Nucleic Acids (DNA, RNA)

This application can generate nucleic acids, and perform molecular dynamics on them. These structures include single and double-stranded DNA and RNA. To access this functionality, use the Nucleic Acids section of the GUI, which can be optionally hidden.

DNA and RNA molecules can be generated directly from primary nucleotide sequence data. This can be input directly, or inferred from an opened protein based on its amino acid residues. In the case of the latter, we make arbitrary choices when multiple nucleotide triplets correspond to a given amino acid.

DNA can be generated as either single-stranded, or double-stranded molecules.

Templates

We load the DNA and RNA building blocks from Amber's ff-nucleic-OL24.lib and RNA.lib's libraries respectively, then assemble them into a single molecule.

Double-stranded molecules

When double-stranded molecule are created (Double selected in the dropdown), a two strand are added in a helix configuration, with the bases aligned in a way that supports hydrogen bonds. During MD runs, the Coulomb and Lennard Jones forces will keep the strands together from these bonds. For the purposes of molecule selection, manipluation, and closing, both strands are considered to be a single molecule. If you wish to treat them as independent, then addd two Single strands instead.

Molecular Dynamics

You can perform molecular dynamics on nucleic acids acids without any special setup. We use Amber's OL24 force field parameters for DNA, and OL3 parameters for RNA. These both are used in conjunction with (e.g. overriding) the base Amber Parm19.dat configuration.