IR fluorophore-modified DNAs and IR fluorescence imaging provide a safe and effective alternative for investigating ligand-DNA interactions than those involving radioactivity. These DNAs can be synthesized by conventional phosphoramidite chemistries and are commercially available. However, they are relatively expensive, which can be prohibitive if many different DNA probes are required. Described here is the design of modular DNA probes that can be synthesized by PCR using conventional templates and a defined set of IR fluorophore-modified primers. These have been found effective for investigating protein-DNA interactions in a variety of assays, including Electrophoretic Mobility Shift Assays (EMSA), Restriction Endonuclease Protection Assays (REPA), and the iterative selection method Restriction Endonuclease Protection, Selection, and Amplification (REPSA).