Simple Screening Method for Double-strand DNA Binders Using Hairpin DNA-modified Magnetic Beads

We designed an effective screening method for double strand DNA (dsDNA) binders using DNA-modified magnetic particles. Hairpin DNA was immobilized on the surface of magnetic particle for a simple screening of dsDNA binding materials in a solution containing various compounds. Through several magnetic separation and incubation processes, four DNA-binding materials, DAPI, 9AA, AQ2A, and DNR, were successfully screened from among five candidates. Efficiency of screening was demonstrated by HPLC analysis using a C2/18 reverse-phase column. In addition, their relative binding strengths were verified by measuring the melting temperature (Tm). If hairpin DNA sequence is modified for other uses, this magnetic bead-based approach can be applied as a high-throughput screening method for various functional materials such as anti-cancer drugs. Key Words: Screening, dsDNA binder, Magnetic bead, Hairpin DNA, HPLC Figure 1. Schematic diagram for screening dsDNA binding materials using hairpin DNA-modified magnetic particles. Red B(n)s are dsDNA binders, and yellow N(n)s represent the non-binding materials for dsDNA. Sequence and structure of hairpin DNA is described in inset.