151
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Cheng G, Zeng X, Shen J, Wang X, Cui X. A metal-free multicomponent cascade reaction for the regiospecific synthesis of 1,5-disubstituted 1,2,3-triazoles. Angew Chem Int Ed Engl 2013; 52:13265-8. [PMID: 24227395 DOI: 10.1002/anie.201307499] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 10/11/2013] [Indexed: 01/02/2023]
Affiliation(s)
- Guolin Cheng
- Engineering Research Center of Molecular Medicine, Ministry of Education, Key Laboratory of Xiamen Marine and Gene Drugs, Institutes of Molecular Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen 361021 (P. R. China)
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152
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Li L, Hao G, Zhu A, Liu S, Zhang G. Three-component assembly of 5-halo-1,2,3-triazoles via aerobic oxidative halogenation. Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2013.08.089] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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153
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Abstract
RNA molecules are highly modular components that can be used in a variety of contexts for building new metabolic, regulatory and genetic circuits in cells. The majority of synthetic RNA systems to date predominately rely on two-dimensional modularity. However, a better understanding and integration of three-dimensional RNA modularity at structural and functional levels is critical to the development of more complex, functional bio-systems and molecular machines for synthetic biology applications.
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Affiliation(s)
- Wade Grabow
- Department of Chemistry and Biochemistry, Seattle Pacific University3307 Third Avenue West, Seattle, WA 98119USA
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, Bio-Molecular Science and Engineering Program, University of CaliforniaSanta Barbara, CA 93106-9510USA
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154
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Abstract
Diazo compounds are in widespread use in synthetic organic chemistry but have untapped potential in chemical biology. We report on the design and optimization of a phosphinoester that mediates the efficient conversion of azides into diazo compounds in phosphate buffer at neutral pH and room temperature. High yields are maintained in the presence of common nucleophilic or electrophilic functional groups, and reaction progress can be monitored by colorimetry. As azido groups are easy to install and maintain in biopolymers or their ligands, this new mode of azide reactivity could have substantial utility in chemical biology.
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Affiliation(s)
- Ho-Hsuan Chou
- Department of Chemistry and ∥Department of Biochemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
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155
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Kayet A, Pathak T. 1,5-Disubstituted 1,2,3-Triazolylation at C1, C2, C3, C4, and C6 of Pyranosides: A Metal-Free Route to Triazolylated Monosaccharides and Triazole-Linked Disaccharides. J Org Chem 2013; 78:9865-75. [DOI: 10.1021/jo401576n] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Anirban Kayet
- Department
of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721 302, India
| | - Tanmaya Pathak
- Department
of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721 302, India
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156
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Heuer-Jungemann A, Kirkwood R, El-Sagheer AH, Brown T, Kanaras AG. Copper-free click chemistry as an emerging tool for the programmed ligation of DNA-functionalised gold nanoparticles. NANOSCALE 2013; 5:7209-7212. [PMID: 23828172 DOI: 10.1039/c3nr02362a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We demonstrate a new method to program the ligation of single stranded DNA-modified gold nanoparticles using copper-free click chemistry. Gold nanoparticles functionalized with a discrete number of 3'-azide or 5'-alkyne modified oligonucleotides, can be brought together via a splint strand and covalently 'clicked', in a simple one-pot reaction. This new approach to the assembly of gold nanoparticles is inherently advantageous in comparison to the traditional enzymatic ligation. The chemical ligation is specific and takes place at room temperature by simply mixing the particles without the need for special enzymatic conditions. The yield of 'clicked' nanoparticles can be as high as 92%. The ease of the copper-free, 'click-ligation' method allows for its universal applicability and opens up new avenues in programmed nanoparticle organization.
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Affiliation(s)
- Amelie Heuer-Jungemann
- Physics and Astronomy, Faculty of Physical Sciences and Engineering, University of Southampton, Southampton, SO17 1BJ, UK
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157
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White JD, Osborn MF, Moghaddam AD, Guzman LE, Haley MM, DeRose VJ. Picazoplatin, an azide-containing platinum(II) derivative for target analysis by click chemistry. J Am Chem Soc 2013; 135:11680-3. [PMID: 23879391 PMCID: PMC4130293 DOI: 10.1021/ja402453k] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Despite the broad use of platinum-based chemotherapeutics, identification of their full range of cellular targets remains a significant challenge. In order to identify, visualize, and isolate cellular targets of Pt(II) complexes, we have modified the chemotherapeutic drug picoplatin with an azide moiety for subsequent click reactivity. The new compound picazoplatin readily binds DNA and RNA oligonucleotides and undergoes facile post-labeling click reactions to alkyne-fluorophore conjugates. Pt-fluorophore click reactions in rRNA purified from drug-treated Saccharomyces cerevisiae demonstrate its potential for future in vivo efforts.
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Affiliation(s)
| | | | - Alan D. Moghaddam
- Department of Chemistry and Institute of Molecular Biology, University of Oregon, Eugene, OR 97403-1253 USA
| | - Lindsay E. Guzman
- Department of Chemistry and Institute of Molecular Biology, University of Oregon, Eugene, OR 97403-1253 USA
| | - Michael M. Haley
- Department of Chemistry and Institute of Molecular Biology, University of Oregon, Eugene, OR 97403-1253 USA
| | - Victoria J. DeRose
- Department of Chemistry and Institute of Molecular Biology, University of Oregon, Eugene, OR 97403-1253 USA
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158
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Stolz RM, Northrop BH. Experimental and Theoretical Studies of Selective Thiol–Ene and Thiol–Yne Click Reactions Involving N-Substituted Maleimides. J Org Chem 2013; 78:8105-16. [DOI: 10.1021/jo4014436] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Robert M. Stolz
- Department of Chemistry, Wesleyan University, Middletown, Connecticut
06459, United States
| | - Brian H. Northrop
- Department of Chemistry, Wesleyan University, Middletown, Connecticut
06459, United States
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159
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Jawalekar AM, Malik S, Verkade JMM, Gibson B, Barta NS, Hodges JC, Rowan A, van Delft FL. Oligonucleotide tagging for copper-free click conjugation. Molecules 2013; 18:7346-63. [PMID: 23884112 PMCID: PMC6270431 DOI: 10.3390/molecules18077346] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 05/24/2013] [Accepted: 06/05/2013] [Indexed: 01/24/2023] Open
Abstract
Copper-free click chemistry between cyclooctynes and azide is a mild, fast and selective technology for conjugation of oligonucleotides. However, technology for site-specific introduction of the requisite probes by automated protocols is scarce, while the reported cyclooctynes are large and hydrophobic. In this work, it is demonstrated that the introduction of bicyclo[6.1.0]nonyne (BCN) into synthetic oligonucleotides is feasible by standard solid-phase phosphoramidite chemistry. A range of phosphoramidite building blocks is presented for incoporation of BCN or azide, either on-support or in solution. The usefulness of the approach is demonstrated by the straightforward and high-yielding conjugation of the resulting oligonucleotides, including biotinylation, fluorescent labeling, dimerization and attachment to polymer.
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Affiliation(s)
- Anup M. Jawalekar
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands; E-Mails: (A.M.J.); (S.M.); (A.R.)
| | - Sudip Malik
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands; E-Mails: (A.M.J.); (S.M.); (A.R.)
| | | | - Brian Gibson
- Berry and Associates, Inc., 2434 Bishop Circle East, Dexter, MI 48130, USA; E-Mails: (B.G.); (N.S.B.); (J.C.H.)
| | - Nancy S. Barta
- Berry and Associates, Inc., 2434 Bishop Circle East, Dexter, MI 48130, USA; E-Mails: (B.G.); (N.S.B.); (J.C.H.)
| | - John C. Hodges
- Berry and Associates, Inc., 2434 Bishop Circle East, Dexter, MI 48130, USA; E-Mails: (B.G.); (N.S.B.); (J.C.H.)
| | - Alan Rowan
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands; E-Mails: (A.M.J.); (S.M.); (A.R.)
| | - Floris L. van Delft
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands; E-Mails: (A.M.J.); (S.M.); (A.R.)
- SynAffix BV, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands; E-Mail:
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160
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Varizhuk AM, Kaluzhny DN, Novikov RA, Chizhov AO, Smirnov IP, Chuvilin AN, Tatarinova ON, Fisunov GY, Pozmogova GE, Florentiev VL. Synthesis of triazole-linked oligonucleotides with high affinity to DNA complements and an analysis of their compatibility with biosystems. J Org Chem 2013; 78:5964-9. [PMID: 23724994 DOI: 10.1021/jo400651k] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
New oligonucleotide analogues with triazole internucleotide linkages were synthesized, and their hybridization properties were studied. The analogues demonstrated DNA binding affinities similar to those of unmodified oligonucleotides. The modification was shown to protect the oligonucleotides from nuclease hydrolysis. The modified oligonucleotides were tested as PCR primers. Modifications remote from the 3'-terminus were tolerated by polymerases. Our results suggest that these new oligonucleotide analogues are among the most promising triazole DNA mimics characterized to date.
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Affiliation(s)
- Anna M Varizhuk
- Institute for Physical-Chemical Medicine of Ministry of Public Health, Malaya Pirogovskaya str. 1a, 117312 Moscow, Russia.
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161
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Astakhova IK, Kumar TS, Campbell MA, Ustinov AV, Korshun VA, Wengel J. Branched DNA nanostructures efficiently stabilised and monitored by novel pyrene-perylene 2'-α-L-amino-LNA FRET pairs. Chem Commun (Camb) 2013. [PMID: 23201901 DOI: 10.1039/c2cc37547h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Novel pyrene-perylene α-L-LNA FRET pairs described herein effectively detect assembly of 2- and 3-way branched DNA nanostructures prepared by postsynthetic microwave-assisted CuAAC click chemistry. The fluorescent signalling of assembly by internally positioned FRET pairs is achieved with low to no fluorescence background signal, remarkably low limit of target detection values and stabilization of the resulting nanostructures.
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Affiliation(s)
- I Kira Astakhova
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark.
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162
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Casarrubios L, de la Torre MC, Sierra MA. The “Click” Reaction Involving Metal Azides, Metal Alkynes, or Both: An Exploration into Multimetal Structures. Chemistry 2013; 19:3534-41. [DOI: 10.1002/chem.201204596] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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163
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Astakhova IK, Pasternak K, Campbell MA, Gupta P, Wengel J. A locked nucleic acid-based nanocrawler: designed and reversible movement detected by multicolor fluorescence. J Am Chem Soc 2013; 135:2423-6. [PMID: 23379691 DOI: 10.1021/ja311250w] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Herein we introduce a novel fluorescent LNA/DNA machine, a nanocrawler, which reversibly moves along a directionally polar complementary road controlled by affinity-enhancing locked nucleic acid (LNA) monomers and additional regulatory strands. Polyaromatic hydrocarbon (PAH) dyes attached to 2'-amino-LNA monomers are incorporated at four stations of the system, enabling simple detection of the position of the nanocrawler via a step-specific color signal. The sensing is provided by highly sensitive, chemically stable, and photostable PAH LNA interstrand communication systems, including pyrene excimer formation and pyrene-perylene interstrand Förster resonance energy transfer. We furthermore demonstrate that the nanocrawler selectively and reversibly moves along the road, followed by a bright and consistent fluorescence response for up to 10 cycles without any loss of signal.
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Affiliation(s)
- I Kira Astakhova
- Nucleic Acid Center and Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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164
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Abdo M, Sun Z, Knapp S. Biohybrid -Se-S- coupling reactions of an amino acid derived seleninate. Molecules 2013; 18:1963-72. [PMID: 23381022 PMCID: PMC6270073 DOI: 10.3390/molecules18021963] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 01/28/2013] [Accepted: 01/30/2013] [Indexed: 11/24/2022] Open
Abstract
We describe the synthesis of the N-(2-seleninatoethyl) amide of N-Boc-phenylalanine, serving here as a peptide model, and its reductive coupling reactions under mild conditions with unprotected thiouridine and glutathione. Selenosulfide products such as these comprise reversibly conjugated bio-components, and can potentially find uses as probes of biological function, such as enzyme inhibitors, delivery systems, or structural mimics.
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Affiliation(s)
| | | | - Spencer Knapp
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-732-445-2627; Fax: +1-732-445-5312
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165
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MoradpourHafshejani S, Hedley JH, Haigh AO, Pike AR, Tuite EM. Synthesis and binding of proflavine diazides as functional intercalators for directed assembly on DNA. RSC Adv 2013. [DOI: 10.1039/c3ra43090a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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166
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Freeman C, Vyle JS, Heaney F. Oligo switches: photoresponsive oligonucleotide conjugates by solid-supported click chemistry. RSC Adv 2013. [DOI: 10.1039/c2ra22815g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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167
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Debets MF, van Hest JCM, Rutjes FPJT. Bioorthogonal labelling of biomolecules: new functional handles and ligation methods. Org Biomol Chem 2013; 11:6439-55. [PMID: 23969529 DOI: 10.1039/c3ob41329b] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Marjoke F Debets
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands.
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