1
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El-Khoury R, Damha MJ. End-ligation can dramatically stabilize i-motifs at neutral pH. Chem Commun (Camb) 2023; 59:3715-3718. [PMID: 36883338 DOI: 10.1039/d2cc07063d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Stabilizing i-motif structures at neutral pH and physiological temperature remains a major challenge. Here, we demonstrate the use of chemical end-ligation to stabilize intramolecular i-motifs at both acidic and neutral pH. We also demonstrate that combining 2'-deoxy-2'-fluoroarabinocytidine substitutions and end-ligation results in an i-motif with an unparalleled thermal stability of 54 °C at neutral pH. Overall, the ligated i-motifs presented herein may be used in screens for selective i-motif ligands and proteins and could find important applications in nanotechnology.
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Affiliation(s)
- Roberto El-Khoury
- Department of Chemistry, McGill University, Montréal, H3A0B8, Canada.
| | - Masad J Damha
- Department of Chemistry, McGill University, Montréal, H3A0B8, Canada.
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2
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Yamaoka K, Oikawa R, Abe N, Nakamoto K, Tomoike F, Hashiya F, Kimura Y, Abe H. Completely Chemically Synthesized Long DNA Can be Transcribed in Human Cells. Chembiochem 2021; 22:3273-3276. [PMID: 34519401 DOI: 10.1002/cbic.202100312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/11/2021] [Indexed: 11/10/2022]
Abstract
Chemical ligation reaction of DNA is useful for the construction of long functional DNA using oligonucleotide fragments that are prepared by solid phase chemical synthesis. However, the unnatural linkage structure formed by the ligation reaction generally impairs the biological function of the resulting ligated DNA. We achieved the complete chemical synthesis of 78 and 258 bp synthetic DNAs via multiple chemical ligation reactions with phosphorothioate and haloacyl-modified DNA fragments. The latter synthetic DNA, coding shRNA for luciferase genes with a designed truncated SV promoter sequence, successfully induced the expected gene silencing effect in HeLa cells.
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Affiliation(s)
- Kazuki Yamaoka
- Graduate School of Science, Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Ryota Oikawa
- Graduate School of Science, Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Naoko Abe
- Graduate School of Science, Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Kosuke Nakamoto
- Graduate School of Science, Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Fumiaki Tomoike
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.,Department of Life Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588, Japan
| | - Fumitaka Hashiya
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Yasuaki Kimura
- Graduate School of Science, Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Hiroshi Abe
- Graduate School of Science, Department of Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.,CREST, Japan Science and Technology Agency, Gobancho, Chiyoda-ku, Tokyo, 102-0076, Japan.,Institute for Glyco-core Research, Tokai National Higher Education and Research System, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
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3
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Obianyor C, Newnam G, Clifton BE, Grover MA, Hud NV. Towards Efficient Nonenzymatic DNA Ligation: Comparing Key Parameters for Maximizing Ligation Rates and Yields with Carbodiimide Activation**. Chembiochem 2020; 21:3359-3370. [DOI: 10.1002/cbic.202000335] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/21/2020] [Indexed: 01/14/2023]
Affiliation(s)
- Chiamaka Obianyor
- Georgia Institute of Technology School of Chemical and Biomolecular Engineering Atlanta Georgia 30332-0400 USA
| | - Gary Newnam
- Georgia Institute of Technology, Chemistry and Biochemistry 311 Ferst Drive Atlanta Georgia 30332-0400 USA
| | - Bryce E. Clifton
- Georgia Institute of Technology, Chemistry and Biochemistry 311 Ferst Drive Atlanta Georgia 30332-0400 USA
| | - Martha A. Grover
- Georgia Institute of Technology School of Chemical and Biomolecular Engineering Atlanta Georgia 30332-0400 USA
| | - Nicholas V. Hud
- Georgia Institute of Technology, Chemistry and Biochemistry 311 Ferst Drive Atlanta Georgia 30332-0400 USA
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4
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Sosson M, Pfeffer D, Richert C. Enzyme-free ligation of dimers and trimers to RNA primers. Nucleic Acids Res 2019; 47:3836-3845. [PMID: 30869145 PMCID: PMC6486630 DOI: 10.1093/nar/gkz160] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 02/25/2019] [Accepted: 02/28/2019] [Indexed: 01/19/2023] Open
Abstract
The template-directed formation of phosphodiester bonds between two nucleic acid components is a pivotal process in biology. To induce such a reaction in the absence of enzymes is a challenge. This challenge has been met for the extension of a primer with mononucleotides, but the ligation of short oligonucleotides (dimers or trimers) has proven difficult. Here we report a method for ligating dimers and trimers of ribonucleotides using in situ activation in aqueous buffer. All 16 different dimers and two trimers were tested. Binding studies by NMR showed low millimolar dissociation constants for complexes between representative dimers and hairpins mimicking primer-template duplexes, confirming that a weak template effect is not the cause of the poor ligating properties of these short oligomers. Rather, cyclization was found to compete with ligation, with up to 90% of dimer being converted to the cyclic form during the course of an assay. This side reaction is strongly sequence dependent and more pronounced for dimers than for trimers. Under optimized reaction conditions, high yields were observed with strongly pairing purines at the 3'-terminus. These results show that short oligomers of ribonucleotides are competent reactants in enzyme-free copying.
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Affiliation(s)
- Marilyne Sosson
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Daniel Pfeffer
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
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5
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Dai Z, Leung HM, Gao Q, Wang F, Wong SW, Liu LS, Au YJ, Lai KWC, Lo PK. Facile construction of a DNA tetrahedron in unconventional ladder-like arrangements at room temperature. NANOSCALE ADVANCES 2019; 1:1240-1248. [PMID: 36133183 PMCID: PMC9473169 DOI: 10.1039/c8na00323h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 12/23/2018] [Indexed: 05/08/2023]
Abstract
A DNA tetrahedron as the most classical and simplest three-dimensional DNA nanostructure has been widely utilized in biomedicine and biosensing. However, the existing assembly approaches usually require harsh thermal annealing conditions, involve the formation of unwanted by-products, and have poor size control. Herein, a facile strategy to fabricate a discrete DNA tetrahedron as a single, thermodynamically stable product in a quantitative yield at room temperature is reported. This system does not require a DNA trigger or thermal annealing treatment to initiate self-assembly. This DNA tetrahedron was made of three chemically ligated triangular-shaped DNAs in unconventional ladder-like arrangements, with measured heights of ∼4.16 ± 0.04 nm, showing extra protections for enzymatic degradation in biological environment. They show substantial cellular uptake in different cell lines via temperature, energy-dependent and clathrin-mediated endocytosis pathways. These characteristics allow our DNA tetrahedron to be used as vehicles for the delivery of very small and temperature-sensitive cargos. This novel assembly strategy developed for DNA tetrahedra could potentially be extended to other highly complex polyhedra; this indicated its generalizability.
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Affiliation(s)
- Ziwen Dai
- Department of Chemistry, City University of Hong Kong Tat Chee Avenue Kowloon Tong Hong Kong SAR
| | - Hoi Man Leung
- Department of Chemistry, City University of Hong Kong Tat Chee Avenue Kowloon Tong Hong Kong SAR
| | - Qi Gao
- Department of Biomedical Engineering, City University of Hong Kong Tat Chee Avenue Kowloon Tong Hong Kong SAR
| | - Fei Wang
- Department of Chemistry, City University of Hong Kong Tat Chee Avenue Kowloon Tong Hong Kong SAR
| | - Sze Wing Wong
- Department of Chemistry, City University of Hong Kong Tat Chee Avenue Kowloon Tong Hong Kong SAR
| | - Ling Sum Liu
- Department of Chemistry, City University of Hong Kong Tat Chee Avenue Kowloon Tong Hong Kong SAR
| | - Yu Ju Au
- Department of Chemistry, City University of Hong Kong Tat Chee Avenue Kowloon Tong Hong Kong SAR
| | - King Wai Chiu Lai
- Department of Biomedical Engineering, City University of Hong Kong Tat Chee Avenue Kowloon Tong Hong Kong SAR
| | - Pik Kwan Lo
- Department of Chemistry, City University of Hong Kong Tat Chee Avenue Kowloon Tong Hong Kong SAR
- Key Laboratory of Biochip Technology, Biotech and Health Care, Shenzhen Research Institute of City University of Hong Kong Shenzhen 518057 China
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6
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Ali M, Afshan N, Jiang C, Xiao SJ. DNA dumbbell tiles with uneven widths for 2D arrays. Org Biomol Chem 2019; 17:1277-1283. [DOI: 10.1039/c8ob02709a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA dumbbell tiles of AO(E) and BO(E), with stem spans of 11 and 16 bp twisting two head loop motifs of each tile into parallel and antiparallel conformations respectively, were constructed to grow planar nanoribbon arrays and nanotubes as well.
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Affiliation(s)
- Mashooq Ali
- State Key Laboratory of Coordination Chemistry
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210093
- China
| | - Noshin Afshan
- Institute of Molecular Medicine
- Renji Hospital Affiliated To Shanghai Jiao Tong University
- School of Medicine
- Shanghai 200001
- China
| | - Chuan Jiang
- State Key Laboratory of Coordination Chemistry
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210093
- China
| | - Shou-Jun Xiao
- State Key Laboratory of Coordination Chemistry
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210093
- China
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7
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Kramer M, Richert C. Enzyme-Free Ligation of 5'-Phosphorylated Oligodeoxynucleotides in a DNA Nanostructure. Chem Biodivers 2017; 14. [PMID: 28710838 DOI: 10.1002/cbdv.201700315] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 07/12/2017] [Indexed: 01/05/2023]
Abstract
Multicomponent reactions are difficult synthetic transformations. For DNA, there is a special opportunity to align multiple strands in a folded nanostructure, so that they are preorganized to give a specific sequence. Multistrand reactions in DNA origami structures have previously been performed using photochemical crosslinking, 1,3-diploar cycloadditions or phosphoramidate-forming reactions. Here we report carbodiimide-driven phosphodiester formation in a small origami sheet that produces DNA strands up to 600 nucleotides in length in a single step. The method uses otherwise unmodified oligodeoxynucleotides with a 5'-terminal phosphate as starting materials. Compared to an enzymatic multistrand ligation involving linear duplexes, the carbodiimide-driven ligation gave fewer side products, as detected by gel electrophoresis. The full-length 600mer product was successfully amplified by polymerase chain reaction.
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Affiliation(s)
- Markus Kramer
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
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8
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Kalinowski M, Haug R, Said H, Piasecka S, Kramer M, Richert C. Phosphoramidate Ligation of Oligonucleotides in Nanoscale Structures. Chembiochem 2016; 17:1150-5. [PMID: 27225865 DOI: 10.1002/cbic.201600061] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Indexed: 01/25/2023]
Abstract
The folding of long DNA strands into designed nanostructures has evolved into an art. Being based on linear chains only, the resulting nanostructures cannot readily be transformed into covalently linked frameworks. Covalently linking strands in the context of folded DNA structures requires a robust method that avoids sterically demanding reagents or enzymes. Here we report chemical ligation of the 3'-amino termini of oligonucleotides and 5'-phosphorylated partner strands in templated reactions that produce phosphoramidate linkages. These reactions produce inter-nucleotide linkages that are isoelectronic and largely isosteric to phosphodiesters. Ligations were performed at three levels of complexity, including the extension of branched DNA hybrids and the ligation of six scaffold strands in a small origami.
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Affiliation(s)
- Matthäus Kalinowski
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Rüdiger Haug
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Hassan Said
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Sylwia Piasecka
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Markus Kramer
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Clemens Richert
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany.
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9
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Riaño A, Arrechea‐Marcos I, Mancheño MJ, Mayorga Burrezo P, de la Peña A, Loser S, Timalsina A, Facchetti A, Marks TJ, Casado J, López Navarrete JT, Ponce Ortiz R, Segura JL. Benzotrithiophene versus Benzo/Naphthodithiophene Building Blocks: The Effect of Star‐Shaped versus Linear Conjugation on Their Electronic Structures. Chemistry 2016; 22:6374-81. [DOI: 10.1002/chem.201504526] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Alberto Riaño
- Department of Organic Chemistry Complutense University of Madrid, Faculty of Chemistry Madrid 28040 Spain
| | | | - María J. Mancheño
- Department of Organic Chemistry Complutense University of Madrid, Faculty of Chemistry Madrid 28040 Spain
| | | | - Alejandro de la Peña
- Department of Organic Chemistry Complutense University of Madrid, Faculty of Chemistry Madrid 28040 Spain
| | - Stephen Loser
- Department of Chemistry and the Materials Research Center Northwestern University 2145 Sheridan Road Evanston Illinois 60208 USA
| | - Amod Timalsina
- Department of Chemistry and the Materials Research Center Northwestern University 2145 Sheridan Road Evanston Illinois 60208 USA
| | - Antonio Facchetti
- Department of Chemistry and the Materials Research Center Northwestern University 2145 Sheridan Road Evanston Illinois 60208 USA
| | - Tobin J. Marks
- Department of Chemistry and the Materials Research Center Northwestern University 2145 Sheridan Road Evanston Illinois 60208 USA
| | - Juan Casado
- Department of Physical Chemistry University of Málaga Málaga 29071 Spain
| | | | - Rocío Ponce Ortiz
- Department of Physical Chemistry University of Málaga Málaga 29071 Spain
| | - José L. Segura
- Department of Organic Chemistry Complutense University of Madrid, Faculty of Chemistry Madrid 28040 Spain
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10
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Tam DY, Dai Z, Chan MS, Liu LS, Cheung MC, Bolze F, Tin C, Lo PK. A Reversible DNA Logic Gate Platform Operated by One- and Two-Photon Excitations. Angew Chem Int Ed Engl 2015; 55:164-8. [DOI: 10.1002/anie.201507249] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 10/15/2015] [Indexed: 12/21/2022]
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11
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Tam DY, Dai Z, Chan MS, Liu LS, Cheung MC, Bolze F, Tin C, Lo PK. A Reversible DNA Logic Gate Platform Operated by One- and Two-Photon Excitations. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507249] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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12
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Dai Z, Tam DY, Xu H, Chan MS, Liu LS, Bolze F, Sun XH, Lo PK. Conformational Change of Self-Assembled DNA Nanotubes Induced by Two-Photon Excitation. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:4090-6. [PMID: 26011412 DOI: 10.1002/smll.201500333] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 04/20/2015] [Indexed: 05/14/2023]
Abstract
Two-photon-regulated, shape-changing DNA nanostructures are demonstrated by integrating a DNA nanotube with a two-photon photocleavable module that enables the opening of the cavities of tube, and becomes partially single-stranded in response to two-photon excitation under 800 nm fs laser pulses.
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Affiliation(s)
- Ziwen Dai
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
| | - Dick Yan Tam
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Hailiang Xu
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Miu Shan Chan
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
| | - Ling Sum Liu
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Frédéric Bolze
- Laboratoire de Conception et Application des Molécules Bioactives, UMR Université of Strasbourg-CNRS 7199, Faculté de Pharmacie, Université de Strasbourg, France
| | - Xiao Hua Sun
- School of Biological Industry, Chengdu University, Shiling Town, Chengdu City, Sichuan Province, China
| | - Pik Kwan Lo
- Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China
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13
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Yoshimura Y, Matsuzaki T, Fujimoto K. Photochemical Ligation of DNA Probe prepared in Click Chemistry. J PHOTOPOLYM SCI TEC 2009. [DOI: 10.2494/photopolymer.22.267] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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14
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Mui TP, Silverman SK. Convergent and general one-step DNA-catalyzed synthesis of multiply branched DNA. Org Lett 2008; 10:4417-20. [PMID: 18808125 DOI: 10.1021/ol801568q] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report a deoxyribozyme (DNA enzyme) that catalyzes the convergent and general synthesis of branched DNA. The 15HA9 deoxyribozyme mediates nucleophilic attack of the 2'-hydroxyl group of a ribonucleotide embedded within one DNA substrate into a 5'-adenylate of the second DNA substrate. This approach can be used to synthesize multiply branched DNA with a wide range of DNA sequences.
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Affiliation(s)
- Timothy P Mui
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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15
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McCullagh M, Zhang L, Karaba AH, Zhu H, Schatz GC, Lewis FD. Effect of Loop Distortion on the Stability and Structural Dynamics of DNA Hairpin and Dumbbell Conjugates. J Phys Chem B 2008; 112:11415-21. [DOI: 10.1021/jp802378a] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Martin McCullagh
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
| | - Ligang Zhang
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
| | - Andrew H. Karaba
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
| | - Huihe Zhu
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
| | - George C. Schatz
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
| | - Frederick D. Lewis
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113
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16
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Arslan P, Ihara T, Mukae M, Jyo A. The effect of local structural disruption on the yield of photochemical ligation between anthracene-oligonucleotide conjugates. ANAL SCI 2008; 24:173-6. [PMID: 18187868 DOI: 10.2116/analsci.24.173] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The techniques of chemical ligation have attracted great attention as an alternative to enzymatic joining of DNA ends. Here we introduce the photoligation of anthracene-modified ODN conjugates through anthracene cyclodimer formation. The effect of the positions and the kinds of single base mismatch on the template was evaluated using eight templates with one-base displacements. We found out that the yield of the ligation was affected by mispairing in a position-dependent manner. Such results would be attributed to the disruption of the local structure at the ligation site.
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Affiliation(s)
- Pelin Arslan
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Kumamoto 860-8555, Japan
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17
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Lietard J, Meyer A, Vasseur JJ, Morvan F. New strategies for cyclization and bicyclization of oligonucleotides by click chemistry assisted by microwaves. J Org Chem 2007; 73:191-200. [PMID: 18067317 DOI: 10.1021/jo702177c] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The synthesis of cyclic, branched, and bicyclic oligonucleotides was performed by copper-catalyzed azide-alkyne cycloaddition assisted by microwaves in solution and on solid support. For that purpose, new phosphoramidite building blocks and new solid supports were designed to introduce alkyne and bromo functions into the same oligonucleotide by solid-phase synthesis on a DNA synthesizer. The bromine atom was then substituted by sodium azide to yield azide oligonucleotides. Cyclizations were found to be more efficient in solution than on solid support. This method allowed the efficient preparation of cyclic (6- to 20-mers), branched (with one or two dangling sequences), and bicyclic (2 x 10-mers) oligonucleotides.
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Affiliation(s)
- Jory Lietard
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université Montpellier 1, Université Montpellier 2, Place Eugène Bataillon, CC1704, 34095 Montpellier Cedex 5, France
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18
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Abstract
Current studies of lariat RNA structure and function are hindered by the lack of access to synthetic lariats. A novel approach to the synthesis of both DNA and RNA lariats is presented here. Noteworthy features of the methodology are the regiospecific formation of the 2'-5'-phosphodiester linkage, the unusual parallel stranded DNA/RNA hybrid (or parallel RNA/RNA duplex) that forms between an RNA template and a folded 22-nt DNA (or RNA) substrate, and the efficiency of the chemical ligation step at an adenosine branchpoint (50-80%). The DNA and RNA lariats were purified by polyacrylamide gel electrophoresis, and their structure and nucleotide composition were confirmed by MALDI-TOF mass spectrometry. Thermal denaturation as well as enzymatic and chemical hydrolysis fully supported the proposed lariat structures. Characterization of control parallel duplexes was conducted by gel shift assays and enzymatic degradation with RNase H. The successful synthesis of the lariat molecules described here will allow structural and biochemical studies aimed at better understanding the splicing and debranching mechanisms in which these unusual nucleic acids are involved.
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Affiliation(s)
- Debbie Mitra
- Department of Chemistry, Otto Maass Chemistry Building, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada
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19
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Ogino M, Fujimoto K. Photochemical synthesis of R-shaped DNA toward DNA recombination and processing in vitro. Angew Chem Int Ed Engl 2007; 45:7223-6. [PMID: 17009378 DOI: 10.1002/anie.200603161] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Masayuki Ogino
- School of Materials Science, Japan Advanced Institute of Science and Technology, Asahidai, Nomi, Ishikawa 923-1292, Japan
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20
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Zhang L, Long H, Schatz GC, Lewis FD. Synthesis and properties of nicked dumbbell and dumbbell DNA conjugates having stilbenedicarboxamide linkers. Org Biomol Chem 2006; 5:450-6. [PMID: 17252127 DOI: 10.1039/b614572h] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis and properties of nicked dumbbell and dumbbell DNA conjugates having A-tract base pair domains connected by rod-like stilbenedicarboxamide linkers are reported. The nicked dumbbells have one to eight dA-dT base pairs and are missing a sugar-phosphate bond either between the linker and a thymine nucleoside residue or between two thymine residues. Chemical ligation of all of the nicked dumbbells with cyanogen bromide affords the dumbbell conjugates in good yield, providing the smallest mini-dumbbells prepared to date. The dumbbells have exceptionally high thermal stability, whereas the nicked dumbbells are only marginally more stable than the hairpin structures on either side of the nick. The structures of the nicked dumbbells and dumbbells have been investigated using a combination of circular dichroism spectroscopy and molecular modeling. The base pair domains are found to adopt normal B'-DNA geometry and thus provide a helical ruler for studies of the distance and angular dependence of electronic interactions between the chromophore linkers.
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Affiliation(s)
- Ligang Zhang
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, USA
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Ogino M, Fujimoto K. Photochemical Synthesis of R-Shaped DNA toward DNA Recombination and Processing In Vitro. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200603161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Hannoush RN, Carriero S, Min KL, Damha MJ. Selective inhibition of HIV-1 reverse transcriptase (HIV-1 RT) RNase H by small RNA hairpins and dumbbells. Chembiochem 2004; 5:527-33. [PMID: 15185377 DOI: 10.1002/cbic.200300831] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We present here the design of a novel class of RNA inhibitors of the RNase H domain of HIV-1 RT, a ribonuclease activity that is essential for viral replication in vivo. Specifically, we show that small RNA hairpins and dumbbells can selectively inhibit the RNase H activity of HIV-1 RT without affecting other cellular RNases H (e.g., E. coli and human RNase H). These results suggest that the inhibitors do not interact with the nucleic acid binding site of RT RNase H, as this region should be well conserved among the various enzymes. The most potent inhibitors displayed IC50 values in the 3-8 microM range. Remarkably, the DNA polymerase activity, an intrinsic property of HIV RT, was not inhibited by the hairpin and dumbbell aptamers, a property not previously observed for any nucleic acid aptamer directed against RT RNase H. The results described here suggest a noncompetitive binding mechanism, as outlined in the differential inhibitory characteristics of each of the nucleic acid aptamers against the bacterial, human, and viral RNase H homologues.
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Affiliation(s)
- Rami N Hannoush
- Department of Chemistry, Otto Maass Chemistry Building, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 2K6, Canada
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Abstract
Nucleic acid "lariats" have been of great interest to the biological community since their discovery two decades ago as splicing intermediates in the biosynthesis of messenger RNA (lariat RNA introns). We report here the first synthesis of lariat DNA and RNA via template-mediated chemical ligation of Y-shaped oligonucleotides. The method allows for the synthesis of lariat DNA of any base composition as well as the more biologically relevant lariat RNA. Typically, branched precursors and complementary linear templates ("splints") were dissolved in an equimolar ratio at a total concentration of 10(-4) M, and ligation was promoted by addition of cyanogen bromide in a pH 7.6 buffer. The template-directed cyclization was very efficient, since the amount of circularized lariat product observed in all cases was in the 40-60% range. The lariats were purified by polyacrylamide gel electrophoresis, and their structure and nucleotide composition confirmed by MALDI-TOF mass spectrometry. Thermal denaturation and circular dichroism studies of lariat:RNA and lariat:DNA duplexes were fully supportive of the isolated "lasso" structures. Further characterization was conducted by enzymatic degradation with spleen phosphodiesterase (a 3'-exonuclease) and the RNA lariat debranching enzyme, a specific 2',5'-phosphodiesterase.
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Affiliation(s)
- Sandra Carriero
- Department of Chemistry, Otto Maass Chemistry Building, McGill University, 801 Sherbrooke Street West, Montreal, QC, H3A 2K6, Canada
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Abstract
Branched RNA molecules with a 2',5'-phosphodiester linkage are important biochemical intermediates. Lariat RNA is a particular type of branched RNA that is formed during intron splicing in vivo. Synthesis of branched and lariat RNA is challenging, and there are few general approaches that are applicable in vitro. Here we report the identification of divalent metal-dependent deoxyribozymes (DNA enzymes) that synthesize branched and lariat RNA. In vitro selection was used to obtain deoxyribozymes that selectively join an internal RNA 2'-hydroxyl with a 5'-terminal triphosphate in a convenient "binding arms" format. At least 85% yield of 2',5'-branched RNA is obtained at 37 degrees C and 20 mM Mn2+, pH 7.5 in </=30 min, and for some DNA enzymes in as little as 2 min (kobs approximately 0.1-2 min-1). This represents a rate enhancement of up to 5 million-fold over the background reaction. Lariat RNA is also synthesized by the new deoxyribozymes, which have significant potential as generalizable reagents for the practical preparation of branched and lariat RNA. Because nucleic acid enzymes apparently create branched RNA in nature (e.g., group II introns and the spliceosome), the new deoxyribozymes are of substantial mechanistic interest as well as practical importance.
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Affiliation(s)
- Yangming Wang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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