Regulation of Gene Editing Activity Directed by Single-Stranded Oligonucleotides and CRISPR/Cas9 Systems

PLoS One. 2015 Jun 8;10(6):e0129308. doi: 10.1371/journal.pone.0129308. eCollection 2015.

Abstract

Single-stranded DNA oligonucleotides (ssODNs) can direct the repair of a single base mutation in human genes. While the regulation of this gene editing reaction has been partially elucidated, the low frequency with which repair occurs has hampered development toward clinical application. In this work a CRISPR/Cas9 complex is employed to induce double strand DNA breakage at specific sites surrounding the nucleotide designated for exchange. The result is a significant elevation in ssODN-directed gene repair, validated by a phenotypic readout. By analysing reaction parameters, we have uncovered restrictions on gene editing activity involving CRISPR/Cas9 complexes. First, ssODNs that hybridize to the non-transcribed strand direct a higher level of gene repair than those that hybridize to the transcribed strand. Second, cleavage must be proximal to the targeted mutant base to enable higher levels of gene editing. Third, DNA cleavage enables a higher level of gene editing activity as compared to single-stranded DNA nicks, created by modified Cas9 (Nickases). Fourth, we calculated the hybridization potential and free energy levels of ssODNs that are complementary to the guide RNA sequences of CRISPRs used in this study. We find a correlation between free energy potential and the capacity of single-stranded oligonucleotides to inhibit specific DNA cleavage activity, thereby indirectly reducing gene editing activity. Our data provide novel information that might be taken into consideration in the design and usage of CRISPR/Cas9 systems with ssODNs for gene editing.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Base Sequence
  • Binding Sites
  • CRISPR-Cas Systems / physiology*
  • Catalysis
  • Cell Line
  • DNA, Single-Stranded*
  • Deoxyribonuclease I / metabolism
  • Gene Expression
  • Gene Targeting
  • Genes, Reporter
  • Genetic Vectors / genetics
  • Humans
  • Molecular Sequence Data
  • Mutation
  • Oligonucleotides*
  • Protein Binding
  • RNA Editing*
  • RNA, Guide / genetics
  • Transfection

Substances

  • DNA, Single-Stranded
  • Oligonucleotides
  • RNA, Guide
  • Deoxyribonuclease I