Middle-out sequence confirmation of CRISPR/Cas9 single guide RNA (sgRNA) using DNA primers and ribonuclease T1 digestion

  • Pickar-Oliver A, Gersbach CA. The next generation of CRISPR–Cas technologies and applications. Nat Rev Mol Cell Bio. 2019;20:490–507. doi.org/10.1038/s41580-019-0131-5.

    Article 
    CAS 

    Google Scholar
     

  • Hendel A, Bak RO, Clark JT, Kennedy AB, Ryan DE, Roy S, Steinfeld I, Lunstad BD, Kaiser RJ, Wilkens AB, Bacchetta R, Tsalenko A, Dellinger D, Bruhn L, Porteus MH. Chemically modified guide RNAs enhance CRISPR-Cas genome editing in human primary cells. Nat Biotechnol. 2015;33:985–9. doi.org/10.1038/nbt.3290.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Moon SB, Kim DY, Ko J-H, Kim J-S, Kim Y-S. Improving CRISPR genome editing by engineering guide RNAs. Trends Biotechnol. 2019;37:870–81. doi.org/10.1016/j.tibtech.2019.01.009.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Basila M, Kelley ML, van Smith A, B. Minimal 2’-O-methyl phosphorothioate linkage modification pattern of synthetic guide RNAs for increased stability and efficient CRISPR-Cas9 gene editing avoiding cellular toxicity. Plos One. 2017;12:e0188593. doi.org/10.1371/journal.pone.0188593.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Li H, Yang Y, Hong W, Huang M, Wu M, Zhao X. Applications of genome editing technology in the targeted therapy of human diseases: mechanisms, advances and prospects. Signal Transduct Target Ther. 2020;5:1. doi.org/10.1038/s41392-019-0089-y.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ryan DE, Taussig D, Steinfeld I, Phadnis SM, Lunstad BD, Singh M, Vuong X, Okochi KD, McCaffrey R, Olesiak M, Roy S, Yung CW, Curry B, Sampson JR, Bruhn L, Dellinger DJ. Improving CRISPR–Cas specificity with chemical modifications in single-guide RNAs. Nucleic Acids Res. 2018;46:792–803. doi.org/10.1093/nar/gkx1199.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Filippova J, Matveeva A, Zhuravlev E, Stepanov G. Guide RNA modification as a way to improve CRISPR/Cas9-based genome-editing systems. Biochimie. 2019;167:49–60. doi.org/10.1016/j.biochi.2019.09.003.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Alfonzo JD, Brown JA, Byers PH, Cheung VG, Maraia RJ, Ross RL. A call for direct sequencing of full-length RNAs to identify all modifications. Nat Genet. 2021;53:1113–6. doi.org/10.1038/s41588-021-00903-1.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Nakayama H, Yamauchi Y, Nobe Y, Sato K, Takahashi N, Shalev-Benami M, Isobe T, Taoka M. Method for direct mass-spectrometry-based identification of monomethylated RNA nucleoside positional isomers and its application to the analysis of Leishmania rRNA. Anal Chem. 2019;91:15634–43. doi.org/10.1021/acs.analchem.9b03735.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Sutton JM, Guimaraes GJ, Annavarapu V, van Dongen WD, Bartlett MG. Current state of oligonucleotide characterization using liquid chromatography–mass spectrometry: insight into critical issues. J Am Soc Mass Spectr. 2020;31:1775–82. doi.org/10.1021/jasms.0c00179.

    Article 
    CAS 

    Google Scholar
     

  • Kimura S, Dedon PC, Waldor MK. Comparative tRNA sequencing and RNA mass spectrometry for surveying tRNA modifications. Nat Chem Biol. 2020;16:964–72. doi.org/10.1038/s41589-020-0558-1.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang J, Yan S, Chang L, Guo W, Wang Y, Wang Y, Zhang P, Chen H-Y, Huang S. Direct microRNA sequencing using nanopore-induced phase-shift sequencing. Iscience. 2020;23:100916. doi.org/10.1016/j.isci.2020.100916.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wei B, Wang J, Cadang L, Goyon A, Chen B, Yang F, Zhang K (2022) Development of an ion pairing reversed-phase liquid chromatography-mass spectrometry method for characterization of clustered regularly interspaced short palindromic repeats guide ribonucleic acid. J Chromatogr A. 462839. doi.org/10.1016/j.chroma.2022.462839

  • Kanavarioti A. HPLC methods for purity evaluation of man-made single-stranded RNAs. Sci Rep-uk. 2019;9:1019. doi.org/10.1038/s41598-018-37642-z.

    Article 
    CAS 

    Google Scholar
     

  • Goyon A, Scott B, Kurita K, Crittenden CM, Shaw D, Lin A, Yehl P, Zhang K. Full sequencing of CRISPR/Cas9 single guide RNA (sgRNA) via parallel ribonuclease digestions and hydrophilic interaction liquid chromatography–high-resolution mass spectrometry analysis. Anal Chem. 2021;93:14792–801. doi.org/10.1021/acs.analchem.1c03533.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Goyon A, Scott B, Kurita K, Maschinot C, Meyer K, Yehl P, Zhang K. On-line sequencing of CRISPR guide RNAs and their impurities via the use of immobilized ribonuclease cartridges attached to a 2D/3D-LC–MS system. Anal Chem. 2021. doi.org/10.1021/acs.analchem.1c04350.

    Article 
    PubMed 

    Google Scholar
     

  • Tao J, Ningxi Y, Jaeah K, John-Ross M, Mildred K, Kanchana R, Edward JM, Vladimir P, Serenus H. Oligonucleotide sequence mapping of large therapeutic mRNAs via parallel ribonuclease digestions and LC-MS/MS. Anal Chem. 2019;91:8500–6. doi.org/10.1021/acs.analchem.9b01664.

    Article 
    CAS 

    Google Scholar
     

  • Paulines MJ, Wetzel C, Limbach PA. Using spectral matching to interpret LC-MS/MS data during RNA modification mapping. J Mass Spectrom. 2019;54:906–14. doi.org/10.1002/jms.4456.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Oberacher H, Pitterl F. On the use of ESI-QqTOF-MS/MS for the comparative sequencing of nucleic acids. Biopolym. 2009;91:401–9. doi.org/10.1002/bip.21156.

    Article 
    CAS 

    Google Scholar
     

  • Taucher M, Breuker K. Characterization of modified RNA by top-down mass spectrometry. Angewandte Chemie Int Ed Engl. 2012;51:11289–92. doi.org/10.1002/anie.201206232.

    Article 
    CAS 

    Google Scholar
     

  • Crittenden CM, Lanzillotti MB, Chen B. Top-down mass spectrometry of synthetic single guide ribonucleic acids enabled by facile sample clean-up. Anal Chem. 2023. doi.org/10.1021/acs.analchem.2c03030.

    Article 
    PubMed 

    Google Scholar
     

  • Hossain M, Limbach PA. Mass spectrometry-based detection of transfer RNAs by their signature endonuclease digestion products. RNA. 2007;13:295–303. doi.org/10.1261/rna.272507.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wolf EJ, Grünberg S, Dai N, Chen T-H, Roy B, Yigit E, Corrêa IR. Human RNase 4 improves mRNA sequence characterization by LC–MS/MS. Nucleic Acids Res. 2022;50:e106–e106. doi.org/10.1093/nar/gkac632.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Vanhinsbergh CJ, Criscuolo A, Sutton JN, Murphy K, Williamson AJK, Cook K, Dickman MJ. Characterization and sequence mapping of large RNA and mRNA Therapeutics using mass spectrometry. Anal Chem. 2022;94:7339–49. doi.org/10.1021/acs.analchem.2c00765.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Edy VG, Szekely M, Loviny T, Dreyer C. Action of nucleases on double-stranded RNA. Eur J Biochem. 1976;61:563–72. doi.org/10.1111/j.1432-1033.1976.tb10051.x.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Loverix S, Winqvist A, Strömberg R, Steyaert J. Mechanism of RNase T1: concerted triester-like phosphoryl transfer via a catalytic three-centered hydrogen bond. Chem Biol. 2000;7:651–8. doi.org/10.1016/s1074-5521(00)00005-3.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Huang M, Xu X, Qiu H, Li N. Analytical characterization of DNA and RNA oligonucleotides by hydrophilic interaction liquid chromatography-tandem mass spectrometry. J Chromatogr A. 2021;1648:462184. doi.org/10.1016/j.chroma.2021.462184.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Birdsall RE, Gilar M, Shion H, Yu YQ, Chen W. Reduction of metal adducts in oligonucleotide mass spectra in ion-pair reversed-phase chromatography/mass spectrometry analysis. Rapid Commun Mass Sp. 2016;30:1667–79. doi.org/10.1002/rcm.7596.

    Article 
    CAS 

    Google Scholar
     

  • Houser WM, Butterer A, Addepalli B, Limbach PA. Combining recombinant ribonuclease U2 and protein phosphatase for RNA modification mapping by liquid chromatography–mass spectrometry. Anal Biochem. 2015;478:52–8. doi.org/10.1016/j.ab.2015.03.016.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Shigematsu M, Kawamura T, Kirino Y. Generation of 2′,3′-cyclic phosphate-containing RNAs as a hidden layer of the transcriptome. Frontiers Gen. 2018;9:562. doi.org/10.3389/fgene.2018.00562.

    Article 
    CAS 

    Google Scholar
     

  • Honda S, Morichika K, Kirino Y. Selective amplification and sequencing of cyclic phosphate–containing RNAs by the cP-RNA-seq method. Nat Protoc. 2016;11:476–89. doi.org/10.1038/nprot.2016.025.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schutz K, Hesselberth JR, Fields S. Capture and sequence analysis of RNAs with terminal 2′,3′-cyclic phosphates. RNA. 2010;16:621–31. doi.org/10.1261/rna.1934910.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Read more here: Source link