thermopar: Nearest neighbor thermodynamic parameters for LNA-modified...

In Santaris/affinity: Functions to do thermodynamics on oligonucleotides

Description

A dataframe bla bla

Usage

data(thermopar)

Format

A data frame with five columns. Each row represents either a dinucleotide xx|yy (where xx is the oligonucleotide sequence 5' to 3' and yy is the RNA target sequence 3' to 5'. For the oligonucleotide, uppercase denotes LNA and lowercase DNA), or a flanking nucleotide flank.x|flank.y (the first or last nucleotide in the sequence), or the symmetry adjustment.

oligo.53

The oligonucleotide dinucleotide sequence from 5' to 3'.

target.35

The RNA target dinucleotide sequence from 3' to 5'.

comb.oligo.target

The combined oligo and target dinucleotides, similar to the rownames.

enthalpy.cal.mol

The contribution to the change in enthalpy (cal/mol).

entropy.cal.mol.K

The contribution to the change in entropy (cal/(mol*K)).

Source

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.

References

See calculate.affinity for additional references.

Examples

data(thermopar)

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