README.md

In Santaris/affinity: Functions to do thermodynamics on oligonucleotides

affinity

This R-package calculates thermodynamic parameters for a perfect pairing between an (chemically modified) oligonucleotide and an RNA target.

The parameters calculated are the melting temperature (tm), Gibbs free energy of binding (dg), enthalpy (dh), entropy (ds), and the equilibrium constant (k), based on a nearest-neigbhbor model.

Currently, the package contains nearest-neigbour parameters from publicly available sources on DNA and LNA. Note that only perfectly matched pairs of oligo and target can be calculated. For algorithms that allow mismatches/bulges/loops refer to e.g. The Vienna RNA Package.

References

Hashem, G, Pham, L, Vaughan, MR, and Gray, DM (1998) Hybrid Oligomer Duplexes Formed with Phosphorothioate DNAs: CD Spectra and Melting Temperatures of S-DNA/RNA Hybrids Are Sequence-Dependent but Consistent with Similar Heteronomous Conformations. Biochemistry 37:61-72.

McTigue, PM, Peterson, RJ and Kahn, JD (2004). Sequence-dependent thermodynamic parameters for locked nucleic acid (LNA)-DNA duplex formation. Biochemistry 43: 5388-5405.

Owczarzy, R, You, Y, Groth, CL and Tataurov, AV (2011). Stability and mismatch discrimination of locked nucleic acid-DNA duplexes. Biochemistry 50: 9352-9367.

Pedersen, L, Hagedorn, P, Lindholm, MW, Lindow, M (2014). A Kinetic Model Explains Why Shorter and Less Affine Enzyme-recruiting Oligonucleotides Can Be More Potent. Molecular Therapy - Nucleic Acids, 3, e149.

SantaLucia, J (1998). A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci USA 95: 1460-1465.

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

Santaris/affinity documentation built on May 9, 2019, 12:43 p.m.