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Ryan D, Diamant-Levi T, Steinfeld I, Taussig D, Visal-Shah S, Thakker S, Lunstad BD, Kaiser RJ, McCaffrey R, Ortiz M, Townsend J, Welch WRW, Singh M, Curry B, Dellinger DJ, Bruhn L. Phosphonoacetate Modifications Enhance the Stability and Editing Yields of Guide RNAs for Cas9 Editors. Biochemistry 2023; 62:3512-3520. [PMID: 35436085 PMCID: PMC10734248 DOI: 10.1021/acs.biochem.1c00768] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
CRISPR gene editing and control systems continue to emerge and inspire novel research and clinical applications. Advances in CRISPR performance such as optimizing the duration of activity in cells, tissues, and organisms, as well as limiting off-target activities, have been extremely important for expanding the utility of CRISPR-based systems. By investigating the effects of various chemical modifications in guide RNAs (gRNAs) at defined positions and combinations, we find that 2'-O-methyl-3'-phosphonoacetate (MP) modifications can be substantially more effective than 2'-O-methyl-3'-phosphorothioate (MS) modifications at the 3' ends of single-guide RNAs (sgRNAs) to promote high editing yields, in some instances showing an order of magnitude higher editing yield in human cells. MP-modified 3' ends are especially effective at promoting the activity of guide RNAs cotransfected with Cas messenger RNA (mRNA), as the gRNA must persist in cells until the Cas protein is expressed. We demonstrate such an MP enhancement for sgRNAs cotransfected with a BE4 mRNA for cytidine base editing and also demonstrate that MP at the 3' ends of prime editing guide RNAs (pegRNAs) cotransfected with PE2 mRNA can promote maximal prime editing yields. In the presence of serum, sgRNAs with MP-modified 3' ends showed marked improvements in editing efficiency over sgRNAs with MS-modified 3' ends codelivered with Cas9 mRNA and showed more modest improvements at enhancing the activity of transfected ribonucleoprotein (RNP) complexes. Our results suggest that MP should be considered as a performance-enhancing modification for the 3' ends of synthetic gRNAs, especially in situations where the guide RNAs may be susceptible to exonuclease-mediated degradation.
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Affiliation(s)
- Daniel
E. Ryan
- Agilent
Research Laboratories, Santa
Clara, California 95051, United States
| | - Tamar Diamant-Levi
- Agilent
Research Laboratories, Santa
Clara, California 95051, United States
| | - Israel Steinfeld
- Agilent
Research Laboratories, Santa
Clara, California 95051, United States
| | - David Taussig
- Agilent
Research Laboratories, Santa
Clara, California 95051, United States
| | - Savita Visal-Shah
- Agilent
Research Laboratories, Santa
Clara, California 95051, United States
| | - Suhani Thakker
- Agilent
Research Laboratories, Santa
Clara, California 95051, United States
| | | | - Robert J. Kaiser
- Agilent
Technologies, Santa Clara, California 95051, United States
| | - Ryan McCaffrey
- Agilent
Technologies, Santa Clara, California 95051, United States
| | - Michael Ortiz
- Agilent
Research Laboratories, Boulder, Colorado 80303, United States
| | - Justin Townsend
- Agilent
Research Laboratories, Boulder, Colorado 80303, United States
| | | | - Mandeep Singh
- Agilent
Research Laboratories, Boulder, Colorado 80303, United States
| | - Bo Curry
- Agilent
Research Laboratories, Santa
Clara, California 95051, United States
| | | | - Laurakay Bruhn
- Agilent
Research Laboratories, Santa
Clara, California 95051, United States
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2
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Sharma P, Sharma BS, Verma RJ. A Guide to RNAseq Data Analysis Using Bioinformatics Approaches. Adv Bioinformatics 2021. [DOI: 10.1007/978-981-33-6191-1_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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3
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Honcharenko M, Honcharenko D, Strömberg R. Efficient Conjugation to Phosphorothioate Oligonucleotides by Cu-Catalyzed Huisgen 1,3-Dipolar Cycloaddition. Bioconjug Chem 2019; 30:1622-1628. [PMID: 31067031 DOI: 10.1021/acs.bioconjchem.9b00217] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Improving oligonucleotide delivery is critical for the further development of oligonucleotide-based therapeutics. Covalent attachment of reporter molecules is one of the most promising approaches toward efficient oligonucleotide-based therapies. An efficient methods for the attachment of a variety of reporter groups is Cu(I)-catalyzed Huisgen azide-alkyne 1,3-dipolar cycloaddition. However, the majority of potential oligonucleotide (ON) therapeutics in clinical trials are carrying phosphorothioate (PS) linkages, and this robust conjugation method is not yet established for these ONs due to a general concern of Cu-S interaction. Here, we developed a method allowing for efficient conjugation of peptides to PS oligonucleotides. The method utilizes solid supported oligonucleotides that can be readily transformed into "clickable ONs" by simple linker conjugation and further reacted with an azido containing moiety (e.g., a peptide) using the CuBr × Me2S complex as a superior catalyst in that reaction. This study opens the way for further development of PS oligonucleotide-conjugates by means of efficient Cu(I)-catalyzed Huisgen azide-alkyne 1,3-dipolar cycloaddition.
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Affiliation(s)
- Malgorzata Honcharenko
- Department of Biosciences and Nutrition , Karolinska Institute , SE-14183 Huddinge , Sweden
| | - Dmytro Honcharenko
- Department of Biosciences and Nutrition , Karolinska Institute , SE-14183 Huddinge , Sweden
| | - Roger Strömberg
- Department of Biosciences and Nutrition , Karolinska Institute , SE-14183 Huddinge , Sweden
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4
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Li L, Leone T, Foley JP, Welch CJ. Separation of small interfering RNA stereoisomers using reversed-phase ion-pairing chromatography. J Chromatogr A 2017; 1500:84-88. [DOI: 10.1016/j.chroma.2017.04.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/05/2017] [Accepted: 04/07/2017] [Indexed: 11/25/2022]
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5
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Capaldi D, Ackley K, Brooks D, Carmody J, Draper K, Kambhampati R, Kretschmer M, Levin D, McArdle J, Noll B, Raghavachari R, Roymoulik I, Sharma BP(B, Thürmer R, Wincott F. Quality Aspects of Oligonucleotide Drug Development: Specifications for Active Pharmaceutical Ingredients. ACTA ACUST UNITED AC 2012. [DOI: 10.1177/0092861512445311] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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6
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Bartoszewicz A, Kalek M, Stawinski J. The case for the intermediacy of monomeric metaphosphate analogues during oxidation of H-phosphonothioate, H-phosphonodithioate, and H-phosphonoselenoate monoesters: mechanistic and synthetic studies. J Org Chem 2008; 73:5029-38. [PMID: 18507440 DOI: 10.1021/jo8006072] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Studies on the reaction of H-phosphonothioate, H-phosphonodithioate, and H-phosphonoselenoate monoesters with iodine in the presence of a base led to identification of a unique oxidation pathway, which consists of the initial oxidation of the sulfur or selenium atom in these compounds, followed by oxidative elimination of hydrogen iodide to generate the corresponding metaphosphate analogues. The intermediacy of the latter species during oxidation of the investigated H-phosphonate monoester derivatives with iodine was supported by various diagnostic experiments. The scope and limitation of these oxidative transformations for the purpose of the synthesis of nucleoside phosphorothioate, nucleoside phosphorodithioate, and nucleoside phosphoroselenoate diesters was also investigated.
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Affiliation(s)
- Agnieszka Bartoszewicz
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
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7
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Kirk Field A, Goodchild J. Section Review: Biologicals & Immunologicals: Antisense oligonucleotides: Rational drug design for genetic pharmacology. Expert Opin Investig Drugs 2008. [DOI: 10.1517/13543784.4.9.799] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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8
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Sanghvi YS, Andrade M, Deshmukh RR, Holmberg L, Scozzari AN, Cole DL. Chemical Synthesis and Purification of Phosphorothioate Antisense Oligonucleotides. ACTA ACUST UNITED AC 1999. [DOI: 10.1007/978-1-4615-5067-9_1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
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9
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Froim D, Hopkins CE, Belenky A, Cohen AS. Method for phosphorothioate antisense DNA sequencing by capillary electrophoresis with UV detection. Nucleic Acids Res 1997; 25:4219-23. [PMID: 9336449 PMCID: PMC147025 DOI: 10.1093/nar/25.21.4219] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The progress of antisense DNA therapy demands development of reliable and convenient methods for sequencing short single-stranded oligonucleotides. A method of phosphorothioate antisense DNA sequencing analysis using UV detection coupled to capillary electrophoresis (CE) has been developed based on a modified chain termination sequencing method. The proposed method reduces the sequencing cost since it uses affordable CE-UV instrumentation and requires no labeling with minimal sample processing before analysis. Cycle sequencing with ThermoSequenase generates quantities of sequencing products that are readily detectable by UV. Discrimination of undesired components from sequencing products in the reaction mixture, previously accomplished by fluorescent or radioactive labeling, is now achieved by bringing concentrations of undesired components below the UV detection range which yields a 'clean', well defined sequence. UV detection coupled with CE offers additional conveniences for sequencing since it can be accomplished with commercially available CE-UV equipment and is readily amenable to automation.
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Affiliation(s)
- D Froim
- Analytical Research, Hybridon, Inc., Cambridge, MA 02139, USA
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10
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Polo LM, McCarley TD, Limbach PA. Chemical Sequencing of Phosphorothioate Oligonucleotides Using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry. Anal Chem 1997. [DOI: 10.1021/ac960840p] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lenore M. Polo
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803
| | | | - Patrick A. Limbach
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803
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11
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Schuette JM, Pieles U, Maleknia SD, Srivatsa GS, Cole DL, Moser HE, Afeyan NB. Sequence analysis of phosphorothioate oligonucleotides via matrix-assisted laser desorption ionization time-of-flight mass spectrometry. J Pharm Biomed Anal 1995; 13:1195-203. [PMID: 8562591 DOI: 10.1016/0731-7085(95)01534-r] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Modification of the natural phosphodiester backbone of deoxyribooligonucleotides can impart increased biostability via nuclease resistance. Further, uniform incorporation of phosphorothioate linkages renders oligonucleotides highly resistant to reagents traditionally used in sequencing reactions. As a consequence, analytical tests crucial for establishing the identity of such oligonucleotide drugs are less informative. To circumvent this problem, chemical oxidation has been employed for converting the phosphorothioate to the uniform phosphodiester, thereby facilitating enzymatic degradation. Following oxidation, exonucleases which sequentially cleave individual bases from the 3' or 5' terminus of the oligonucleotide or base-specific cleavage chemicals were used to facilitate sequence identification of the oligonucleotide. Matrix-assisted laser desorption ionization-time-of-flight/mass spectrometry (MALDI-TOF/MS), previously used to sequence natural phosphodiester DNA, was then used to sequence the chemically oxidized phosphorothioate. Sequential enzymatic cleavage of desulphurized phosphorothioates in combination with MALDI analysis not only provides a viable alternative to radiolabeling as used in conventional sequencing approaches (e.g. Maxam-Gilbert), but also enables rapid sequencing of phosphorothioate oligonucleotides, for routine drug analysis.
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12
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Ravikumar VT, Andrade M, Wyrzykiewicz TK, Scozzari A, Cole DL. Large-Scale Synthesis of Oligodeoxyribonucleotide Phosphorothioate Using Controlled-Pore Glass as Support. ACTA ACUST UNITED AC 1995. [DOI: 10.1080/15257779508010685] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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13
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Zhaoda Zhang, Tang JX, Jin Yan Tang. Syntheses and properties of novel thiono triester modified antisense oligodeoxynucleotide phosphorothioates. Bioorg Med Chem Lett 1995. [DOI: 10.1016/0960-894x(95)00292-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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