deltaSrules: Change in Entropy of Hybridization of DNA/DNA Quadruplets in...

In DECIPHER: Tools for curating, analyzing, and manipulating biological sequences

Description

An 8D array with four adjacent base pairs of the DNA duplex. 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" ...

Details

The first four dimensions correspond to the four top strand positions from 5' to 3'. The fifth to eighth dimensions correspond to the four bottom strand positions from 5' to 3'.

Source

Data from a variety of publications by SantaLucia et al.

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 the duplex AGCT / A-CT pairing
deltaSrules["A", "G", "C", "T", "A", "-", "C", "T"]

DECIPHER documentation built on Nov. 8, 2020, 8:30 p.m.