A programmable DNA roadblock system using dCas9 and multivalent target sites

PLoS One. 2022 May 6;17(5):e0268099. doi: 10.1371/journal.pone.0268099. eCollection 2022.

Abstract

A protein roadblock forms when a protein binds DNA and hinders translocation of other DNA binding proteins. These roadblocks can have significant effects on gene expression and regulation as well as DNA binding. Experimental methods for studying the effects of such roadblocks often target endogenous sites or introduce non-variable specific sites into DNAs to create binding sites for artificially introduced protein roadblocks. In this work, we describe a method to create programmable roadblocks using dCas9, a cleavage deficient mutant of the CRISPR effector nuclease Cas9. The programmability allows us to custom design target sites in a synthetic gene intended for in vitro studies. These target sites can be coded with multivalency-in our case, internal restriction sites which can be used in validation studies to verify complete binding of the roadblock. We provide full protocols and sequences and demonstrate how to use the internal restriction sites to verify complete binding of the roadblock. We also provide example results of the effect of DNA roadblocks on the translocation of the restriction endonuclease NdeI, which searches for its cognate site using one dimensional diffusion along DNA.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Binding Sites
  • CRISPR-Cas Systems
  • DNA* / metabolism
  • DNA-Binding Proteins / genetics
  • Endonucleases* / metabolism
  • RNA, Guide, CRISPR-Cas Systems / genetics

Substances

  • DNA-Binding Proteins
  • RNA, Guide, CRISPR-Cas Systems
  • DNA
  • Endonucleases

Grants and funding

ACP received grant # MCB-2120878 from the National Science Foundation (www.nsf.gov). The funders have not had and will not have a role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.