site-directed mutagenesis via PCR. If oligo and template were
> complementary, the standard nearest-neighbour calculation would apply. But in
> this case?

The nearest neighbour approximation still applies but you have a mismatch
at the site of the base exchange which can be treated as small symmetric
internal loop (at least to a first approximation). There's a lot of
publications on the stability parameters available, see appended list (I
bet it's not completely up to date but you'll get an idea). The
destabilization by a symmetric mismatch 
would be -13.2 cal/mol*K for RNA, I can't find data for DNA at the moment. 

If you are looking for the predicted melting temperature and melting
profile rather than the free energy, the service at  

http://www.biophys.uni-duesseldorf.de/POLAND/poland.html

might be what you need. 

	Michael


Stacking parameters:
--------------------

for RNA in 1 M NaCl

Freier, S.M., Kierzek, R., Jaeger, J.A., Sugimoto, N., Caruthers, M.H.,
Neilson, T. & Turner, D.H. (1986). Proc. Natl. Acad. Sci. USA 83,
9373-9377.
Improved free-energy parameters for predictions of RNA duplex stability. 
for RNA in 1 M NaCl

Pörschke, D., Uhlenbeck, O.C. & Martin, F.H. (1973). Biopolymers 12,
1313-1335.
Thermodynamics and kinetics of the helix-coil transition of oligomers
containing GC base pairs. 

for DNA in 0.019 M NaCl
Gotoh, O. (1983). Adv. Biophys. 16, 1-52.
Prediction of melting profiles and local helix stability for sequenced
DNA. 

for DNA in 1 M NaCl
Breslauer, K.J., Frank, R., Bloecker, H. & Marky, L.A. (1986). Proc. Natl.
Acad. Sci. USA 83, 3746-3750.
Predicting DNA duplex stability from the base sequence. 

for DNA in 0.1 M NaCl
Klump, H.H. (1987). Canad. J. Chem. 66, 804-809.
Energetics of order/order transitions in nucleic acids.

Klump, H. (1990). in Landolt-Börnstein, New Series, Group VII Biophysics,
Vol. 1 Nucleic Acids, Subvol. c Spectroscopic and Kinetic Data, Physical
Data I, (W. Saenger, ed.), Springer-Verlag Berlin, p. 244-245.
Calorimetric studies on DNAs and RNAs. 

for DNA in 1 M NaCl
SantaLucia, J. Jr., Allawi, H.T. & Seneviratne, P.A. (1996). Biochemistry
35, 3555-3562.
Improved nearest-neighbor parameters for predicting DNA duplex stability. 

for DNA in 1 M NaCl
Allawi, H.T. & SantaLucia, J. Jr. (1997). Biochemistry 36, 10581-10594.
Thermodynamics and NMR of Internal G·T Mismatches in DNA. 
    

for RNA/DNA hybrids in 1 M NaCl

Sugimoto, N., Nakano, S., Katoh, M., Matsumura, A., Nakamuta, H., Ohmichi,
T., Yoneyama, M. & Sasaki, M. (1995).
Biochemistry 34, 11211-11216.
Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes. 

Loop entropy parameters:
------------------------

Poland, D. (1974) Biopolymers 13, 1859-1871. Recursion Relation Generation
of Probability Profiles for Specific-Sequence
Macromolecules with Long-Range Correlations. 

Fixman and Freire (1977) Biopolymers 16, 2693-2704. Theory of DNA melting
curves. 

Gralla, J. & Crothers, D.M. (1973) J. Mol. Biol. 78, 301-319. Free energy
of imperfect nucleic acid helices. III. Small internal loops resulting
from mismatches. 

Freier, S.M., Kierzek, R., Jaeger, J.A., Sugimoto, N., Caruthers, M.H.,
Neilson, T. & Turner, D.H. (1986) Proc. Natl. Acad. Sci. USA 83,
9373-9377. Improved free-energy parameters for predictions of RNA duplex
stability.




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