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Jin C, EI‐Sagheer AH, Li S, Vallis KA, Tan W, Brown T. Engineering Enzyme-Cleavable Oligonucleotides by Automated Solid-Phase Incorporation of Cathepsin B Sensitive Dipeptide Linkers. Angew Chem Int Ed Engl 2022; 61:e202114016. [PMID: 34953094 PMCID: PMC9306542 DOI: 10.1002/anie.202114016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Indexed: 12/04/2022]
Abstract
Oligonucleotides containing cleavable linkers have emerged as versatile tools to achieve stimulus-responsive and site-specific cleavage of DNA. However, the limitations of previously reported cleavable linkers including photolabile and disulfide linkers have restricted their applications in vivo. Inspired by the cathepsin B-sensitive dipeptide linkers in antibody-drug conjugates (ADCs) such as Adcetris, we have developed Val-Ala-02 and Val-Ala-Chalcone phosphoramidites for the automated synthesis of enzyme-cleavable oligonucleotides. Cathepsin B digests Val-Ala-02 and Val-Ala-Chalcone linkers efficiently, enabling cleavage of oligonucleotides into two components or release of small-molecule payloads. Based on the prior success of dipeptide linkers in ADCs, we believe that these dipeptide linker phosphoramidites will promote new clinical applications of therapeutic oligonucleotides.
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Affiliation(s)
- Cheng Jin
- Department of Chemistry, Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Afaf H. EI‐Sagheer
- Department of Chemistry, Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
- Department of Science and MathematicsSuez University, Faculty of Petroleum and Mining EngineeringSuez43721Egypt
| | - Siqi Li
- Medical Research CouncilOxford Institute for Radiation OncologyDepartment of OncologyUniversity of OxfordOxfordOX3 7DQUK
| | - Katherine A. Vallis
- Medical Research CouncilOxford Institute for Radiation OncologyDepartment of OncologyUniversity of OxfordOxfordOX3 7DQUK
| | - Weihong Tan
- The Cancer Hospital of the University of Chinese Academy of SciencesZhejiang Cancer Hospital)Institute of Basic Medicine and Cancer (IBMC)Chinese Academy of SciencesHangzhouZhejiang310022China
- Institute of Molecular Medicine (IMM)Renji HospitalShanghai Jiao Tong University School of MedicineShanghai200240China
| | - Tom Brown
- Department of Chemistry, Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
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2
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Jin C, EI‐Sagheer AH, Li S, Vallis KA, Tan W, Brown T. Engineering Enzyme-Cleavable Oligonucleotides by Automated Solid-Phase Incorporation of Cathepsin B Sensitive Dipeptide Linkers. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202114016. [PMID: 38505643 PMCID: PMC10946720 DOI: 10.1002/ange.202114016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Indexed: 11/09/2022]
Abstract
Oligonucleotides containing cleavable linkers have emerged as versatile tools to achieve stimulus-responsive and site-specific cleavage of DNA. However, the limitations of previously reported cleavable linkers including photolabile and disulfide linkers have restricted their applications in vivo. Inspired by the cathepsin B-sensitive dipeptide linkers in antibody-drug conjugates (ADCs) such as Adcetris, we have developed Val-Ala-02 and Val-Ala-Chalcone phosphoramidites for the automated synthesis of enzyme-cleavable oligonucleotides. Cathepsin B digests Val-Ala-02 and Val-Ala-Chalcone linkers efficiently, enabling cleavage of oligonucleotides into two components or release of small-molecule payloads. Based on the prior success of dipeptide linkers in ADCs, we believe that these dipeptide linker phosphoramidites will promote new clinical applications of therapeutic oligonucleotides.
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Affiliation(s)
- Cheng Jin
- Department of Chemistry, Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
| | - Afaf H. EI‐Sagheer
- Department of Chemistry, Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
- Department of Science and MathematicsSuez University, Faculty of Petroleum and Mining EngineeringSuez43721Egypt
| | - Siqi Li
- Medical Research CouncilOxford Institute for Radiation OncologyDepartment of OncologyUniversity of OxfordOxfordOX3 7DQUK
| | - Katherine A. Vallis
- Medical Research CouncilOxford Institute for Radiation OncologyDepartment of OncologyUniversity of OxfordOxfordOX3 7DQUK
| | - Weihong Tan
- The Cancer Hospital of the University of Chinese Academy of SciencesZhejiang Cancer Hospital)Institute of Basic Medicine and Cancer (IBMC)Chinese Academy of SciencesHangzhouZhejiang310022China
- Institute of Molecular Medicine (IMM)Renji HospitalShanghai Jiao Tong University School of MedicineShanghai200240China
| | - Tom Brown
- Department of Chemistry, Chemistry Research LaboratoryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
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Highly enhanced activity and stability via affinity induced immobilization β-glucosidase from Aspergillus niger onto amino-based silica for the biotransformation of ginsenoside Rb1. J Chromatogr A 2021; 1653:462388. [PMID: 34280789 DOI: 10.1016/j.chroma.2021.462388] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 01/15/2023]
Abstract
In this study, an enzyme immobilization method for the effective biotransformation of ginsenoside Rb1 to impart activity and stability was developed. Using a hydrolase enzyme model, β-glucosidase from Aspergillus niger, immobilization within chemically affinity-linked amino-based silica provided an immobilization efficiency 5.86-fold higher than that of free enzyme. Compared with the free enzyme, the immobilized enzyme functioned optimally at a wider pH range and had higher thermostability. The optimum pH for the free and immobilized enzymes was 5.5. The optimal reaction temperature of the immobilized enzyme was 45 °C, which was 5 °C higher than that of the free enzyme. The Michaelis constant (Km) values before and after immobilization were 0.482 mmol•L-1 and 0.387 mmol•L-1, respectively. The catalytic rate (Kcat) for the immobilized and free enzymes was 22.269 mmol•L-1and 8.800 mmol•L-1, respectively, and the catalytic efficiency (Kcat/Km) activity of the immobilized enzyme was 3.30-fold higher than that of the free enzyme. The immobilized enzyme could preserve 97 % of the activity after 45 cycles of repeated use. The high catalytic activity and significant operational stability are beneficial for industrial applications.
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4
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Biotin oligonucleotide labeling reactions: A method to assess their effectiveness and reproducibility. Anal Biochem 2020; 593:113590. [PMID: 31962102 DOI: 10.1016/j.ab.2020.113590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 01/16/2020] [Indexed: 11/24/2022]
Abstract
The strong molecular interaction between biotin and streptavidin is widely used in the growing field of nucleic acid nanotechnology. Several biotin labeled oligonucleotide tools have been developed for the detection of biological molecules as well as for protein purification. For these reasons, biotinylation can be considered one of the main chemical reactions for nucleic acid labeling. However, despite its widespread application and the presence on the market of many reagents for the conjugation of biotin to oligonucleotides, it is not yet available a cheap, easy and sensitive system able to assess the effectiveness and reproducibility of this reaction. Here, we present an accurate and reliable method to achieve a qualitative and quantitative analysis of oligonucleotide biotinylation. The protocol employs basic laboratory instruments and standard software for molecular biology applications and does not require advanced expertise for its execution. Most importantly, our method is independent from complex kinetic equilibrium parameters and shows a limit of detection more than one order of magnitude lower than the current fluorometric gold standard assay. Therefore, this method could become a standard, inexpensive and routinely used quality test for post-synthesis evaluation of biotin conjugation reactions.
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5
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Eriyagama DNAM, Shahsavari S, Halami B, Lu BY, Wei F, Fang S. Parallel, Large-Scale, and Long Synthetic Oligodeoxynucleotide Purification Using the Catching Full-Length Sequence by Polymerization Technique. Org Process Res Dev 2018; 22:1282-1288. [PMID: 30906183 PMCID: PMC6428204 DOI: 10.1021/acs.oprd.8b00209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The catching by polymerization synthetic oligodeoxynucleotide (ODN) purification technique was shown to be potentially suitable for high throughput purification by purifying 12 ODNs simultaneously, to be convenient for large-scale purification by purifying at 60 μmol synthesis scale, and to be highly powerful for long ODN purification by purifying ODNs as long as 303-mer. LC-MS analysis indicated that the ODNs purified with the technique have excellent purity.
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Affiliation(s)
| | - Shahien Shahsavari
- Department of Chemistry, Michigan Technological
University, 1400 Townsend Drive, Houghton, MI 49931, USA
| | - Bhaskar Halami
- Department of Chemistry, Michigan Technological
University, 1400 Townsend Drive, Houghton, MI 49931, USA
| | - Bao-Yuan Lu
- Nalco Champion, an Ecolab Company, 11177 S. Stadium
Drive, Sugar Land, TX 77478, USA
| | - Fengping Wei
- CGeneTech, Inc., 7202 E. 87th Street, Suite#100,
Indianapolis, IN 46256, USA
| | - Shiyue Fang
- Department of Chemistry, Michigan Technological
University, 1400 Townsend Drive, Houghton, MI 49931, USA
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Grajkowski A, Cieślak J, Beaucage SL. A High-Throughput Process for the Solid-Phase Purification of Synthetic DNA Sequences. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2017; 69:10.17.1-10.17.30. [PMID: 28628204 PMCID: PMC5568675 DOI: 10.1002/cpnc.31] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
An efficient process for the purification of synthetic phosphorothioate and native DNA sequences is presented. The process is based on the use of an aminopropylated silica gel support functionalized with aminooxyalkyl functions to enable capture of DNA sequences through an oximation reaction with the keto function of a linker conjugated to the 5'-terminus of DNA sequences. Deoxyribonucleoside phosphoramidites carrying this linker, as a 5'-hydroxyl protecting group, have been synthesized for incorporation into DNA sequences during the last coupling step of a standard solid-phase synthesis protocol executed on a controlled pore glass (CPG) support. Solid-phase capture of the nucleobase- and phosphate-deprotected DNA sequences released from the CPG support is demonstrated to proceed near quantitatively. Shorter than full-length DNA sequences are first washed away from the capture support; the solid-phase purified DNA sequences are then released from this support upon reaction with tetra-n-butylammonium fluoride in dry dimethylsulfoxide (DMSO) and precipitated in tetrahydrofuran (THF). The purity of solid-phase-purified DNA sequences exceeds 98%. The simulated high-throughput and scalability features of the solid-phase purification process are demonstrated without sacrificing purity of the DNA sequences. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Andrzej Grajkowski
- Laboratory of Biological Chemistry, Food and Drug Administration, Silver Spring, Maryland
| | - Jacek Cieślak
- Laboratory of Biological Chemistry, Food and Drug Administration, Silver Spring, Maryland
| | - Serge L Beaucage
- Laboratory of Biological Chemistry, Food and Drug Administration, Silver Spring, Maryland
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7
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Grajkowski A, Cieslak J, Beaucage SL. Solid-Phase Purification of Synthetic DNA Sequences. J Org Chem 2016; 81:6165-75. [PMID: 27382974 DOI: 10.1021/acs.joc.6b01020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although high-throughput methods for solid-phase synthesis of DNA sequences are currently available for synthetic biology applications and technologies for large-scale production of nucleic acid-based drugs have been exploited for various therapeutic indications, little has been done to develop high-throughput procedures for the purification of synthetic nucleic acid sequences. An efficient process for purification of phosphorothioate and native DNA sequences is described herein. This process consists of functionalizing commercial aminopropylated silica gel with aminooxyalkyl functions to enable capture of DNA sequences carrying a 5'-siloxyl ether linker with a "keto" function through an oximation reaction. Deoxyribonucleoside phosphoramidites functionalized with the 5'-siloxyl ether linker were prepared in yields of 75-83% and incorporated last into the solid-phase assembly of DNA sequences. Capture of nucleobase- and phosphate-deprotected DNA sequences released from the synthesis support is demonstrated to proceed near quantitatively. After shorter than full-length DNA sequences were washed from the capture support, the purified DNA sequences were released from this support upon treatment with tetra-n-butylammonium fluoride in dry DMSO. The purity of released DNA sequences exceeds 98%. The scalability and high-throughput features of the purification process are demonstrated without sacrificing purity of the DNA sequences.
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Affiliation(s)
- Andrzej Grajkowski
- Laboratory of Biological Chemistry, Division of Biotechnology Review and Research IV, Center for Drug Evaluation and Research, Food and Drug Administration , 10903 New Hampshire Avenue, Silver Spring, Maryland 20933, United States
| | - Jacek Cieslak
- Laboratory of Biological Chemistry, Division of Biotechnology Review and Research IV, Center for Drug Evaluation and Research, Food and Drug Administration , 10903 New Hampshire Avenue, Silver Spring, Maryland 20933, United States
| | - Serge L Beaucage
- Laboratory of Biological Chemistry, Division of Biotechnology Review and Research IV, Center for Drug Evaluation and Research, Food and Drug Administration , 10903 New Hampshire Avenue, Silver Spring, Maryland 20933, United States
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8
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Lin X, Chen J, Shahsavari S, Green N, Goyal D, Fang S. Synthesis of Oligodeoxynucleotides Containing Electrophilic Groups. Org Lett 2016; 18:3870-3. [PMID: 27447361 DOI: 10.1021/acs.orglett.6b01878] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
By use of 1,3-dithian-2-yl-methoxycarbonyl (Dmoc) as a protecting group and linker for oligodeoxynucleotide (ODN) synthesis, deprotection and cleavage are achieved under non-nucleophilic oxidative conditions. The nucleophile-sensitive thioester and α-chloroacetyl groups are conveniently incorporated into ODN sequences. The technology could be universally useful for electrophilic ODN synthesis.
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Affiliation(s)
- Xi Lin
- Department of Chemistry, Michigan Technological University , 1400 Townsend Drive, Houghton, Michigan 49931, United States
| | - Jinsen Chen
- Department of Chemistry, Michigan Technological University , 1400 Townsend Drive, Houghton, Michigan 49931, United States
| | - Shahien Shahsavari
- Department of Chemistry, Michigan Technological University , 1400 Townsend Drive, Houghton, Michigan 49931, United States
| | - Nathanael Green
- Department of Chemistry, Michigan Technological University , 1400 Townsend Drive, Houghton, Michigan 49931, United States
| | - Deepti Goyal
- Department of Chemistry, Michigan Technological University , 1400 Townsend Drive, Houghton, Michigan 49931, United States
| | - Shiyue Fang
- Department of Chemistry, Michigan Technological University , 1400 Townsend Drive, Houghton, Michigan 49931, United States
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9
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Pokharel D, Yuan Y, Fueangfung S, Fang S. Synthetic oligodeoxynucleotide purification by capping failure sequences with a methacrylamide phosphoramidite followed by polymerization. RSC Adv 2014. [DOI: 10.1039/c3ra46986g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Synthetic oligodeoxynucleotides are simply purified by capping failure sequences with a methacrylamide phosphoramidite, co-polymerization with N,N-dimethylacrylamide and extraction with water.
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Affiliation(s)
- Durga Pokharel
- Department of Chemistry
- Michigan Technological University
- Houghton, USA
| | - Yinan Yuan
- School of Forest Resources and Environmental Science
- Michigan Technological University
- Houghton, USA
| | | | - Shiyue Fang
- Department of Chemistry
- Michigan Technological University
- Houghton, USA
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10
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Trippier PC. Synthetic strategies for the biotinylation of bioactive small molecules. ChemMedChem 2013; 8:190-203. [PMID: 23303486 DOI: 10.1002/cmdc.201200498] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 12/07/2012] [Indexed: 01/19/2023]
Abstract
Biotinylation, the functional appendage of a biotin moiety to a bioactive compound (including small molecules and biological macromolecules), represents a common technique for identification of the intracellular binding partners that underlie the foundation of observed biological activity. Introduction of an attachment tether to the framework of a compound of interest must be planned at an early stage of development, and many considerations apply: 1) region of attachment, so as not to impede the pharmacophore; 2) stability of the parent molecular architecture to biotinylation conditions; 3) regioselectivity for the chosen tethering location over other reactive functionalities; 4) toxicity of reagents if biotinylation is to be performed in vitro; and 5) overall ease of synthesis. This review is intended to serve as a guide for the selection of appropriate tethering modalities. Examples of the common techniques used to affix biotin, including amide bond formation, [3+2] cycloadditions through "click" chemistry, Staudinger ligation, and thioether formation will be discussed, along with analysis of the wider applications of synthetic methodology that have been applied toward the biotinylation of small molecules.
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Affiliation(s)
- Paul C Trippier
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX, USA.
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11
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Cieślak J, Ausín C, Grajkowski A, Beaucage SL. Convenient and efficient approach to the permanent or reversible conjugation of RNA and DNA sequences with functional groups. ACTA ACUST UNITED AC 2012; Chapter 4:Unit4.52. [PMID: 22956458 DOI: 10.1002/0471142700.nc0452s50] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The conversion of 3',5'-disilylated 2'-O-(methylthiomethyl)ribonucleosides to 2'-O-(phthalimidooxymethyl)ribonucleosides is achieved in yields of 66% to 94%. Desilylation and dephtalimidation of these ribonucleosides by treatment with NH(4)F in MeOH produce 2'-O-aminooxymethylated ribonucleosides, which are efficient in producing stable and yet reversible 2'-conjugates upon reaction with 1-pyrenecarboxaldehyde. Exposure of 2'-pyrenylated ribonucleosides to 0.5 M tetra-n-butylammonium fluoride (TBAF) in THF or DMSO results in the cleavage of their iminoether functions to give the native ribonucleosides along with an innocuous nitrile side product. Conversely, the reaction of 2'-O-(aminooxymethyl)uridine with 5-cholesten-3-one leads to a permanent uridine 2'-conjugate, which is left unreacted when treated with TBAF. The versatility and uniqueness of 2'-O-(aminooxymethyl)ribonucleosides is demonstrated by the single or double incorporation of a reversible pyrenylated uridine 2'-conjugate into an RNA sequence. Furthermore, the conjugation of 2'-O-(aminooxymethyl)ribonucleosides with various aldehydes, including those generated from their acetals, is also presented. The preparation of 5'-O-(aminooxymethyl)thymidine is also achieved, albeit in modest yields, from the conversion of 5'-O-methylthiomethyl-3'-O-(levulinyl)thymidine to 5'-O-phthalimidooxymethyl-3'-O-(levuliny)lthymidine followed by hydrazinolysis of both 5'-phthalimido and 3'-levulinyl groups. Pyrenylation of the 5'-O-(aminooxymethyl)deoxyribonucleoside also provides a reversible 5'-conjugate that is sensitive to TBAF, thereby further demonstrating the usefulness of 5'-O-(aminooxymethyl)deoxyribonucleosides for permanent or reversible modification of DNA sequences. Curr. Protoc. Nucleic Acid Chem. 50:4.52.1-4.52.36. © 2012 by John Wiley & Sons, Inc.
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Affiliation(s)
- Jacek Cieślak
- Food and Drug Administration, Bethesda, Maryland, USA
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12
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Fang S, Fueangfung S, Yuan Y. Purification of synthetic oligonucleotides via catching by polymerization. ACTA ACUST UNITED AC 2012; Chapter 10:Unit10.14. [PMID: 22700335 DOI: 10.1002/0471142700.nc1014s49] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This unit describes the purification of synthetic oligodeoxyribonucleotides (ODN) using a catching-by-polymerization approach. In a crude ODN, the major impurity is the failure sequences generated in the coupling step of each synthetic cycle. They are difficult to remove due to the similarity of their physical properties to the full-length sequences. Two non-chromatographic methods are described in the unit to solve the problem. In the first one, during automated synthesis, the failure sequences are tagged with a methacrylamide group, which is polymerizable and can participate in acrylamide radical polymerization reactions; the full-length sequences are not tagged. After synthesis, the crude mixture is subjected to polymerization. The failure sequences are incorporated into an insoluble polymer; the full-length sequences are extracted with water. In the second method, the full-length sequences are tagged with a methacrylamide group via a cleavable linker; the failure sequences are not tagged. After synthesis, the full-length sequences are incorporated into a polymer; the failure sequences are washed away with water. Pure full-length sequences are cleaved from the polymer. The two methods are complementary. .
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Affiliation(s)
- Shiyue Fang
- Department of Chemistry, Michigan Technological University, Houghton, MI, USA
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13
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Yuan Y, Fueangfung S, Lin X, Pokharel D, Fang S. Synthetic 5′-phosphorylated oligodeoxynucleotide purification through catching full-length sequences by polymerization. RSC Adv 2012. [DOI: 10.1039/c2ra01357f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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14
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Cleavable linkers in chemical biology. Bioorg Med Chem 2012; 20:571-82. [DOI: 10.1016/j.bmc.2011.07.048] [Citation(s) in RCA: 157] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 07/08/2011] [Accepted: 07/23/2011] [Indexed: 01/11/2023]
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15
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York KT, Smith RC, Yang R, Melnyk PC, Wiley MM, Turk CM, Ronaghi M, Gunderson KL, Steemers FJ. Highly parallel oligonucleotide purification and functionalization using reversible chemistry. Nucleic Acids Res 2011; 40:e4. [PMID: 22039155 PMCID: PMC3245951 DOI: 10.1093/nar/gkr910] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We have developed a cost-effective, highly parallel method for purification and functionalization of 5′-labeled oligonucleotides. The approach is based on 5′-hexa-His phase tag purification, followed by exchange of the hexa-His tag for a functional group using reversible reaction chemistry. These methods are suitable for large-scale (micromole to millimole) production of oligonucleotides and are amenable to highly parallel processing of many oligonucleotides individually or in high complexity pools. Examples of the preparation of 5′-biotin, 95-mer, oligonucleotide pools of >40K complexity at micromole scale are shown. These pools are prepared in up to ~16% yield and 90–99% purity. Approaches for using this method in other applications are also discussed.
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Affiliation(s)
- Kerri T York
- Illumina, Inc., Advanced Research Group, San Diego, CA 92121, USA
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16
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Fang S, Fueangfung S, Lin X, Zhang X, Mai W, Bi L, Green SA. Synthetic oligodeoxynucleotide purification by polymerization of failure sequences. Chem Commun (Camb) 2010; 47:1345-7. [PMID: 21082113 DOI: 10.1039/c0cc04374e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Synthetic oligodeoxynucleotide is purified by capping failure sequences with an acrylated phosphoramidite followed by polymerization and product extraction. The method is suitable for large scale oligonucleotide drug purification.
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Affiliation(s)
- Shiyue Fang
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, USA.
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17
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Fang S, Fueangfung S. Scalable synthetic oligodeoxynucleotide purification with use of a catching by polymerization, washing, and releasing approach. Org Lett 2010; 12:3720-3. [PMID: 20704419 DOI: 10.1021/ol101316g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Synthetic oligodeoxynucleotides are purified with use of a catching by polymerization, washing, and releasing approach. The method does not require any chromatography, and purification is achieved by simple operations such as shaking, washing, and extraction. It is therefore useful for large-scale purification of synthetic oligonucleotide drugs. In addition to purification of oligonucleotides, this catching by polymerization concept is expected to be equally useful for purification of other synthetic oligomers such as peptides and oligosaccharides.
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Affiliation(s)
- Shiyue Fang
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, USA.
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18
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Yokoshima S, Abe Y, Watanabe N, Kita Y, Kan T, Iwatsubo T, Tomita T, Fukuyama T. Development of photoaffinity probes for γ-secretase equipped with a nitrobenzenesulfonamide-type cleavable linker. Bioorg Med Chem Lett 2009; 19:6869-71. [DOI: 10.1016/j.bmcl.2009.10.086] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Revised: 10/19/2009] [Accepted: 10/20/2009] [Indexed: 10/20/2022]
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19
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Navakouski MJ, Vashkevich II, Sviridov OV. The effect of precipitation of the complexes of streptavidin with biotinylated proteins in agar gel. APPL BIOCHEM MICRO+ 2009. [DOI: 10.1134/s0003683809010177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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21
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Fang S, Bergstrom DE. Reversible biotinylation of the 5'-terminus of oligodeoxyribonucleotides and its application in affinity purification. ACTA ACUST UNITED AC 2008; Chapter 4:Unit 4.20. [PMID: 18428910 DOI: 10.1002/0471142700.nc0420s14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The preparation of two reversible biotinylation phosphoramidites and their application in labeling and affinity purification of synthetic oligodeoxyribonucleotides will be described. In both cases, the biotin is linked to the 5'-terminus of DNA through a diisopropyl silyl acetal functionality. This linkage is completely stable under certain postsynthetic cleavage/deprotection conditions, but can be readily broken by fluoride ions, releasing unmodified 5'-OH and 5'-phosphate DNA, respectively. To demonstrate the use of these reversible biotinylation methods, crude DNA was incubated with NeutrAvidin-coated microspheres, full-length biotinylated DNA was efficiently attached to the solid phase, and nonbiotinylated failure sequences and other impurities were readily removed by washing with buffer. Cleavage of the silyl acetal linkage afforded high-quality, full-length, unmodified 5'-OH and 5'-phosphate DNA, respectively, depending on which of the two phosphoramidites was used. It is anticipated that this method will find applications in areas that require efficient isolation of DNA from a complex mixture.
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Affiliation(s)
- Shiyue Fang
- Purdue University, West Lafayette, Indiana, USA
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Hashimoto M, Hatanaka Y. Recent Progress in Diazirine‐Based Photoaffinity Labeling. European J Org Chem 2008. [DOI: 10.1002/ejoc.200701069] [Citation(s) in RCA: 153] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Makoto Hashimoto
- Department of Agricultural and Life Science, Obihiro University of Agriculture and Veterinary Medicine, Inada‐cho, Obihiro 080‐8555, Hokkaido, Japan, Fax: +81‐155‐495577
| | - Yasumaru Hatanaka
- Faculty of Pharmaceutical Sciences, Toyama Medical and Pharmaceutical University, 2360 Sugitani, Toyama 930‐0194, Japan
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Fang S, Guan Y, Blatchley ER, Shen C, Bergstrom DE. Conjugation of (E)-5-[2-(Methoxycarbonyl)ethenyl]cytidine to Hydrophilic Microspheres: Development of a Mobile Microscale UV Light Actinometer. Bioconjug Chem 2008; 19:592-7. [PMID: 18266312 DOI: 10.1021/bc700336x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shiyue Fang
- School of Civil Engineering, Purdue University, West Lafayette, Indiana 47907-2051, Birck Nanotechnology Center, Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Cancer Center, Purdue University, West Lafayette, Indiana 47907, and The Walther Cancer Institute, Indianapolis, Indiana 46208
| | - Yousheng Guan
- School of Civil Engineering, Purdue University, West Lafayette, Indiana 47907-2051, Birck Nanotechnology Center, Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Cancer Center, Purdue University, West Lafayette, Indiana 47907, and The Walther Cancer Institute, Indianapolis, Indiana 46208
| | - Ernest R. Blatchley
- School of Civil Engineering, Purdue University, West Lafayette, Indiana 47907-2051, Birck Nanotechnology Center, Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Cancer Center, Purdue University, West Lafayette, Indiana 47907, and The Walther Cancer Institute, Indianapolis, Indiana 46208
| | - Chengyue Shen
- School of Civil Engineering, Purdue University, West Lafayette, Indiana 47907-2051, Birck Nanotechnology Center, Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Cancer Center, Purdue University, West Lafayette, Indiana 47907, and The Walther Cancer Institute, Indianapolis, Indiana 46208
| | - Donald E. Bergstrom
- School of Civil Engineering, Purdue University, West Lafayette, Indiana 47907-2051, Birck Nanotechnology Center, Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Cancer Center, Purdue University, West Lafayette, Indiana 47907, and The Walther Cancer Institute, Indianapolis, Indiana 46208
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Mahajan S, Patnaik S, Kumar P, Gandhi RP, Gupta KC. A new synthetic protocol for labeled oligonucleotides, using a chemically cleavable universal linker. Bioorg Med Chem 2006; 14:4302-9. [PMID: 16495059 DOI: 10.1016/j.bmc.2006.01.063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2005] [Revised: 01/21/2006] [Accepted: 01/23/2006] [Indexed: 10/25/2022]
Abstract
A two-step general method for labeling of synthetic oligonucleotides is described. The protocol employs a cleavable universal linker, 5'-O-(4,4'-dimethoxytrityl)-3'-O-benzoyl-2'-O-(2-cyanoethyl-N,N-diisopropyl)-uridine phosphoramidite, to effect coupling to polymer-bound oligonucleotide chains. Sequentially, coupling with commercially available phosphoramidite reagent of an appropriate label (Biotin, HEX etc.) in an automated DNA synthesizer is carried out. The labeled oligomers, obtained after cleavage and deprotection reactions, are analyzed on RP-HPLC. A distinctive feature of this protocol is the recovery of free oligomers from their labeled analogs under mild conditions. The oligomers obtained are comparable to the corresponding standard oligonucleotides (HPLC).
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Affiliation(s)
- Shweta Mahajan
- Nucleic Acids Research Laboratory, Institute of Genomics and Integrative Biology, Mall Road, Delhi University Campus, Delhi 110 007, India
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Hashimoto M, Hatanaka Y. Post-biotinylation of photocrosslinking by Staudinger-Bertozzi ligation of preinstalled alkylazide tag. Chem Pharm Bull (Tokyo) 2006; 53:1510-2. [PMID: 16272745 DOI: 10.1248/cpb.53.1510] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Post-biotinylation of the alkyl azide derivative of trifluoromethyl phenyldiazirine (TPD) was elucidated to apply a photoaffinity biotinylation technique. A photo-modified polyvinilidene difluoride (PVDF) membrane was used as a photolabeled component and we introduced biotin by Staudinger-Bertozzi ligation. The 15 pmol amount of biotinylated reagent was still effective for the visualization of cross-linked product on the matrix. The results show the potential utility of alkyl azide carrying TPD derivatives in the application of photoaffinity biotinylation, which could be useful for the ligands with tight structural requirements.
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Affiliation(s)
- Makoto Hashimoto
- Department of Agricultural and Life Science, Obihiro University of Agriculture and Veterinary Medicine, Hokkaido, Japan.
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Upadhya K, Khattak IK, Mullah B. Oxidation of biotin during oligonucleotide synthesis. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 24:919-22. [PMID: 16248062 DOI: 10.1081/ncn-200059277] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A new "polystyrene biotin support" has been synthesized for the solid support synthesis of the 3'-biotinylated oligonucleotides. Several oligos were synthesized and were analyzed by the HPLC and Mass Spec. Oligo analysis revealed that the biotin gets oxidized to "biotin sulfoxide" during the synthesis.
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Affiliation(s)
- Krishna Upadhya
- Applied Biosystems, 8a50 Lincoln Centre Drive, Foster City, CA 94404, USA.
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Park JJ, Sadakane Y, Masuda K, Tomohiro T, Nakano T, Hatanaka Y. Synthesis of Diazirinyl Photoprobe Carrying a Novel Cleavable Biotin. Chembiochem 2005; 6:814-8. [PMID: 15825213 DOI: 10.1002/cbic.200400342] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jong-jip Park
- Faculty of Pharmaceutical Sciences, Toyama Medical and Pharmaceutical University, 2630 Sugitani, Toyama 930-0194, Japan
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30
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Fang S, Bergstrom DE. Reversible 5′-end biotinylation and affinity purification of synthetic RNA. Tetrahedron Lett 2004. [DOI: 10.1016/j.tetlet.2004.09.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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31
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Pon RT, Yu S. Linker phosphoramidite reagents for the attachment of the first nucleoside to underivatized solid-phase supports. Nucleic Acids Res 2004; 32:623-31. [PMID: 14752050 PMCID: PMC373346 DOI: 10.1093/nar/gkh222] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
New linker phosphoramidite reagents containing a cleavable 3'-ester linkage are used for attaching the first nucleoside to the surface of a solid- phase support. Inexpensive, underivatized amino supports, such as long chain alkylamine controlled-pore glass, can serve as universal supports. No modifications to phosphoramidite coupling conditions are required and, after synthesis, treatment with NH(4)OH releases the products with 3'-OH ends. No 3'-dephosphorylation is required. Phosphoramidite reagents containing a succinate and sulfonyl diethanol linkage between the nucleoside and phosphoramidite group are particularly advantageous and can be used to create both 3'-OH and 5'-phosphate ends on oligonucleotides. Reproducibility and quality of oligonucleotide synthesis is demonstrated for either column and 96-well plate formats on low-, medium- or high-loading CPG supports.
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Affiliation(s)
- Richard T Pon
- Department of Biochemistry and Molecular Biology, University of Calgary, 3550 Hospital Drive N.W., Calgary, Alberta, Canada T2N 4N1.
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