deltaSrulesRNA {DECIPHER} | R Documentation

## Change in Entropy of Hybridization of RNA/RNA Quadruplets in Solution

### Description

An 8D array with four adjacent base pairs of the RNA 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(deltaSrulesRNA)

### Format

The format is: num [1:5, 1:5, 1:5, 1:5, 1:5, 1:5, 1:5, 1:5] -0.0182 0 0 0 0 ... - attr(*, "dimnames")=List of 8 ..$ : chr [1:5] "A" "C" "G" "U" ... ..$ : chr [1:5] "A" "C" "G" "U" ... ..$ : chr [1:5] "A" "C" "G" "U" ... ..$ : chr [1:5] "A" "C" "G" "U" ... ..$ : chr [1:5] "A" "C" "G" "U" ... ..$ : chr [1:5] "A" "C" "G" "U" ... ..$ : chr [1:5] "A" "C" "G" "U" ... ..$ : chr [1:5] "A" "C" "G" "U" ...

### 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(deltaSrulesRNA)
    # dS of the duplex AGCU / A-CU pairing
    deltaSrulesRNA["A", "G", "C", "U", "A", "-", "C", "U"]

[Package DECIPHER version 2.20.0 Index]