High-throughput sequencing SELEX for the determination of DNA-binding protein specificities in vitro

Raphaël Pantier, Kashyap Chhatbar, Grace Alston, Heng Yang Lee, Adrian Bird

Research output: Contribution to journalArticlepeer-review

Abstract

High-throughput sequencing SELEX (HT-SELEX) is a powerful technique for unbiased determination of preferred target motifs of DNA-binding proteins in vitro. The procedure depends upon selection of DNA binding sites from a random library of oligonucleotides by purifying protein-DNA complexes and amplifying bound DNA using the polymerase chain reaction. Here, we describe an optimized step-by-step protocol for HT-SELEX compatible with Illumina sequencing. We also introduce a bioinformatic pipeline (eme_selex) facilitating the detection of promiscuous DNA binding by analyzing the enrichment of all possible k-mers. For complete details on the use and execution of this protocol, please refer to Pantier et al. (2021).

Original languageEnglish
Article number101490
Number of pages21
JournalStar Protocols
Volume3
Issue number3
Early online date22 Jun 2022
DOIs
Publication statusPublished - 16 Sep 2022

Keywords

  • bioinformatics
  • high throughput screening
  • molecular biology
  • sequence analysis
  • sequencing

Fingerprint

Dive into the research topics of 'High-throughput sequencing SELEX for the determination of DNA-binding protein specificities in vitro'. Together they form a unique fingerprint.

Cite this