High-Throughput Sequencing With Fluorescent Ligand Interaction Profiling

HiTS-FLIP is a technique for measuring quantitative protein-DNA binding affinity at unprecedented depth. In this approach, the optics built into a high-throughput sequencer are used to visualize in vitro binding of a protein to sequenced DNA in a flow cell (Nutiu et al., 2011).

A microfluidic flow cell with anchored single-stranded DNA is sequenced by synthesis. Second-strand DNA is stripped and rebuilt using Klenow polymerase and unmodified dNTPs to form double-stranded DNA clusters. Fluorescently labeled binding protein is introduced at different concentrations, and binding is imaged.


  • Quantitative and comprehensive


  • Requires specialized hardware
  • Not yet adopted widely by the scientific community


Illumina Library prep and Array Kit Selector


None available yet


Nutiu R., Friedman R. C., Luo S., et al. Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument. Nat Biotechnol. 2011;29:659-664