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New PAM Improves the Single-Base Specificity of crRNA-Guided LbCas12a Nuclease

The RNA-guided Cas12a nuclease forms a complex with a CRISPR RNA (crRNA) to cleave the double-stranded DNA target. Among others, Cas12a protein from Lachnospiraceae bacterium (LbCas12a) is widely used for biomedical research. For target recognition, LbCas12a requires a specific nucleotide sequence,...

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Autores principales: Misiurina, Mariia A., Chirinskaite, Angelina V., Fotina, Aleksandra S., Zelinsky, Andrey A., Sopova, Julia V., Leonova, Elena I.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9698171/
https://www.ncbi.nlm.nih.gov/pubmed/36431062
http://dx.doi.org/10.3390/life12111927
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author Misiurina, Mariia A.
Chirinskaite, Angelina V.
Fotina, Aleksandra S.
Zelinsky, Andrey A.
Sopova, Julia V.
Leonova, Elena I.
author_facet Misiurina, Mariia A.
Chirinskaite, Angelina V.
Fotina, Aleksandra S.
Zelinsky, Andrey A.
Sopova, Julia V.
Leonova, Elena I.
author_sort Misiurina, Mariia A.
collection PubMed
description The RNA-guided Cas12a nuclease forms a complex with a CRISPR RNA (crRNA) to cleave the double-stranded DNA target. Among others, Cas12a protein from Lachnospiraceae bacterium (LbCas12a) is widely used for biomedical research. For target recognition, LbCas12a requires a specific nucleotide sequence, named a protospacer adjacent motif (PAM). Besides the canonical TTTV PAM, LbCas12a can recognize other suboptimal PAMs. We examined a novel TTAA PAM for the LbCas12a nuclease and found that the specificity of cleavage was increased. We found that single nucleotide substitutions at all positions of the guide RNA except the 20th position blocked the cleavage of the target DNA. The type of nucleotide substitutions (U-A, U-C or U-G) did not affect the efficiency of cleavage in the 20th position. When we used the canonical PAM under the same conditions, we observed the cleavage of target DNA by LbCas12a in many positions, showing less specificity in given conditions. The efficiency and specificity of the LbCas12a nuclease were evaluated both by gel-electrophoresis and using FAM-labeled single-stranded probes. We were able to assess the change in fluorescence intensity only for several variants of guide RNAs. High specificity allows us to type single nucleotide substitutions and small deletions/insertions (1–2 nucleotides) and look for target mutations when knocking out.
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spelling pubmed-96981712022-11-26 New PAM Improves the Single-Base Specificity of crRNA-Guided LbCas12a Nuclease Misiurina, Mariia A. Chirinskaite, Angelina V. Fotina, Aleksandra S. Zelinsky, Andrey A. Sopova, Julia V. Leonova, Elena I. Life (Basel) Article The RNA-guided Cas12a nuclease forms a complex with a CRISPR RNA (crRNA) to cleave the double-stranded DNA target. Among others, Cas12a protein from Lachnospiraceae bacterium (LbCas12a) is widely used for biomedical research. For target recognition, LbCas12a requires a specific nucleotide sequence, named a protospacer adjacent motif (PAM). Besides the canonical TTTV PAM, LbCas12a can recognize other suboptimal PAMs. We examined a novel TTAA PAM for the LbCas12a nuclease and found that the specificity of cleavage was increased. We found that single nucleotide substitutions at all positions of the guide RNA except the 20th position blocked the cleavage of the target DNA. The type of nucleotide substitutions (U-A, U-C or U-G) did not affect the efficiency of cleavage in the 20th position. When we used the canonical PAM under the same conditions, we observed the cleavage of target DNA by LbCas12a in many positions, showing less specificity in given conditions. The efficiency and specificity of the LbCas12a nuclease were evaluated both by gel-electrophoresis and using FAM-labeled single-stranded probes. We were able to assess the change in fluorescence intensity only for several variants of guide RNAs. High specificity allows us to type single nucleotide substitutions and small deletions/insertions (1–2 nucleotides) and look for target mutations when knocking out. MDPI 2022-11-18 /pmc/articles/PMC9698171/ /pubmed/36431062 http://dx.doi.org/10.3390/life12111927 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Misiurina, Mariia A.
Chirinskaite, Angelina V.
Fotina, Aleksandra S.
Zelinsky, Andrey A.
Sopova, Julia V.
Leonova, Elena I.
New PAM Improves the Single-Base Specificity of crRNA-Guided LbCas12a Nuclease
title New PAM Improves the Single-Base Specificity of crRNA-Guided LbCas12a Nuclease
title_full New PAM Improves the Single-Base Specificity of crRNA-Guided LbCas12a Nuclease
title_fullStr New PAM Improves the Single-Base Specificity of crRNA-Guided LbCas12a Nuclease
title_full_unstemmed New PAM Improves the Single-Base Specificity of crRNA-Guided LbCas12a Nuclease
title_short New PAM Improves the Single-Base Specificity of crRNA-Guided LbCas12a Nuclease
title_sort new pam improves the single-base specificity of crrna-guided lbcas12a nuclease
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9698171/
https://www.ncbi.nlm.nih.gov/pubmed/36431062
http://dx.doi.org/10.3390/life12111927
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