NET-Seq
HiTS-FLIP
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. 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.
Pros:
- Quantitative and comprehensive
Cons:
- Requires specialized hardware
- Not yet adopted widely by the scientific community