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Rosenqvist P, Saari V, Ora M, Molina AG, Horvath A, Virta P. Tuning the Solubility of Soluble Support Constructs in Liquid Phase Oligonucleotide Synthesis. J Org Chem 2024; 89:13005-13015. [PMID: 39250641 DOI: 10.1021/acs.joc.4c01053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Solubility of the growing oligonucleotide-soluble support constructs in the liquid phase oligonucleotide synthesis (LPOS) is a critical parameter, which affects coupling efficiency, purity, and recovery of the growing oligonucleotides during the chain elongation. In the present study, oligonucleotides have been assembled on a 4-oxoheptanedioic acid (OHDA) linker-derived tetrapodal soluble support using 5'-O-(2-methoxyprop-2-yl)-protected 2'-deoxyribonucleotide phosphoroamidite building blocks with different nucleobase protecting groups [isobutyryl (Gua), 1-butylpyrrolidin-2-ylidene (Gua, Cyt), 2,4-dimethylbenzoyl (Ade, Cyt), and Bz (Thy)]. The solubility of the oligonucleotide-soluble support constructs (molecular mass varying between 3 and 10 kDa) as models of protected tetra-, octa-, dodeca-, hexadeca-, and eicosa-nucleotides was measured in different solvent systems and in potential antisolvents. By tuning the nucleobase protecting group scheme, the solubility can be improved in aprotic organic solvent systems, while the recovery of the constructs in the precipitation, used for the isolation and purification of the growing oligonucleotide intermediates in a protic antisolvent (2-propanol), remained near quantitative. The precipitation-based yield of the protected tetrapodal oligonucleotides varied from a quantitative to 90% yield. Overall yield (for di-: 95%, tri-: 79-96%, tetra-: 82-88%, and pentanucleotides: 68-75%) and purity of the LPOS were evaluated by RP HPLC and MS-spectroscopy of the released oligonucleotide aliquots. In addition, the orthogonality of the OHDA linker was applied to release authentic protected nucleotides from the soluble supports.
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Affiliation(s)
- Petja Rosenqvist
- Department of Chemistry, University of Turku, 20500 Turku, Finland
| | - Verneri Saari
- Department of Chemistry, University of Turku, 20500 Turku, Finland
| | - Mikko Ora
- Department of Chemistry, University of Turku, 20500 Turku, Finland
| | | | - Andras Horvath
- Janssen Pharmaceutica N.V., 30 Turnhoutseweg, B-2340 Beerse, Belgium
| | - Pasi Virta
- Department of Chemistry, University of Turku, 20500 Turku, Finland
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2
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Preuss I, Rosenberg M, Yakhini Z, Anavy L. Efficient DNA-based data storage using shortmer combinatorial encoding. Sci Rep 2024; 14:7731. [PMID: 38565928 PMCID: PMC11369284 DOI: 10.1038/s41598-024-58386-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 03/28/2024] [Indexed: 04/04/2024] Open
Abstract
Data storage in DNA has recently emerged as a promising archival solution, offering space-efficient and long-lasting digital storage solutions. Recent studies suggest leveraging the inherent redundancy of synthesis and sequencing technologies by using composite DNA alphabets. A major challenge of this approach involves the noisy inference process, obstructing large composite alphabets. This paper introduces a novel approach for DNA-based data storage, offering, in some implementations, a 6.5-fold increase in logical density over standard DNA-based storage systems, with near-zero reconstruction error. Combinatorial DNA encoding uses a set of clearly distinguishable DNA shortmers to construct large combinatorial alphabets, where each letter consists of a subset of shortmers. We formally define various combinatorial encoding schemes and investigate their theoretical properties. These include information density and reconstruction probabilities, as well as required synthesis and sequencing multiplicities. We then propose an end-to-end design for a combinatorial DNA-based data storage system, including encoding schemes, two-dimensional (2D) error correction codes, and reconstruction algorithms, under different error regimes. We performed simulations and show, for example, that the use of 2D Reed-Solomon error correction has significantly improved reconstruction rates. We validated our approach by constructing two combinatorial sequences using Gibson assembly, imitating a 4-cycle combinatorial synthesis process. We confirmed the successful reconstruction, and established the robustness of our approach for different error types. Subsampling experiments supported the important role of sampling rate and its effect on the overall performance. Our work demonstrates the potential of combinatorial shortmer encoding for DNA-based data storage and describes some theoretical research questions and technical challenges. Combining combinatorial principles with error-correcting strategies, and investing in the development of DNA synthesis technologies that efficiently support combinatorial synthesis, can pave the way to efficient, error-resilient DNA-based storage solutions.
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Affiliation(s)
- Inbal Preuss
- School of Computer Science, Reichman University, 4610101, Herzliya, Israel.
- Faculty of Computer Science, Technion, 3200003, Haifa, Israel.
| | - Michael Rosenberg
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002, Ramat Gan, Israel
| | - Zohar Yakhini
- School of Computer Science, Reichman University, 4610101, Herzliya, Israel
- Faculty of Computer Science, Technion, 3200003, Haifa, Israel
| | - Leon Anavy
- School of Computer Science, Reichman University, 4610101, Herzliya, Israel
- Faculty of Computer Science, Technion, 3200003, Haifa, Israel
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3
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Suchsland R, Appel B, Virta P, Müller S. Synthesis of fully protected trinucleotide building blocks on a disulphide-linked soluble support. RSC Adv 2021; 11:3892-3896. [PMID: 35424330 PMCID: PMC8694130 DOI: 10.1039/d0ra10941j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 01/12/2021] [Indexed: 11/30/2022] Open
Abstract
In recent years, preparation of fully protected trinucleotide phosphoramidites as synthons for the codon-based synthesis of gene libraries as well as for the assembly of oligonucleotides from blockmers has gained much attention. We here describe the preparation of such trinucleotide synthons on a soluble support using a disulphide linker. Fully protected trinucleotides are synthesized on a tetrapodal soluble support using a disulphide linkage that upon reductive cleavage allows release of the trinucleotide with free 3′-OH group for further conversion to a phosphoramidite.![]()
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Affiliation(s)
- Ruth Suchsland
- University Greifswald
- Institute for Biochemistry
- 17487 Greifswald
- Germany
| | - Bettina Appel
- University Greifswald
- Institute for Biochemistry
- 17487 Greifswald
- Germany
| | - Pasi Virta
- University of Turku
- Department of Chemistry
- 20014 Turku
- Finland
| | - Sabine Müller
- University Greifswald
- Institute for Biochemistry
- 17487 Greifswald
- Germany
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4
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Solemani Zadeh A, Grässer A, Dinter H, Hermes M, Schindowski K. Efficient Construction and Effective Screening of Synthetic Domain Antibody Libraries. Methods Protoc 2019; 2:mps2010017. [PMID: 31164599 PMCID: PMC6481084 DOI: 10.3390/mps2010017] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 01/27/2019] [Accepted: 02/11/2019] [Indexed: 01/02/2023] Open
Abstract
Phage display is a powerful technique for drug discovery in biomedical research in particular for antibody libraries. But, several technical challenges are associated with the selection process. For instance, during the panning step, the successful elution of the phages bound to the antigen is critical in order to avoid losing the most promising binders. Here, we present an efficient protocol to establish, screen and select synthetic libraries of domain antibodies using phage display. We do not only present suitable solutions to the above-mentioned challenges to improve elution by 50-fold, but we also present a step by step in-depth protocol with miniaturized volumes and optimized procedures to save material, costs and time for a successful phage display with domain antibodies. Hence, this protocol improves the selection process for an efficient handling process. The here presented library is based on the variable domain (vNAR) of the naturally occurring novel antibody receptor (IgNAR) from cartilage fishes. Diversity was introduced in the Complementarity-Determining Region 3 (CDR3) of the antigen-binding site with different composition and length.
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Affiliation(s)
- Arghavan Solemani Zadeh
- Institute for Applied Biotechnology, Biberach University of Applied Science, Hubertus-Liebrecht-Strasse 35, 88400 Biberach, Germany.
- Faculty of Medicine, Graduate School "Molecular Medicine", University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany.
- Faculty of Natural Sciences, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany.
| | - Alissa Grässer
- Institute for Applied Biotechnology, Biberach University of Applied Science, Hubertus-Liebrecht-Strasse 35, 88400 Biberach, Germany.
- Faculty of Natural Sciences, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany.
| | - Heiko Dinter
- Institute for Applied Biotechnology, Biberach University of Applied Science, Hubertus-Liebrecht-Strasse 35, 88400 Biberach, Germany.
| | - Maximilian Hermes
- Institute for Applied Biotechnology, Biberach University of Applied Science, Hubertus-Liebrecht-Strasse 35, 88400 Biberach, Germany.
- Faculty of Natural Sciences, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany.
| | - Katharina Schindowski
- Institute for Applied Biotechnology, Biberach University of Applied Science, Hubertus-Liebrecht-Strasse 35, 88400 Biberach, Germany.
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5
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Suchsland R, Appel B, Müller S. Synthesis of Trinucleotide Building Blocks in Solution and on Solid Phase. ACTA ACUST UNITED AC 2018; 75:e60. [PMID: 30375750 DOI: 10.1002/cpnc.60] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We have developed two methods, in solution and on solid phase, that give easy access to trinucleotide phosphoramidites capable of undergoing coupling reactions by the solid-phase phosphoramidite approach. The solution protocol is characterized by application of 5'-O-dimethoxytrityl (DMT) and 3'-O-tert-butyldimethylsilyl (TBDMS) as a pair of orthogonal protecting groups and 2-cyanoethyl (CE) for protection of the phosphate. Starting with suitably functionalized monomers, synthesis proceeds in the 3'- to 5'-direction, delivering the fully protected trinucleotide. The 3'-O-protecting group is cleaved followed by phosphitylation of the free 3'-OH group. The solid-phase protocol is based on standard phosphoramidite chemistry in conjunction with a dithiomethyl linkage connecting the 3'-starting nucleoside to the polymer. The disulfide bridge can be cleaved under neutral conditions for release of the trinucleotide from the support preserving all other protecting groups. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Ruth Suchsland
- Institute for Biochemistry, University Greifswald, Greifswald, Germany
| | - Bettina Appel
- Institute for Biochemistry, University Greifswald, Greifswald, Germany
| | - Sabine Müller
- Institute for Biochemistry, University Greifswald, Greifswald, Germany
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6
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Suchsland R, Appel B, Müller S. Preparation of trinucleotide phosphoramidites as synthons for the synthesis of gene libraries. Beilstein J Org Chem 2018. [PMID: 29520304 PMCID: PMC5827815 DOI: 10.3762/bjoc.14.28] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The preparation of protein libraries is a key issue in protein engineering and biotechnology. Such libraries can be prepared by a variety of methods, starting from the respective gene library. The challenge in gene library preparation is to achieve controlled total or partial randomization at any predefined number and position of codons of a given gene, in order to obtain a library with a maximum number of potentially successful candidates. This purpose is best achieved by the usage of trinucleotide synthons for codon-based gene synthesis. We here review the strategies for the preparation of fully protected trinucleotides, emphasizing more recent developments for their synthesis on solid phase and on soluble polymers, and their use as synthons in standard DNA synthesis.
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Affiliation(s)
- Ruth Suchsland
- Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Str. 4, D-17489 Greifswald, Germany
| | - Bettina Appel
- Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Str. 4, D-17489 Greifswald, Germany
| | - Sabine Müller
- Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Str. 4, D-17489 Greifswald, Germany
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7
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Polypharmacy through Phage Display: Selection of Glucagon and GLP-1 Receptor Co-agonists from a Phage-Displayed Peptide Library. Sci Rep 2018; 8:585. [PMID: 29330364 PMCID: PMC5766609 DOI: 10.1038/s41598-017-18494-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/16/2017] [Indexed: 02/07/2023] Open
Abstract
A promising emerging area for the treatment of obesity and diabetes is combinatorial hormone therapy, where single-molecule peptides are rationally designed to integrate the complementary actions of multiple endogenous metabolically-related hormones. We describe here a proof-of-concept study on developing unimolecular polypharmacy agents through the use of selection methods based on phage-displayed peptide libraries (PDL). Co-agonists of the glucagon (GCG) and GLP-1 receptors were identified from a PDL sequentially selected on GCGR- and GLP1R-overexpressing cells. After two or three rounds of selection, 7.5% of randomly picked clones were GLP1R/GCGR co-agonists, and a further 1.53% were agonists of a single receptor. The phages were sequenced and 35 corresponding peptides were synthesized. 18 peptides were potent co-agonists, 8 of whom showed EC50 ≤ 30 pM on each receptor, comparable to the best rationally designed co-agonists reported in the literature. Based on literature examples, two sequences were engineered to stabilize against dipeptidyl peptidase IV cleavage and prolong the in vivo half-life: the engineered peptides were comparably potent to the parent peptides on both receptors, highlighting the potential use of phage-derived peptides as therapeutic agents. The strategy described here appears of general value for the discovery of optimized polypharmacology paradigms across several metabolically-related hormones.
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8
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Matsuno Y, Shoji T, Kim S, Chiba K. Synthetic Method for Oligonucleotide Block by Using Alkyl-Chain-Soluble Support. Org Lett 2016; 18:800-3. [PMID: 26845521 DOI: 10.1021/acs.orglett.6b00077] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A straightforward method for the synthesis of oligonucleotide blocks using a Cbz-type alkyl-chain-soluble support (Z-ACSS) attached to the 3'-OH group of 3'-terminal nucleosides was developed. The Z-ACSS allowed for the preparation of fully protected deoxyribo- and ribo-oligonucleotides without chromatographic purification and released dimer- to tetramer-size oligonucleotide blocks via hydrogenation using a Pd/C catalyst without significant loss or migration of protective groups such as 5'-end 4,4'-dimethoxtrityl, 2-cyanoethyl on internucleotide bonds, or 2'-TBS.
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Affiliation(s)
- Yuki Matsuno
- Laboratory of Bio-organic Chemistry, Tokyo University of Agriculture and Technology , 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Takao Shoji
- Laboratory of Bio-organic Chemistry, Tokyo University of Agriculture and Technology , 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Shokaku Kim
- Laboratory of Bio-organic Chemistry, Tokyo University of Agriculture and Technology , 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Kazuhiro Chiba
- Laboratory of Bio-organic Chemistry, Tokyo University of Agriculture and Technology , 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
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9
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Kungurtsev V, Lönnberg H, Virta P. Synthesis of protected 2′-O-deoxyribonucleotides on a precipitative soluble support: a useful procedure for the preparation of trimer phosphoramidites. RSC Adv 2016. [DOI: 10.1039/c6ra22316h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
A straightforward procedure for the preparation of protected 2′-O-deoxyribonucleotide trimers, using the phosphotriester chemistry on a precipitative soluble support, was described.
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Affiliation(s)
- V. Kungurtsev
- Department of Chemistry
- University of Turku
- FI-20014 Turku
- Finland
| | - H. Lönnberg
- Department of Chemistry
- University of Turku
- FI-20014 Turku
- Finland
| | - P. Virta
- Department of Chemistry
- University of Turku
- FI-20014 Turku
- Finland
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10
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Barreto K, Geyer CR. Screening combinatorial libraries of cyclic peptides using the yeast two-hybrid assay. Methods Mol Biol 2014; 1163:273-309. [PMID: 24841315 DOI: 10.1007/978-1-4939-0799-1_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Peptides are useful reagents for reverse analysis of protein function in a variety of organisms, as they have a dominant mode of action that can inhibit protein interactions or activities. Further, peptides are important tools for validating proteins as therapeutic targets, for determining structure/activity relationships, and for designing small molecules. Genetic selection strategies have been developed for screening combinatorial peptide libraries to rapidly isolate peptides that interact with a given target. In genetic selections and biological assays, linear peptides are not very stable and are rapidly degraded. In contrast, cyclic peptides are more stable and bind with higher affinity. Genetic selections of cyclic peptides are difficult as they are not compatible with most selection technologies. Thus, there has been limited number of applications that use cyclic peptides for the reverse analysis of protein function.Here, we describe a protocol to isolate cyclic peptides that bind proteins in the yeast two-hybrid assay. Cyclic peptides used in the yeast two-hybrid assay are referred to as "lariat" peptides. Lariat peptides are made by blocking the intein-producing cyclic peptide reaction at an intermediate step. They consist of a lactone cyclic peptide or "noose" region connected by an amide bond to a transcription activation domain. Combinatorial libraries of >10(7) lariat peptides can be screened using the yeast two-hybrid assay to isolate lariat peptides for studying the function or validating the therapeutic potential of protein targets.
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Affiliation(s)
- Kris Barreto
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, Canada, S7N 5E5
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11
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Huovinen T, Syrjanpaa M, Sanmark H, Brockmann EC, Azhayev A, Wang Q, Vehniainen M, Lamminmaki U. Two ScFv antibody libraries derived from identical VL-VH framework with different binding site designs display distinct binding profiles. Protein Eng Des Sel 2013; 26:683-93. [DOI: 10.1093/protein/gzt037] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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12
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Huang J, Xi Z. Chemical synthesis of bioactive siRNA in solution phase by using 2-(azidomethyl)benzoyl as 3′-hydroxyl group protecting group. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.05.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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13
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Arunachalam TS, Wichert C, Appel B, Müller S. Mixed oligonucleotides for random mutagenesis: best way of making them. Org Biomol Chem 2012; 10:4641-50. [PMID: 22552713 DOI: 10.1039/c2ob25328c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The generation of proteins, especially enzymes, with pre-deliberated, novel properties is a big challenge in the field of protein engineering. This aim, over the years was critically facilitated by newly emerging methods of combinatorial and evolutionary techniques, such as combinatorial gene synthesis followed by functional screening of many structural variants generated in parallel (library). Libraries can be generated by a large number of available methods. Therein the use of mixtures of pre-formed trinucleotide blocks representing codons for the 20 canonical amino acids for oligonucleotide synthesis stands out as allowing fully controlled partial (or total) randomization individually at any number of arbitrarily chosen codon positions of a given gene. This has created substantial demand of fully protected trinucleotide synthons of good reactivity in standard oligonucleotide synthesis. We here review methods for the preparation of oligonucleotide mixtures with a strong focus on codon-specific trinucleotide blocks.
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Affiliation(s)
- Tamil Selvi Arunachalam
- Institut für Biochemie, Ernst Moritz Arndt Universität, Felix Hausdorff Strasse 4, Greifswald, D-17487, Germany
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14
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Huovinen T, Brockmann EC, Akter S, Perez-Gamarra S, Ylä-Pelto J, Liu Y, Lamminmäki U. Primer extension mutagenesis powered by selective rolling circle amplification. PLoS One 2012; 7:e31817. [PMID: 22355397 PMCID: PMC3280210 DOI: 10.1371/journal.pone.0031817] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 01/18/2012] [Indexed: 11/18/2022] Open
Abstract
Primer extension mutagenesis is a popular tool to create libraries for in vitro evolution experiments. Here we describe a further improvement of the method described by T.A. Kunkel using uracil-containing single-stranded DNA as the template for the primer extension by additional uracil-DNA glycosylase treatment and rolling circle amplification (RCA) steps. It is shown that removal of uracil bases from the template leads to selective amplification of the nascently synthesized circular DNA strand carrying the desired mutations by phi29 DNA polymerase. Selective RCA (sRCA) of the DNA heteroduplex formed in Kunkel's mutagenesis increases the mutagenesis efficiency from 50% close to 100% and the number of transformants 300-fold without notable diversity bias. We also observed that both the mutated and the wild-type DNA were present in at least one third of the cells transformed directly with Kunkel's heteroduplex. In contrast, the cells transformed with sRCA product contained only mutated DNA. In sRCA, the complex cell-based selection for the mutant strand is replaced with the more controllable enzyme-based selection and less DNA is needed for library creation. Construction of a gene library of ten billion members is demonstrated with the described method with 240 nanograms of DNA as starting material.
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Affiliation(s)
- Tuomas Huovinen
- Department of Biochemistry and Food Chemistry, University of Turku, Turku, Finland.
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15
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Janczyk M, Appel B, Springstubbe D, Fritz HJ, Müller S. A new and convenient approach for the preparation of β-cyanoethyl protected trinucleotide phosphoramidites. Org Biomol Chem 2012; 10:1510-3. [PMID: 22231393 DOI: 10.1039/c2ob06934b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein we report a convenient approach for the preparation of fully protected trinucleotide synthons to be used for the synthesis of gene libraries. The trinucleotide synthons bear β-cyanoethyl groups at the phosphate residues, and thus can be used in standard oligonucleotide synthesis without additional steps for deprotection and work-up.
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Affiliation(s)
- Matthäus Janczyk
- Ernst-Moritz-Arndt-Universität Greifswald, Institut für Biochemie, Felix-Hausdorff-Str., 4, 17487 Greifswald, Germany
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16
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Yagodkin A, Weisel J, Azhayev A. Versatile solid supports for oligonucleotide synthesis that incorporate urea bridge. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2011; 30:475-89. [PMID: 21888540 DOI: 10.1080/15257770.2011.582851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The universal solid support, USIII, representing a new and improved version of commercial USII, as well as 2 '-deoxynucleoside and 2 '-deoxy-2 '-fluoronucleoside bound supports, incorporating a labile phenoxyacetyl fragment, was synthesized by an aminomethyl polystyrene carbamoylation with corresponding azides in the presence of aqueous triethylammonium bicarbonate. All three solid phases incorporate a stable urea tether, thus bridging the polymer and functional linker. These new matrices proved to be potent solid phases for the synthesis of DNA, RNA, or modified oligonucleotides as well as randomized mixed 2 '-ribo/2 '-deoxy-2 '-fluoro-RNA libraries and/or DNA libraries, randomized with trinucleotides (codons).
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Affiliation(s)
- Andrey Yagodkin
- Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
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17
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Brockmann EC, Akter S, Savukoski T, Huovinen T, Lehmusvuori A, Leivo J, Saavalainen O, Azhayev A, Lövgren T, Hellman J, Lamminmäki U. Synthetic single-framework antibody library integrated with rapid affinity maturation by VL shuffling. Protein Eng Des Sel 2011; 24:691-700. [PMID: 21680620 DOI: 10.1093/protein/gzr023] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Affinity maturation is often applied to improve the properties of antibodies isolated from universal antibody libraries in vitro. A synthetic human scFv antibody library was constructed in single immunoglobulin framework to enable rapid affinity maturation by updated Kunkel's mutagenesis. The initial diversity was generated predominantly in the V(H) domain combined with only 36 V(L) domain variants yielding 3 × 10(10) unique members in the phage-displayed library. After three rounds of panning the enriched V(H) genes from the primary library selections against lysozyme were incorporated into a ready-made circular single-stranded affinity maturation library containing 7 × 10(8) V(L) gene variants. Several unique antibodies with 0.8-10 nM (K(d), dissociation constant) affinities against lysozyme were found after panning from the affinity maturation library, contrasted by only one anti-lysozyme scFv clone with K(d) <20 nM among the clones panned from the primary universal library. The presented single-framework strategy provides a way to convey significant amount of functional V(H) domain diversity to affinity maturation without bimolecular ligation leading to a diverse set of antibodies with binding affinities in the low nanomolar range.
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Affiliation(s)
- E-C Brockmann
- Department of Biotechnology, University of Turku, Turku, Finland.
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18
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Lindner T, Kolmar H, Haberkorn U, Mier W. DNA libraries for the construction of phage libraries: statistical and structural requirements and synthetic methods. Molecules 2011; 16:1625-41. [PMID: 21326140 PMCID: PMC6259622 DOI: 10.3390/molecules16021625] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 01/26/2011] [Accepted: 02/11/2011] [Indexed: 01/19/2023] Open
Abstract
Peptide-based molecular probes identified by bacteriophage (phage) display technology expand the peptide repertoire for in vivo diagnosis and therapy of cancer. Numerous peptides that bind cancer-associated antigens have been discovered by panning phage libraries. However, until now only few of the peptides selected by phage display have entered clinical applications. The success of phage derived peptides essentially depends on the quality of the library screened. This review summarizes the methods to achieve highly homogenous libraries that cover a maximal sequence space. Biochemical and chemical strategies for the synthesis of DNA libraries and the techniques for their integration into the viral genome are discussed in detail. A focus is set on the methods that enable the exclusion of disturbing sequences. In addition, the parameters that define the variability, the minimal numbers of copies per library and the use of alternating panning cycles to avoid the loss of selected hits are evaluated.
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Affiliation(s)
- Thomas Lindner
- Department of Nuclear Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 400, D-69120 Heidelberg, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Darmstadt University of Technology, Petersenstrase 22, 64287 Darmstadt, Germany
| | - Uwe Haberkorn
- Department of Nuclear Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 400, D-69120 Heidelberg, Germany
| | - Walter Mier
- Department of Nuclear Medicine, University Hospital Heidelberg, Im Neuenheimer Feld 400, D-69120 Heidelberg, Germany
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +49-6221-56-7720; Fax: +49-6221-56-33629
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19
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Efimov VA, Aralov AV, Klykov VN, Chakhmakhcheva OG. Synthesis of RNA by the rapid phosphotriester method using azido-based 2'-O-protecting groups. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2010; 28:846-65. [PMID: 20183623 DOI: 10.1080/15257770903170286] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The azidomethyl and 2-(azidomethyl)benzoyl as 2'-OH protecting groups are reported for preparation of oligoribonucleotides by the phosphotriester solid-phase method using O-nucleophilic intramolecular catalysis. The procedures for the synthesis of the corresponding monomer synthons were developed and the usefulness of the application of 2'-O-azidomethyl and 2'-O-2-(azidomethyl)benzoyl groups was examined in the synthesis of different RNA fragments with a chain length of 15-22 nucleotides. The azidomethyl group was found to be more preferable for effective synthesis of oligoribonucleotides. Hybridization properties of RNAs toward their complementary oligonucleotides were examined before and after the removal of 2'-O-azidomethyl groups.
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Affiliation(s)
- V A Efimov
- Russian Academy of Sciences, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
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20
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Straightforward carbamoylation of nucleophilic compounds employing organic azides, phosphines, and aqueous trialkylammonium hydrogen carbonate. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.01.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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21
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Gaytán P, Contreras-Zambrano C, Ortiz-Alvarado M, Morales-Pablos A, Yáñez J. TrimerDimer: an oligonucleotide-based saturation mutagenesis approach that removes redundant and stop codons. Nucleic Acids Res 2009; 37:e125. [PMID: 19783828 PMCID: PMC2764442 DOI: 10.1093/nar/gkp602] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
9-fluorenylmethoxycarbonyl (Fmoc) and 4,4'-dimethoxytrityl (DMTr) are orthogonal hydroxyl protecting groups that have been used in conjunction to assemble oligonucleotide libraries whose variants contain wild-type and mutant codons randomly interspersed throughout a focused DNA region. Fmoc is labile to organic bases and stable to weak acids, whereas DMTr behaves oppositely. Based on these chemical characteristics, we have now devised TrimerDimer, a novel codon-based saturation mutagenesis approach that removes redundant and stop codons during the assembly of degenerate oligonucleotides. In this approach, five DMTr-protected trinucleotide phosphoramidites (dTGG, dATG, dTTT, dTAT and dTGC) and five Fmoc-protected dinucleotide phosphoramidites (dAA, dTT, dAT, dGC and dCG) react simultaneously with a starting oligonucleotide growing on a solid support. The Fmoc group is then removed and the incorporated dimers react with a mixture of three DMTr-protected monomer phosphoramidites (dC, dA and dG) to produce 15 trinucleotides: dCAA, dAAA, dGAA, dCTT, dATT, dGTT, dCAT, dAAT, dGAT, dCGC, dAGC, dGGC, dCCG, dACG and dGCG. After one mutagenic cycle, 20 codons are generated encoding the 20 natural amino acids. TrimerDimer was tested by randomizing the four contiguous codons that encode amino acids L64-G67 of an engineered, nonfluorescent GFP protein. Sequencing of 89 nonfluorescent mutant clones and isolation of two fluorescent mutants confirmed the principle.
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Affiliation(s)
- Paul Gaytán
- Instituto de Biotecnología-Universidad Nacional Autónoma de México, Ap. Postal 510-3 Cuernavaca, Morelos 62250, México.
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