1
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Wang J, Feng Y, Sun T, Zhang Q, Chai Y. Photolabile 2-(2-Nitrophenyl)-propyloxycarbonyl (NPPOC) for Stereoselective Glycosylation and Its Application in Consecutive Assembly of Oligosaccharides. J Org Chem 2022; 87:3402-3421. [PMID: 35171610 DOI: 10.1021/acs.joc.1c03006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A photolabile protecting group (PPG) 2-(2-nitrophenyl)-propyloxycarbonyl (NPPOC) was explored in glycosylation and applied in the consecutive synthesis of oligosaccharides. NPPOC displays a strong neighboring group participation (NGP) effect to facilitate the construction of 1,2-trans glycosides in excellent yield. Notably, NPPOC could be efficiently removed by photolysis, and the deprotection conditions are friendly to typical protecting groups. A branched and asymmetric oligomannose Man6 was rapidly prepared, and the consecutive assembly of oligosaccharides without intermediate purification was further investigated owing to the compatibility conditions between NPPPOC's photolysis and glycosylation.
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Affiliation(s)
- Jincai Wang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education and School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China.,School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, P. R. China
| | - Yingle Feng
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education and School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China.,School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, P. R. China
| | - Taotao Sun
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education and School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China.,School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, P. R. China
| | - Qi Zhang
- School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, P. R. China
| | - Yonghai Chai
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education and School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, P. R. China.,School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, P. R. China
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2
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Lietard J, Leger A, Erlich Y, Sadowski N, Timp W, Somoza MM. Chemical and photochemical error rates in light-directed synthesis of complex DNA libraries. Nucleic Acids Res 2021; 49:6687-6701. [PMID: 34157124 PMCID: PMC8266620 DOI: 10.1093/nar/gkab505] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/24/2021] [Accepted: 06/17/2021] [Indexed: 11/30/2022] Open
Abstract
Nucleic acid microarrays are the only tools that can supply very large oligonucleotide libraries, cornerstones of the nascent fields of de novo gene assembly and DNA data storage. Although the chemical synthesis of oligonucleotides is highly developed and robust, it is not error free, requiring the design of methods that can correct or compensate for errors, or select for high-fidelity oligomers. However, outside the realm of array manufacturers, little is known about the sources of errors and their extent. In this study, we look at the error rate of DNA libraries synthesized by photolithography and dissect the proportion of deletion, insertion and substitution errors. We find that the deletion rate is governed by the photolysis yield. We identify the most important substitution error and correlate it to phosphoramidite coupling. Besides synthetic failures originating from the coupling cycle, we uncover the role of imperfections and limitations related to optics, highlight the importance of absorbing UV light to avoid internal reflections and chart the dependence of error rate on both position on the array and position within individual oligonucleotides. Being able to precisely quantify all types of errors will allow for optimal choice of fabrication parameters and array design.
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Affiliation(s)
- Jory Lietard
- Institute of Inorganic Chemistry, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Adrien Leger
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Norah Sadowski
- Johns Hopkins University, Department of Molecular Biology and Genetics, Baltimore, MD, USA
| | - Winston Timp
- Johns Hopkins University, Department of Molecular Biology and Genetics, Baltimore, MD, USA.,Johns Hopkins University, Departments of Biomedical Engineering, Molecular Biology and Genetics and Medicine, Division of Infectious Disease, Baltimore, MD, USA
| | - Mark M Somoza
- Institute of Inorganic Chemistry, University of Vienna, Althanstraße 14, 1090 Vienna, Austria.,Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany.,Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
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3
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Weinstain R, Slanina T, Kand D, Klán P. Visible-to-NIR-Light Activated Release: From Small Molecules to Nanomaterials. Chem Rev 2020; 120:13135-13272. [PMID: 33125209 PMCID: PMC7833475 DOI: 10.1021/acs.chemrev.0c00663] [Citation(s) in RCA: 242] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Indexed: 02/08/2023]
Abstract
Photoactivatable (alternatively, photoremovable, photoreleasable, or photocleavable) protecting groups (PPGs), also known as caged or photocaged compounds, are used to enable non-invasive spatiotemporal photochemical control over the release of species of interest. Recent years have seen the development of PPGs activatable by biologically and chemically benign visible and near-infrared (NIR) light. These long-wavelength-absorbing moieties expand the applicability of this powerful method and its accessibility to non-specialist users. This review comprehensively covers organic and transition metal-containing photoactivatable compounds (complexes) that absorb in the visible- and NIR-range to release various leaving groups and gasotransmitters (carbon monoxide, nitric oxide, and hydrogen sulfide). The text also covers visible- and NIR-light-induced photosensitized release using molecular sensitizers, quantum dots, and upconversion and second-harmonic nanoparticles, as well as release via photodynamic (photooxygenation by singlet oxygen) and photothermal effects. Release from photoactivatable polymers, micelles, vesicles, and photoswitches, along with the related emerging field of photopharmacology, is discussed at the end of the review.
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Affiliation(s)
- Roy Weinstain
- School
of Plant Sciences and Food Security, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Tomáš Slanina
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Dnyaneshwar Kand
- School
of Plant Sciences and Food Security, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Petr Klán
- Department
of Chemistry and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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4
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Jeong Y, Jwa DG, You A, Park S, Kim JG, Kang SM, Kim M. Photochemical Control of Polydopamine Coating in an Aprotic Organic Solvent. ASIAN J ORG CHEM 2019. [DOI: 10.1002/ajoc.201900246] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Yeonwoo Jeong
- Department of Chemistry and BK21Plus Research TeamChungbuk National University 1 Chungdae-ro Seowon-gu, Cheongju, Chungbuk 28644 Korea
| | - Dong Gyun Jwa
- Department of Chemistry and BK21Plus Research TeamChungbuk National University 1 Chungdae-ro Seowon-gu, Cheongju, Chungbuk 28644 Korea
| | - Ahrom You
- Department of Chemistry and BK21Plus Research TeamChungbuk National University 1 Chungdae-ro Seowon-gu, Cheongju, Chungbuk 28644 Korea
| | - Sora Park
- Department of Chemistry and Research Institute of Physics and ChemistryChonbuk National University 567 Baekje-DAero, Deokjin-gu, Jeonju Jeonbuk 54896 Korea
| | - Jeung Gon Kim
- Department of Chemistry and Research Institute of Physics and ChemistryChonbuk National University 567 Baekje-DAero, Deokjin-gu, Jeonju Jeonbuk 54896 Korea
| | - Sung Min Kang
- Department of Chemistry and BK21Plus Research TeamChungbuk National University 1 Chungdae-ro Seowon-gu, Cheongju, Chungbuk 28644 Korea
| | - Min Kim
- Department of Chemistry and BK21Plus Research TeamChungbuk National University 1 Chungdae-ro Seowon-gu, Cheongju, Chungbuk 28644 Korea
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5
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Zivic N, Kuroishi PK, Dumur F, Gigmes D, Dove AP, Sardon H. Recent Advances and Challenges in the Design of Organic Photoacid and Photobase Generators for Polymerizations. Angew Chem Int Ed Engl 2019; 58:10410-10422. [DOI: 10.1002/anie.201810118] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Nicolas Zivic
- POLYMATUniversity of the Basque Country UPV/EHUJose Mari Korta Center Avda Tolosa 72 20018 Donostia-San Sebastian Spain
| | - Paula K. Kuroishi
- Department of ChemistryUniversity of Warwick Coventry CV4 7AL UK
- School of ChemistryUniversity of Birmingham, Edgbaston Birmingham B15 2TT UK
| | - Frédéric Dumur
- Aix Marseille Univ, CNRS, ICR UMR7273 13397 Marseille France
| | - Didier Gigmes
- Aix Marseille Univ, CNRS, ICR UMR7273 13397 Marseille France
| | - Andrew P. Dove
- School of ChemistryUniversity of Birmingham, Edgbaston Birmingham B15 2TT UK
| | - Haritz Sardon
- POLYMATUniversity of the Basque Country UPV/EHUJose Mari Korta Center Avda Tolosa 72 20018 Donostia-San Sebastian Spain
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6
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Zivic N, Kuroishi PK, Dumur F, Gigmes D, Dove AP, Sardon H. Organische Photosäuren‐ und Photobasenbildner für Polymerisationen: Jüngste Fortschritte und Herausforderungen. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201810118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Nicolas Zivic
- POLYMATUniversity of the Basque Country UPV/EHUJose Mari Korta Center Avda Tolosa 72 20018 Donostia-San Sebastian Spanien
| | - Paula K. Kuroishi
- Department of ChemistryUniversity of Warwick Coventry CV4 7AL Großbritannien
- School of ChemistryUniversity of Birmingham, Edgbaston Birmingham B15 2TT Großbritannien
| | - Frédéric Dumur
- Aix Marseille Univ, CNRS, ICR UMR7273 13397 Marseille Frankreich
| | - Didier Gigmes
- Aix Marseille Univ, CNRS, ICR UMR7273 13397 Marseille Frankreich
| | - Andrew P. Dove
- School of ChemistryUniversity of Birmingham, Edgbaston Birmingham B15 2TT Großbritannien
| | - Haritz Sardon
- POLYMATUniversity of the Basque Country UPV/EHUJose Mari Korta Center Avda Tolosa 72 20018 Donostia-San Sebastian Spanien
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7
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Faggi E, Aguilera J, Sáez R, Pujol F, Marquet J, Hernando J, Sebastián RM. Wavelength-Tunable Light-Induced Polymerization of Cyanoacrylates Using Photogenerated Amines. Macromolecules 2019. [DOI: 10.1021/acs.macromol.8b02318] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Enrico Faggi
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Jordi Aguilera
- CUANTUM
Medical
Cosmetics S.L., 08193 Cerdanyola del Vallès, Spain
| | - Rubén Sáez
- CUANTUM
Medical
Cosmetics S.L., 08193 Cerdanyola del Vallès, Spain
| | - Ferran Pujol
- CUANTUM
Medical
Cosmetics S.L., 08193 Cerdanyola del Vallès, Spain
| | - Jordi Marquet
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Jordi Hernando
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Rosa María Sebastián
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
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8
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Hölz K, Hoi JK, Schaudy E, Somoza V, Lietard J, Somoza MM. High-Efficiency Reverse (5'→3') Synthesis of Complex DNA Microarrays. Sci Rep 2018; 8:15099. [PMID: 30305718 PMCID: PMC6180089 DOI: 10.1038/s41598-018-33311-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 09/26/2018] [Indexed: 11/18/2022] Open
Abstract
DNA microarrays are important analytical tools in genetics and have recently found multiple new biotechnological roles in applications requiring free 3' terminal hydroxyl groups, particularly as a starting point for enzymatic extension via DNA or RNA polymerases. Here we demonstrate the highly efficient reverse synthesis of complex DNA arrays using a photolithographic approach. The method is analogous to conventional solid phase synthesis but makes use of phosphoramidites with the benzoyl-2-(2-nitrophenyl)-propoxycarbonyl (BzNPPOC) photolabile protecting group on the 3'-hydroxyl group. The use of BzNPPOC, with more than twice the photolytic efficiency of the 2-(2-nitrophenyl)-propoxycarbonyl (NPPOC) previously used for 5'→3' synthesis, combined with additional optimizations to the coupling and oxidation reactions results in an approximately 3-fold improvement in the reverse synthesis efficiency of complex arrays of DNA oligonucleotides. The coupling efficiencies of the reverse phosphoramidites are as good as those of regular phosphoramidites, resulting in comparable yields. Microarrays of DNA surface tethered on the 5' end and with free 3' hydroxyl termini can be synthesized quickly and with similarly high stepwise coupling efficiency as microarrays using conventional 3'→5' synthesis.
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Affiliation(s)
- Kathrin Hölz
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Julia K Hoi
- Department of Physiological Chemistry, Christian Doppler Laboratory for Bioactive Aroma Compounds, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Erika Schaudy
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Veronika Somoza
- Department of Physiological Chemistry, Christian Doppler Laboratory for Bioactive Aroma Compounds, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Jory Lietard
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.
| | - Mark M Somoza
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.
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9
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Farahani PE, Adelmund SM, Shadish JA, DeForest CA. Photomediated oxime ligation as a bioorthogonal tool for spatiotemporally-controlled hydrogel formation and modification. J Mater Chem B 2017; 5:4435-4442. [PMID: 32263971 PMCID: PMC8296977 DOI: 10.1039/c6tb03400d] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Click chemistry has proved a valuable tool in biocompatible hydrogel formation for 3D cell culture, owing to its bioorthogonal nature and high efficiency under physiological conditions. While traditional click reactions can be readily employed to create uniform functional materials about living cells, their spontaneity prohibits spatiotemporal control of material properties, thereby limiting their utility in recapitulating the dynamic heterogeneity characteristic of the in vivo microenvironment. Photopolymerization-based techniques gain this desired level of 4D programmability, but often at the expense of introducing propagating free radicals that are prone to non-specific reactions with biological systems. Here we present a strategy for bioorthogonal hydrogel formation and modification that does not rely on propagating free radicals, proceeding through oxime ligation moderated by a photocaged alkoxyamine. Upon mild near UV light exposure, the photocage is cleaved, liberating the alkoxyamine and permitting localized condensation with an aldehyde. Multi-arm crosslinkers, functionalized with either benzaldehydes or photocaged alkoxyamines, formed oxime-based hydrogels within minutes of light exposure in the presence of live cells. Polymerization rates and final mechanical properties of these gels could be systematically tuned by varying crosslinker concentrations, light intensity, aniline catalyst equivalents, and pH. Moreover, hydrogel geometry and final mechanical properties were controlled by the location and extent of UV exposure, respectively. Photomediated oxime ligation was then translated to the biochemical modification of hydrogels, where full-length proteins containing photocaged alkoxyamines were immobilized in user-defined regions exposed to UV light. The programmability afforded by photomediated oxime ligation can recapitulate dynamically anisotropic mechanical and biochemical aspects of the native extracellular matrix. Consequently, photopolymerized oxime-based hydrogels are expected to enable an enhanced understanding of cell-matrix interactions by serving as improved 4D cell culture platforms.
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Affiliation(s)
- Payam E Farahani
- Department of Chemical Engineering, University of Washington, 4000 15th Ave NE, Seattle, WA 98195, USA.
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10
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Sack M, Hölz K, Holik AK, Kretschy N, Somoza V, Stengele KP, Somoza MM. Express photolithographic DNA microarray synthesis with optimized chemistry and high-efficiency photolabile groups. J Nanobiotechnology 2016; 14:14. [PMID: 26936369 PMCID: PMC4776362 DOI: 10.1186/s12951-016-0166-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 02/17/2016] [Indexed: 12/16/2022] Open
Abstract
Background DNA microarrays are a core element of modern genomics research and medical diagnostics, allowing the simple and simultaneous determination of the relative abundances of hundreds of thousands to millions of genomic DNA or RNA sequences in a sample. Photolithographic in situ synthesis, using light projection from a digitally-controlled array of micromirrors, has been successful at both commercial and laboratory scales. The advantages of this synthesis method are its ability to reliably produce high-quality custom microarrays with a very high spatial density of DNA features using a compact device with few moving parts. The phosphoramidite chemistry used in photolithographic synthesis is similar to that used in conventional solid-phase synthesis of oligonucleotides, but some unique differences require an independent optimization of the synthesis chemistry to achieve fast and low-cost synthesis without compromising microarray quality. Results High microarray quality could be maintained while reducing coupling time to a few seconds using DCI activator. Five coupling activators were compared, which resulted in microarray hybridization signals following the order ETT > Activator 42 > DCI ≫ BTT ≫ pyridinium chloride, but only the use of DCI led to both high signal and highly uniform feature intensities. The photodeprotection time was also reduced to a few seconds by replacing the NPPOC photolabile group with the new thiophenyl-NPPOC group. Other chemical parameters, such as oxidation and washing steps were also optimized. Conclusions Highly optimized and microarray-specific phosphoramidite chemistry, along with the use of the very photosensitive thiophenyl-NPPOC protecting group allow for the synthesis of high-complexity DNA arrays using coupling times of 15 s and deprotection times of 9 s. The resulting overall cycle time (coupling to coupling) of about 50 s, results in a three-fold reduction in synthesis time.
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Affiliation(s)
- Matej Sack
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.
| | - Kathrin Hölz
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.
| | - Ann-Katrin Holik
- Department of Nutritional and Physiological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.
| | - Nicole Kretschy
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.
| | - Veronika Somoza
- Department of Nutritional and Physiological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria. .,Christian Doppler Laboratory for Bioactive Aroma Compounds, University of Vienna, Vienna, Austria.
| | | | - Mark M Somoza
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.
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11
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Kretschy N, Holik AK, Somoza V, Stengele KP, Somoza MM. o-Nitrobenzyl-photolabile Gruppen der nächsten Generation in der lichtgesteuerten Chemie und der Synthese von Mikroarrays. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502125] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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12
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Kretschy N, Holik AK, Somoza V, Stengele KP, Somoza MM. Next-Generation o-Nitrobenzyl Photolabile Groups for Light-Directed Chemistry and Microarray Synthesis. Angew Chem Int Ed Engl 2015; 54:8555-9. [PMID: 26036777 PMCID: PMC4531821 DOI: 10.1002/anie.201502125] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Indexed: 01/11/2023]
Abstract
Light as an external trigger is a valuable and easily controllable tool for directing chemical reactions with high spatial and temporal accuracy. Two o-nitrobenzyl derivatives, benzoyl- and thiophenyl-NPPOC, undergo photo-deprotection with significantly improved efficiency over that of the commonly used NPPOC group. The two- and twelvefold increase in photo-deprotection efficiency was proven using photolithograph synthesis of microarrays.
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Affiliation(s)
- Nicole Kretschy
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Althanstrasse 14 (UZA II), 1090 Vienna (Austria)
| | - Ann-Katrin Holik
- Department of Nutritional and Physiological Chemistry, Faculty of Chemistry, University of Vienna (Austria)
| | - Veronika Somoza
- Department of Nutritional and Physiological Chemistry, Faculty of Chemistry, University of Vienna (Austria).,Christian Doppler Laboratory for Bioactive Aroma Compounds, University of Vienna (Austria)
| | | | - Mark M Somoza
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Althanstrasse 14 (UZA II), 1090 Vienna (Austria).
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13
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Wang G, Peng T, Zhang S, Wang J, Wen X, Yan H, Hu L, Wang L. 2-(2-Nitrophenyl) propyl: a rapidly released photolabile COOH-protecting group for solid-phase peptide synthesis. RSC Adv 2015. [DOI: 10.1039/c5ra01210d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We developed a new efficient photolabile protecting group, 2-(2-nitrophenyl) propyl (Npp) that blocks the carboxyl group in peptide synthesis.
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Affiliation(s)
- Gang Wang
- College of Life Science and Bio-engineering
- Beijing University of Technology
- Beijing
- P. R. China
- Beijing Institute of Radiation Medicine
| | - Tao Peng
- Beijing Institute of Radiation Medicine
- Beijing
- P. R. China
| | - Shouguo Zhang
- Beijing Institute of Radiation Medicine
- Beijing
- P. R. China
| | - Junyi Wang
- School of Basic Medical Sciences
- Peking University
- Beijing
- P. R. China
| | - Xiaoxue Wen
- Beijing Institute of Radiation Medicine
- Beijing
- P. R. China
| | - Haiyan Yan
- Beijing Institute of Radiation Medicine
- Beijing
- P. R. China
| | - Liming Hu
- College of Life Science and Bio-engineering
- Beijing University of Technology
- Beijing
- P. R. China
| | - Lin Wang
- College of Life Science and Bio-engineering
- Beijing University of Technology
- Beijing
- P. R. China
- Beijing Institute of Radiation Medicine
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14
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Xi W, Krieger M, Kloxin CJ, Bowman CN. A new photoclick reaction strategy: photo-induced catalysis of the thiol-Michael addition via a caged primary amine. Chem Commun (Camb) 2013; 49:4504-6. [DOI: 10.1039/c3cc41123k] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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Zhao H, Sterner ES, Coughlin EB, Theato P. o-Nitrobenzyl Alcohol Derivatives: Opportunities in Polymer and Materials Science. Macromolecules 2012. [DOI: 10.1021/ma201924h] [Citation(s) in RCA: 432] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Hui Zhao
- Institute for Technical and Macromolecular Chemistry, University of Hamburg, Bundesstrasse 45, D-20146 Hamburg, Germany
| | - Elizabeth S. Sterner
- Department of Polymer Science & Engineering, University of Massachusetts, 120 Governors Drive, Amherst, Massachusetts 01003-4530, United States
| | - E. Bryan Coughlin
- Department of Polymer Science & Engineering, University of Massachusetts, 120 Governors Drive, Amherst, Massachusetts 01003-4530, United States
| | - Patrick Theato
- Institute for Technical and Macromolecular Chemistry, University of Hamburg, Bundesstrasse 45, D-20146 Hamburg, Germany
- World Class University (WCU) program of Chemical Convergence for Energy & Environment (C2E2), School of Chemical and Biological Engineering, College of Engineering, Seoul National University (SNU), Seoul, Korea
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16
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Stupi BP, Li H, Wang J, Wu W, Morris SE, Litosh VA, Muniz J, Hersh MN, Metzker ML. Stereochemistry of benzylic carbon substitution coupled with ring modification of 2-nitrobenzyl groups as key determinants for fast-cleaving reversible terminators. Angew Chem Int Ed Engl 2012; 51:1724-7. [PMID: 22231919 PMCID: PMC3326374 DOI: 10.1002/anie.201106516] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Indexed: 01/20/2023]
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17
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Stupi BP, Li H, Wang J, Wu W, Morris SE, Litosh VA, Muniz J, Hersh MN, Metzker ML. Stereochemischer Verlauf einer Benzyl-Kohlenstoff-Substitution kombiniert mit Ringmodifikation der 2-Nitrobenzylgruppen als Schlüsselfaktoren für schnell spaltende, reversible Terminatoren. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201106516] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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18
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Chmielewski MK, Tykarska E, Markiewicz WT, Rypniewski W. Engineering N-(2-pyridyl)aminoethyl alcohols as potential precursors of thermolabile protecting groups. NEW J CHEM 2012. [DOI: 10.1039/c1nj20584f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Pirrung MC, Roy BG, Gadamsetty S. Structure-reactivity relationships in (2-hydroxyethyl)benzophenone photoremovable protecting Groups. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.02.087] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Cheng JY, Chen HY. Microfluidic ARray Synthesizer (MArS) for rapid preparation and hybridization of custom DNA microarray. Biotechnol Bioeng 2009; 104:400-7. [DOI: 10.1002/bit.22383] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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21
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Drexler K, Smirnova J, Galetskaya M, Voss S, Fonin M, Boneberg J, Rüdiger U, Leiderer P, Steiner UE. X-ray photoelectron spectroscopy- and surface plasmon resonance-detected photo release of photolabile protecting groups from nucleoside self-assembled monolayers on gold surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:10794-10801. [PMID: 19603744 DOI: 10.1021/la901346s] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The formation of self-assembled monolayers (SAMs) on gold by 2-(5-iodo-2-nitrophenyl) propoxycarbonyl (I-NPPOC)-protected thymidine with an attached mercaptohexyl succinate linker and the kinetics of photochemical release of the I-NPPOC group were monitored using X-ray photoelectron spectroscopy (XPS) and surface plasmon resonance (SPR) detection. In the XPS spectra, the iodine peaks allowed for specific and accurate monitoring of the presence and loss of I-NPPOC groups on the surface. In the SPR experiment, the overall signal change on photoillumination is in accord with a theoretical estimation of the density of I-NPPOC groups in a dense monolayer. The kinetics roughly follow a biexponential time dependence with two very different time constants, corresponding to photochemical quantum yields of 0.22 and 0.0032, respectively.
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Affiliation(s)
- Katja Drexler
- Department of Chemistry, University of Konstanz, Konstanz, Germany
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22
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Yi H, Maisonneuve S, Xie J. Synthesis, glycosylation and photolysis of photolabile 2-(2-nitrophenyl)propyloxycarbonyl (NPPOC) protected glycopyranosides. Org Biomol Chem 2009; 7:3847-54. [DOI: 10.1039/b908404e] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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23
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Wöll D, Smirnova J, Galetskaya M, Prykota T, Bühler J, Stengele KP, Pfleiderer W, Steiner UE. Intramolecular sensitization of photocleavage of the photolabile 2-(2-nitrophenyl)propoxycarbonyl (NPPOC) protecting group: photoproducts and photokinetics of the release of nucleosides. Chemistry 2008; 14:6490-7. [PMID: 18537211 DOI: 10.1002/chem.200800613] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Novel photolabile protecting groups based on the 2-(2-nitrophenyl)propoxycarbonyl (NPPOC) group with a covalently linked thioxanthone as an intramolecular triplet sensitizer exhibit significantly enhanced light sensitivity under continuous illumination. Herein we present a detailed study of the photokinetics and photoproducts of nucleosides caged with these new protecting groups. Relative to the parent NPPOC group, the light sensitivity of the new photolabile protecting groups is enhanced by up to a factor of 21 at 366 nm and is still quite high at 405 nm, the wavelength at which the sensitivity of the parent compound is practically zero. A new pathway for deprotection of the NPPOC group proceeding through a nitroso benzylalcohol intermediate has been discovered to complement the main mechanism, which involves beta elimination. Under standard conditions of lithographic DNA-chip synthesis, some of the new compounds, while maintaining the same chip quality, react ten times faster than the unmodified NPPOC-protected nucleosides.
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Affiliation(s)
- Dominik Wöll
- Fachbereich Chemie, Universität Konstanz, Universitätsstrasse 10, Konstanz, Germany.
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24
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Beier M, Hoheisel JD. Synthesis of 5'-O-phosphoramidites with a photolabile 3'-O-protecting group. ACTA ACUST UNITED AC 2008; Chapter 12:Unit 12.3. [PMID: 18428919 DOI: 10.1002/0471142700.nc1203s17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
This unit describes the chemical synthesis of phosphoramidite building blocks that carry a protecting group at the 3' position. These inversely oriented synthons expose a 2-(2-nitrophenyl)propoxycarbonyl (NPPOC) group as the photolabile protecting group of choice. Among other applications, the building blocks can be employed for light-controlled in situ synthesis of DNA microarrays, producing arrayed oligonucleotides that are attached to the support via their 5' ends, leaving their 3' termini available to act as substrates for polymerases.
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Affiliation(s)
- Markus Beier
- Deutsches Krebsforschungszentrum, Heidelberg, Germany
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25
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Wöll D, Laimgruber S, Galetskaya M, Smirnova J, Pfleiderer W, Heinz B, Gilch P, Steiner UE. On the Mechanism of Intramolecular Sensitization of Photocleavage of the 2-(2-Nitrophenyl)propoxycarbonyl (NPPOC) Protecting Group. J Am Chem Soc 2007; 129:12148-58. [PMID: 17877342 DOI: 10.1021/ja072355p] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A spectroscopic study of a variety of covalently linked thioxanthone(TX)-linker-2-(2-nitrophenyl)propoxycarbonyl(NPPOC)-substrate conjugates is presented. Herein, the TX chromophore functions as an intramolecular sensitizer to the NPPOC moiety, a photolabile protecting group used in photolithographic DNA chip synthesis. The rate of electronic energy transfer between TX and NPPOC was quantified by means of stationary fluorescence as well as nanosecond and femtosecond time-resolved laser spectroscopy. A dual mechanism of triplet-triplet energy transfer has been observed comprising a slower mechanism involving the T1(pipi*) state of TX with linker-length-dependent time constants longer than 20 ns and a fast mechanism with linker-length-dependent time constants shorter than 3 ns. Evidence is provided that the latter mechanism is due to energy transfer from the T2(npi*) state which is in fast equilibrium with the fluorescent S1(pipi*) state. In the case of direct linkage between the aromatic rings of TX and NPPOC, the spectroscopic properties are indicative of one united chromophore which, however, still shows the typical NPPOC cleavage reaction triggered by intramolecular hydrogen atom transfer to the nitro group.
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Affiliation(s)
- Dominik Wöll
- Contribution from the Fachbereich Chemie, Universität Konstanz, 78465 Konstanz, Germany
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26
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Flickinger ST, Patel M, Binkowski BF, Lowe AM, Li MH, Kim C, Cerrina F, Belshaw PJ. Spatial photorelease of oligonucleotides, using a safety-catch photolabile linker. Org Lett 2007; 8:2357-60. [PMID: 16706525 DOI: 10.1021/ol060644x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[reaction: see text] We report the development of a safety-catch photolabile linker that allows the light-directed synthesis and spatially selective photorelease of oligonucleotides from microarrays. The linker remains stable to light during DNA synthesis, and is activated for photorelease after acidic hydrolysis. We demonstrate that the photoreleased oligonucleotides can be amplified by PCR to produce double stranded DNA. The advantages offered by this linker could aid the development of an automated gene synthesis platform.
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Affiliation(s)
- Shane T Flickinger
- The Department of Chemistry, University of Wisconsin-Madison, 53706, USA
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27
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Kröck L, Heckel A. Photoinduced transcription by using temporarily mismatched caged oligonucleotides. Angew Chem Int Ed Engl 2006; 44:471-3. [PMID: 15624132 DOI: 10.1002/anie.200461779] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Lenz Kröck
- Rheinische Friedrich-Wilhelms-Universität Bonn, Kekulé-Institut für Organische Chemie und Biochemie, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
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28
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Wöll D, Smirnova J, Pfleiderer W, Steiner UE. Highly Efficient Photolabile Protecting Groups with Intramolecular Energy Transfer. Angew Chem Int Ed Engl 2006; 45:2975-8. [PMID: 16555354 DOI: 10.1002/anie.200504091] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Dominik Wöll
- Fachbereich Chemie, Universität Konstanz, Universitätstrasse 10, 78464 Konstanz, Germany
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29
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Wöll D, Smirnova J, Pfleiderer W, Steiner UE. Hocheffiziente photolabile Schutzgruppen mit intramolekularem Energietransfer. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200504091] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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30
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Smirnova J, Wöll D, Pfleiderer W, Steiner U. Synthesis of Caged Nucleosides with Photoremovable Protecting Groups Linked to Intramolecular Antennae. Helv Chim Acta 2005. [DOI: 10.1002/hlca.200590067] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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31
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Beier M, Hoheisel JD. DNA Microarray Preparation by Light‐Controlled In Situ Synthesis. ACTA ACUST UNITED AC 2005; Chapter 12:Unit 12.5. [DOI: 10.1002/0471142700.nc1205s20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Markus Beier
- Deutsches Krebsforschungszentrum Heidelberg Germany
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32
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Suzuki I, Uno S, Tsuchiya Y, Shigenaga A, Nemoto H, Shibuya M. Synthesis and DNA damaging ability of enediyne model compounds possessing photo-triggering devices. Bioorg Med Chem Lett 2005; 14:2959-62. [PMID: 15125968 DOI: 10.1016/j.bmcl.2004.02.096] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2004] [Accepted: 02/28/2004] [Indexed: 10/26/2022]
Abstract
Enediyne model compounds possessing photo-triggering devices were developed. These enediynes afforded biradicals by UV irradiation and showed DNA cleaving activity. The DNA damage was confirmed to be mainly caused by the biradical, not singlet oxygen.
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Affiliation(s)
- Ichiro Suzuki
- Faculty of Pharmaceutical Sciences, University of Tokushima, Sho-machi 1-78, Tokushima, Japan.
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33
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Papageorgiou G, Barth A, Corrie JET. Flash photolytic release of alcohols from photolabile carbamates or carbonates is rate-limited by decarboxylation of the photoproduct. Photochem Photobiol Sci 2005; 4:216-20. [PMID: 15696240 DOI: 10.1039/b417153e] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Flash photolysis of a 7-nitroindolinyl carbamate derivative in neutral aqueous solution rapidly generated a monoalkyl carbonate salt. The rate constant for subsequent decarboxylation of this salt [mono(2-phosphoryloxyethyl) carbonate], determined by rapid scan IR difference spectroscopy, was 0.4 s(-1) at pH 7.0, 20 degrees C. This rate reflects release of the product alcohol upon photolysis of the parent compound. In general, alcohols protected as photolabile carbamate (or carbonate) derivatives will therefore be released too slowly for studies of the kinetics of millisecond time scale biological processes.
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Affiliation(s)
- George Papageorgiou
- National Institute for Medical Research, The Ridgeway, Mill Hill, London, UK NW7 1AA
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34
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Kröck L, Heckel A. Lichtinduzierte Transkription mit vorübergehend fehlgepaarten Oligonucleotiden. Angew Chem Int Ed Engl 2004. [DOI: 10.1002/ange.200461779] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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35
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Marchán V, Cieślak J, Livengood V, Beaucage SL. 2,2,5,5-tetramethylpyrrolidin-3-one-1-sulfinyl group for 5'-hydroxyl protection of deoxyribonucleoside phosphoramidites in the solid-phase preparation of DNA oligonucleotides. J Am Chem Soc 2004; 126:9601-10. [PMID: 15291564 DOI: 10.1021/ja048377i] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Several nitrogen-sulfur reagents have been investigated as potential 5'-hydroxyl protecting groups for deoxyribonucleoside phosphoramidites to improve the synthesis of oligonucleotides on glass microarrays. Out of the nitrogen-sulfur-based protecting groups so far investigated, the 2,2,5,5-tetramethylpyrrolidin-3-one-1-sulfinyl group exhibited near optimal properties for 5'-hydroxyl protection by virtue of the mildness of its deprotection conditions. Specifically, the iterative cleavage of a terminal 5'-sulfamidite group in the synthesis of 5'-d(ATCCGTAGCCAAGGTCATGT) on controlled-pore glass is efficiently accomplished by treatment with iodine in the presence of an acidic salt. Hydrolysis of the oligonucleotide to its 2'-deoxyribonucleosides upon exposure to snake venom phosphodiesterase and bacterial alkaline phosphatase did not reveal the formation of any nucleobase adducts or other modifications. These findings indicate that the 2,2,5,5-tetramethylpyrrolidin-3-one-1-sulfinyl group for 5'-hydroxyl protection of phosphoramidites, such as 10a-d, may lead to the production of oligonucleotide microarrays exhibiting enhanced specificity and sensitivity in the detection of nucleic acid targets.
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Affiliation(s)
- Vicente Marchán
- Division of Therapeutic Proteins, Center for Drug Evalution and Research, Food and Drug Administration, 8800 Rockville Pike, Bethesda, Maryland 20892, USA
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36
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Abstract
This contribution presents a brief overall look of the methods for the preparation of various types of DNA microarrays and a thorough examination of the methods for in situ synthesis of oligonucleotide microarrays.
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Affiliation(s)
- Xiaolian Gao
- Department of Chemistry, University of Houston, Houston, TX 77004-5003, USA.
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37
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Chmielewski MK, Marchán V, Cieślak J, Grajkowski A, Livengood V, Münch U, Wilk A, Beaucage SL. Thermolytic carbonates for potential 5'-hydroxyl protection of deoxyribonucleosides. J Org Chem 2004; 68:10003-12. [PMID: 14682694 DOI: 10.1021/jo035089g] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thermolytic groups structurally related to well-studied heat-sensitive phosphate/thiophosphate protecting groups have been evaluated for 5'-hydroxyl protection of deoxyribonucleosides as carbonates and for potential use in solid-phase oligonucleotide synthesis. The spatial arrangement of selected functional groups forming an asymmetric nucleosidic 5'-O-carbonic acid ester has been designed to enable heat-induced cyclodecarbonation reactions, which would result in the release of carbon dioxide and the generation of a nucleosidic 5'-hydroxyl group. The nucleosidic 5'-O-carbonates 3-8, 10-15, and 19-21 were prepared and were isolated in yields ranging from 45 to 83%. Thermolytic deprotection of these carbonates is preferably performed in aqueous organic solvent at 90 degrees C under near neutral conditions. The rates of carbonate deprotection are dependent on the nucleophilicity of the functional group involved in the postulated cyclodecarbonation reaction and on solvent polarity. Deprotection kinetics increase according to the following order: 4 < 5 < 10 < 6 < 12 < 7 < 13 < 8 < 14 congruent with 19-21 and CCl4 < dioxane < MeCN < t-BuOH < MeCN:phosphate buffer (3:1 v/v, pH 7.0) < EtOH:phosphate buffer (1:1 v/v, pH 7.0). Complete thermolytic deprotection of carbonates 7, 8, 13, and 14 is achieved within 20 min to 2 h under optimal conditions in phosphate buffer-MeCN. The 2-(2-pyridyl)amino-1-phenylethyl and 2-[N-methyl-N-(2-pyridyl)]aminoethyl groups are particularly promising for 5'-hydroxyl protection of deoxyribonucleosides as thermolytic carbonates.
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Affiliation(s)
- Marcin K Chmielewski
- Division of Therapeutic Proteins, Center for Biologics Evaluation and Research, Food and Drug Administration, 8800 Rockville Pike, Bethesda, Maryland 20892, USA
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38
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Wöll D, Walbert S, Stengele KP, Green R, Albert T, Pfleiderer W, Steiner UE. More efficient photolithographic synthesis of DNA-chips by photosensitization. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2003; 22:1395-8. [PMID: 14565427 DOI: 10.1081/ncn-120022994] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- D Wöll
- University of Konstanz, Konstanz, Germany
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39
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Abstract
Several analogues of the 9-phenylthioxanthyl (S-pixyl) photocleavable protecting group have been synthesized, containing substituents on the 9-aryl ring and on the thioxanthyl backbone. Each analogue protected the 5'-hydroxy moiety of thymidine in good to excellent yield. The protected substrates were deprotected in 1:1 water:acetonitrile with irradiation at 300 nm, resulting in recovered thymidine in excellent yield, except for the nitro-substituted analogues which gave substantially lower yields. Substrates with 2,7-dibromo or 3-methoxy substitution on the thioxanthyl backbone were also deprotected efficiently with irradiation at 350 nm. Shorter irradiation times were observed in the less nucleophilic solvent mixture of 1:9 trifluoroethanol:acetonitrile, with no formation of secondary photooxidation products. Photodeprotection with high yields was also achieved in the absence of solvent, with no secondary photoproducts.
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Affiliation(s)
- Michael P Coleman
- Department of Chemistry, Loyola University Chicago, Illinois 60626, USA
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40
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Abstract
In this review, recent advances in DNA microarray technology and their applications are examined. The many varieties of DNA microarray or DNA chip devices and systems are described along with their methods for fabrication and their use. This includes both high-density microarrays for high-throughput screening applications and lower-density microarrays for various diagnostic applications. The methods for microarray fabrication that are reviewed include various inkjet and microjet deposition or spotting technologies and processes, in situ or on-chip photolithographic oligonucleotide synthesis processes, and electronic DNA probe addressing processes. The DNA microarray hybridization applications reviewed include the important areas of gene expression analysis and genotyping for point mutations, single nucleotide polymorphisms (SNPs), and short tandem repeats (STRs). In addition to the many molecular biological and genomic research uses, this review covers applications of microarray devices and systems for pharmacogenomic research and drug discovery, infectious and genetic disease and cancer diagnostics, and forensic and genetic identification purposes. Additionally, microarray technology being developed and applied to new areas of proteomic and cellular analysis are reviewed.
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Affiliation(s)
- Michael J Heller
- Department of Bioengineering/Electronic, University of California, San Diego, La Jolla 92093, USA.
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41
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Pelliccioli AP, Wirz J. Photoremovable protecting groups: reaction mechanisms and applications. Photochem Photobiol Sci 2002; 1:441-58. [PMID: 12659154 DOI: 10.1039/b200777k] [Citation(s) in RCA: 538] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photolabile protecting groups enable biochemists to control the release of bioactive compounds in living tissue. 'Caged compounds' (photoactivatable bioagents) have become an important tool to study the events that follow chemical signalling in, e.g., cell biology and the neurosciences. The possibilities are by no means exhausted. Progress will depend on the development of photoremovable protecting groups that satisfy the diverse requirements of new applications--a challenging task for photochemists.
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Affiliation(s)
- Anna Paola Pelliccioli
- Institut für Physikalische Chemie, Universität Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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42
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Pirrung MC, Wang L, Montague-Smith MP. 3'-nitrophenylpropyloxycarbonyl (NPPOC) protecting groups for high-fidelity automated 5' --> 3' photochemical DNA synthesis. Org Lett 2001; 3:1105-8. [PMID: 11348170 DOI: 10.1021/ol0069150] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[structure: see text]. The most powerful DNA microarrays would be prepared by photolithography with free 3'-ends that could be processed enzymatically. A photoremovable group that could be removed in quantitative yield would ensure high purity of the synthesized probes. We have developed new pyrimidine building blocks for 5' --> 3' DNA synthesis with high cycle yields using the NPPOC (3'-nitrophenylpropyloxycarbonyl) protecting group. These phosphoramidites were proved in automated photochemical DNA synthesis on a modified synthesizer.
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Affiliation(s)
- M C Pirrung
- Department of Chemistry, Levine Science Research Center, Duke University, Box 90317, Durham, North Carolina 27708, USA.
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