DAP-Seq (DNA Affinity Purification Sequencing) Service

Transcription factors (TFs) are sequence-specific DNA-binding proteins that regulate gene expression in all organisms, and they account for 4-10% of all protein-coding genes in all species. For example, the model plant Arabidopsis has 2492 genes encoding TFs, accounting for more than 9% of its total protein-coding genes.

ChIP-seq is the main method to perform in vivo detection of TFBS, and the cumbersome steps and material requirements have blocked many scientific processes. The DNA Affinity Purification Sequencing (DAP-seq) method has successfully transferred in vivo binding experiments to in vitro, solved the problem of ChIP antibody preparation, and greatly improved the efficiency of DNA Binding Site discovery. DAP-seq is not only able to find TFBS with ultra-high throughput, but also provides insight into the biological properties and binding site structures of numerous TFs, showing great value in cis-trans and epistatic studies of any organism.

Creative Proteomics offers cutting-edge DAP-Seq technology, which is a powerful tool for studying protein-DNA interactions. With our expertise and advanced instrumentation, we provide reliable and accurate results that enable researchers to gain a deeper understanding of gene regulation and other important biological processes.

DAP-seq expresses TF with tags by in vitro protein expression technology, binds to genomic DNA libraries in vitro, and then isolates the DNA bound to the TF, and then uses high-throughput sequencing to find the binding site of the TF.

Routine Analytical Procedures for DAP-seq

a) Obtain genomic DNA, interrupt and ligate sequencing junction

b) Expression of fusion protein with ligand (target TF)

c) The fusion protein is attached to antibody direct-labeled magnetic beads

d) Genomic DNA is incubated with the target TF fusion protein, and the DNA fragment bound to the target TF is enriched using the magnet and sequenced

DAP-seq protocol overviewDAP-seq protocol overview (Bartlett et al., 2017)

Choose DAP-Seq or ChIP-seq?

You can refer to the following information to select the appropriate research method for your project:

Advantages of DAP-seq service:

  • Overcomes the limitations of ChIP-seq that relies on the availability of high-quality antibodies.
  • No need for transgenic approaches, making it more accessible and efficient for studying TFBS in non-model organisms and less studied TFs.
  • Can detect TFBS in high-throughput and gain insight into TF biology and TFBS structure in epigenetic research.

Limitations of DAP-seq service:

  • Some TFs require co-factors or specific cellular conditions to function, which may not be present in the in vitro environment of DAP-seq.
  • Some TFs may not properly fold or form multimers in vitro, limiting their functionality in DAP-seq.
  • DAP-seq cannot capture the dynamic changes in TF-DNA interactions due to factors such as chromatin modification and accessibility, making it less suitable for studying dynamic TFBS.
DAP-seq ChIP-seq
Protein and DNA binding in in vitro in vivo
Requires specific antibodies No Yes
Suitable for non-model species Yes No
Experimental cycle Short Long
Suitable for large-scale transcription factor studies Yes No

Creative Proteomics has accumulated a wealth of experience in DNA-protein interaction research. Our team of technical professionals also offers other techniques for DNA-protein interaction analysis, including ChIP-seq, DNA pull down, DNase l footprinting, etc. Contact us to learn more.


  1. Bartlett, Anna, et al. "Mapping genome-wide transcription-factor binding sites using DAP-seq." Nature protocols 12.8 (2017): 1659-1672.
* This service is for RESEARCH USE ONLY, not intended for any clinical use.