DECIPHER (version 2.0.2)

deltaSrules: Change in Entropy of Hybridization of Primer/Target Quadruplets in Solution

Description

An 8D array with four adjacent base pairs of the primer and target sequences at a time. Each dimension has five elements defining the residue at that position ("A", "C", "G", "T", or "-"). The array contains the standard entropy change of probe binding (dS, [kcal/mol]) for every quadruple base pairing.

Usage

data(deltaSrules)

Format

The format is: num [1:5, 1:5, 1:5, 1:5, 1:5, 1:5, 1:5, 1:5] -0.0226 0 0 0 0 ... - attr(*, "dimnames")=List of 8 ..$ : chr [1:5] "A" "C" "G" "T" ... ..$ : chr [1:5] "A" "C" "G" "T" ... ..$ : chr [1:5] "A" "C" "G" "T" ... ..$ : chr [1:5] "A" "C" "G" "T" ... ..$ : chr [1:5] "A" "C" "G" "T" ... ..$ : chr [1:5] "A" "C" "G" "T" ... ..$ : chr [1:5] "A" "C" "G" "T" ... ..$ : chr [1:5] "A" "C" "G" "T" ...

Source

Data from a variety of publications by SantaLucia et al.

Details

The first four dimensions correspond to the 4 primer positions from 5' to 3'. The fifth to eighth dimensions correspond to the 4 positions from 5' to 3' of the target sequence.

References

SantaLucia, J., Jr., & Hicks, D. (2004) The Thermodynamics of DNA Structural Motifs. Annual Review of Biophysics and Biomolecular Structure, 33(1), 415-440. doi:10.1146/annurev.biophys.32.110601.141800.

Examples

data(deltaSrules)
# dS of primer = AGCT / target = A-CT pairing
deltaSrules["A", "G", "C", "T", "A", "-", "C", "T"]