CSI-FID: high throughput label-free detection of DNA binding molecules.
Determining the sequence specifity of DNA binding molecules is a non-trivial task. Here we describe the development of a platform for assaying the sequence specificity of DNA ligands using label free detection on high density DNA microarrays. This is achieved by combining Cognate Site Identification (CSI) with Fluorescence Intercalation Displacement (FID) to create CSI-FID. We use the well-studied small molecule DNA ligand netropsin to develop this high throughput platform. Analysis of the DNA binding properties of protein- and small molecule-based libraries with CSI-FID will advance the development of genome-anchored molecules for therapeutic purposes.
Hauschild
Karl E
KE
Genome Center of Wisconsin, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
Stover
James S
JS
Boger
Dale L
DL
Ansari
Aseem Z
AZ
D001665:Binding Sites; D004247:DNA / Q000737:chemistry*; D004996:Ethidium / Q000737:chemistry; D005456:Fluorescent Dyes / Q000737:chemistry; D007364:Intercalating Agents / Q000737:chemistry; D008024:Ligands; D009429:Netropsin / Q000737:chemistry; D020411:Oligonucleotide Array Sequence Analysis; D054852:Small Molecule Libraries
D005456:Fluorescent Dyes; D007364:Intercalating Agents; D008024:Ligands; D054852:Small Molecule Libraries; D009429:Netropsin; D004247:DNA; D004996:Ethidium