Methods for identifying ligands that target nucleic acid molecules and nucleic acid structural motifs

A method for selecting, from a plurality of candidate ligands, one or more ligands that have increased likelihood of binding to a nucleic acid molecule comprising a particular nucleic acid motif, said method comprising:

• providing a database which correlates various ligands' abilities to bind to the particular nucleic acid motif and various other nucleic acid motifs;
• comparing the candidate ligands' ability to bind to the particular nucleic acid motif;
• and
• choosing one or more ligands based on their ability to bind to the particular nucleic acid motif.

A method for selecting, from a plurality of candidate ligands, one or more ligands that have increased likelihood of binding to a first nucleic acid molecule comprising a first particular nucleic acid motif and that have decreased likelihood of binding to a second nucleic acid molecule comprising a second particular nucleic acid motif, said method comprising:

• providing a database which correlates various ligands' abilities to bind to the first particular nucleic acid motif, to the second particular nucleic acid motif, and to various other nucleic acid motifs;
• comparing the candidate ligands' ability to bind to the first particular nucleic acid motif and to the second particular nucleic acid motif;
• and
• choosing one or more ligands based on their ability to bind to the first particular nucleic acid motif and their inability to the second particular nucleic acid motif.

A method for identifying a nucleic acid which interacts with a ligand, said method comprising:

• providing a plurality of ligands immobilized on a support, wherein each particular ligand is immobilized at a discrete location on the support;
• contacting the plurality of immobilized ligands with a nucleic acid library under conditions effective for one or more members of the nucleic acid library to bind with the immobilized ligands;
• and
• identifying members of the nucleic acid library that are bound to a particular immobilized ligand.