1
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Ghosh U, Gupta S, Sinha S. Synthesis of 5'-Thiol Functionalized Morpholino Oligo-Nucleotide and Subsequent Conjugation with IGT to Improve Delivery and Antisense Efficacy In Vitro. Bioconjug Chem 2023; 34:174-180. [PMID: 36538654 DOI: 10.1021/acs.bioconjchem.2c00587] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Thiol functionalized oligonucleotides are useful intermediates for a wide range of applications including DNA nanobiotechnology field through conjugation with various types of probes and cargos. Due to the limitation of synthetic process, phosphorodiamidate morpholino oligonucleotides (PMOs) have not been explored like other oligonucleotides through SH conjugation as mentioned above. In this paper, we report the synthesis of 5'-SH functionalized PMO using a solid support synthesis protocol with an optimized cysteine derived linker so that loading and coupling efficiency of morpholino monomers were effective enough to get a 25-mer 5'-SH functionalized PMO against human Nanog. The PMO with SH functionality was subsequently conjugated with our previously reported Internal Oligo-guanidinium Transporter (IGT) in solution phase to obtain the IGT-PMO conjugate. Interestingly, 5'-conjugated PMO (IGT-PMO) showed 2.5 times better antisense efficacy than 3'-conjugated PMO with IGT (PMO-IGT). 5'-Conjugation enables us to use IGT-PMO for further conjugation at the 3'-N terminal of PMO which was not possible earlier with 5'-OH-PMO-IGT. PMO has become an important class of antisense reagents because four PMO-based drugs have been approved for the treatment of Duchenne muscular dystrophy; hence such an improved result with 5'-modified PMO could be useful for enhancing the therapeutic efficacy of DMD drugs. Similarly, thiol-modified PMO could also be explored like other thiol-containing oligonucleotides for various other applications.
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Affiliation(s)
- Ujjwal Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, West Bengal, India
| | - Shalini Gupta
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, West Bengal, India
| | - Surajit Sinha
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, West Bengal, India
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2
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Modular synthesis of diphosphoramidite ligands derived from 1,8,10,9-triazaboradecalin and their complexes with Ni, Pd, and Pt. Polyhedron 2022. [DOI: 10.1016/j.poly.2022.115877] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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3
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Wang J, Shang J, Xiang Y, Tong A. Post-Synthetic Modification of Oligonucleotides Through Oxidative Amination of 4-Thio-2'-Deoxyuridine. Curr Protoc 2021; 1:e274. [PMID: 34644451 DOI: 10.1002/cpz1.274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Functionalized oligonucleotides (ONs) are widely applied as target recognition molecules for biosensing and gene regulation. Herein, we describe a general method for post-synthetic modification of ONs based on the oxidative amination of 4-thio-2'-deoxyuridine (4SdU) with sodium periodate and several amines. Alkyne-/azide-, biotin-, and fluorophore-modified ONs were prepared by modifying 4SdU-containing ONs with the corresponding amines and characterized for their bioorthogonal reactivity, streptavidin-binding affinity, and fluorescence properties, respectively. We synthesized three fluorophore-modified ONs with and without the aromatic fluorophores conjugated to modified nucleobases and investigated their emission properties. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Post-synthetic modification of ONs Supporting Protocol: Preparation of dansyl ethylenediamine Basic Protocol 2: Quantification of ON reaction yields Basic Protocol 3: Characterization of modified ONs.
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Affiliation(s)
- Jingyi Wang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, China
| | - Jiachen Shang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, China
| | - Yu Xiang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, China
| | - Aijun Tong
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, China
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4
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Single-molecule junction spontaneously restored by DNA zipper. Nat Commun 2021; 12:5762. [PMID: 34599166 PMCID: PMC8486845 DOI: 10.1038/s41467-021-25943-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Accepted: 09/07/2021] [Indexed: 11/09/2022] Open
Abstract
The electrical properties of DNA have been extensively investigated within the field of molecular electronics. Previous studies on this topic primarily focused on the transport phenomena in the static structure at thermodynamic equilibria. Consequently, the properties of higher-order structures of DNA and their structural changes associated with the design of single-molecule electronic devices have not been fully studied so far. This stems from the limitation that only extremely short DNA is available for electrical measurements, since the single-molecule conductance decreases sharply with the increase in the molecular length. Here, we report a DNA zipper configuration to form a single-molecule junction. The duplex is accommodated in a nanogap between metal electrodes in a configuration where the duplex is perpendicular to the nanogap axis. Electrical measurements reveal that the single-molecule junction of the 90-mer DNA zipper exhibits high conductance due to the delocalized π system. Moreover, we find an attractive self-restoring capability that the single-molecule junction can be repeatedly formed without full structural breakdown even after electrical failure. The DNA zipping strategy presented here provides a basis for novel designs of single-molecule junctions. The versatility of DNA has inspired many single-molecule investigations utilizing nanotechnology. Harashima et al. have a somewhat different take on the subject and study a zipper configuration bridging electrodes that resembles an active electro-mechanical component instead.
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5
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Wang J, Shang J, Xiang Y, Tong A. General Method for Post-Synthetic Modification of Oligonucleotides Based on Oxidative Amination of 4-Thio-2'-deoxyuridine. Bioconjug Chem 2021; 32:721-728. [PMID: 33730486 DOI: 10.1021/acs.bioconjchem.1c00016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Functionalized oligonucleotides (ONs) are widely applied as target binding molecules for biosensing and regulators for gene expression. Numerous efforts have been focused on developing facile methods for preparing these useful ONs carrying diverse modifications. Herein, we present a general method for postsynthetic modification of ONs via oxidative amination of 4-thio-2'-deoxyuridine (4SdU). 4SdU-containing ON can be derived by both alkyl and aromatic amines. Using this approach, ONs are successfully attached with alkyne/azide, biotin and dansylamide moieties, and these as-prepared ONs possess the expected biorthogonal reactivity, streptavidin affinity and fluorescent property, respectively. Furthermore, we also directly install fluorophores to the ON nucleobase based on oxidative amination of 4SdU, and these fluorophores exhibit distinct luminescence behaviors before and after conjugation. We believe our method will be a versatile strategy for constructing various functionalized ONs used in a wide range of nucleic acid applications.
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Affiliation(s)
- Jingyi Wang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Jiachen Shang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Yu Xiang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Aijun Tong
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
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6
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Matray T, Singh S, Sherif H, Farber K, Kwang E, VanBrunt M, Matsui E, Yada H. A novel class of polymeric fluorescent dyes assembled using a DNA synthesizer. PLoS One 2020; 15:e0243218. [PMID: 33275644 PMCID: PMC7717558 DOI: 10.1371/journal.pone.0243218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/17/2020] [Indexed: 12/02/2022] Open
Abstract
In the pursuit of a novel class of fluorescent dyes we have developed a programmable polymer system that enables the rational design and control of macromolecular constructs through simple control of polymer primary sequence. These polymers are assembled using standard phosphoramidite chemistry on a DNA synthesizer which allows for extremely rapid prototyping and enables many permutations due to the large selection of phosphoramidite monomers presently available on the market. This programmability to some extent allows us to control the interactions/spacing of payload molecules distributed along the designed polymeric backbone. Control of molecular architecture using this technology has allowed us to address the long-standing technical issue of contact quenching between fluorescent dyes offering new possibilities in the life sciences arena. Much like peptidic sequences coding for enzymes, cofactors, and receptors (all needing control of tertiary structure for proper function via primary sequence) our programmable system approaches a similar endpoint using a phosphate based polymeric backbone assembled in a completely automated fashion. Using this novel technology, we have efficiently synthesized several types of fluorescent dyes and demonstrated the programmability in molecule design, including the increases in brightness of the fluorescence emission.
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Affiliation(s)
- Tracy Matray
- R and D Department, Sony Biotechnology, Bothell, Washington, United States of America
- * E-mail:
| | - Sharat Singh
- Independent Consultant, Sony Biotechnology, Bothell, Washington, United States of America
| | - Hesham Sherif
- R and D Department, Sony Biotechnology, Bothell, Washington, United States of America
| | - Kenneth Farber
- R and D Department, Sony Biotechnology, Bothell, Washington, United States of America
| | - Erin Kwang
- R and D Department, Sony Biotechnology, Bothell, Washington, United States of America
| | - Michael VanBrunt
- R and D Department, Sony Biotechnology, Bothell, Washington, United States of America
| | - Eriko Matsui
- Medical Business Group, Sony Imaging Products & Solutions Inc., Atsugi-shi, Kanagawa, Japan
| | - Hiroaki Yada
- Medical Business Group, Sony Imaging Products & Solutions Inc., Atsugi-shi, Kanagawa, Japan
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7
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Seth PP, Swayze EE. The Medicinal Chemistry of RNase H-activating Antisense Oligonucleotides. ADVANCES IN NUCLEIC ACID THERAPEUTICS 2019. [DOI: 10.1039/9781788015714-00032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
This review focuses on the properties that an RNase H-activating antisense oligonucleotide (ASO) drug must have to function effectively in animals, as well as on medicinal chemistry strategies to achieve these properties. The biochemistry and structural requirements for activating RNase H are briefly summarized, as well as chemical modifications that can effect activation of RNase H when an ASO is bound to target RNA. The key modifications available to the medicinal chemist to engineer desired properties of the ASO are briefly reviewed, as are ASO design strategies to achieve optimal activity in animal systems. Lastly, the interactions of ASOs with proteins and strategies to control these interactions to improve the profile of ASOs are discussed.
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Affiliation(s)
- Punit P. Seth
- Ionis Pharmaceuticals 2855 Gazelle Court Carlsbad CA 92010 USA
| | - Eric E. Swayze
- Ionis Pharmaceuticals 2855 Gazelle Court Carlsbad CA 92010 USA
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8
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9
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Han X, Domaille DW, Fairbanks BD, He L, Culver HR, Zhang X, Cha JN, Bowman CN. New Generation of Clickable Nucleic Acids: Synthesis and Active Hybridization with DNA. Biomacromolecules 2018; 19:4139-4146. [PMID: 30212619 DOI: 10.1021/acs.biomac.8b01164] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Due to the ability to generate oligomers of precise sequence, sequential and stepwise solid-phase synthesis has been the dominant method of producing DNA and other oligonucleotide analogues. The requirement for a solid support, however, and the physical restrictions of limited surface area thereon significantly diminish the efficiency and scalability of these syntheses, thus, negatively affecting the practical applications of synthetic polynucleotides and other similarly created molecules. By employing the robust photoinitiated thiol-ene click reaction, we developed a new generation of clickable nucleic acids (CNAs) with a polythioether backbone containing repeat units of six atoms, matching the spacing of the phosphodiester backbone of natural DNA. A simple, inexpensive, and scalable route was utilized to produce CNA monomers in gram-scale, which indicates the potential to dramatically lower the cost of these DNA mimics and thereby expand the scope of these materials. The efficiency of this approach was demonstrated by the completion of CNA polymerization in 30 seconds, as characterized by size-exclusive chromatography (SEC) and infrared (IR) spectroscopy. CNA/DNA hybridization was demonstrated by gel electrophoresis and used in CdS nanoparticle assembly.
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Affiliation(s)
- Xun Han
- Department of Chemical and Biological Engineering , University of Colorado , UCB 596 , Boulder , Colorado 80309 , United States
| | - Dylan W Domaille
- Department of Chemistry , Colorado School of Mines , 1500 Illinois Street , Golden , Colorado 80401 , United States
| | - Benjamin D Fairbanks
- Department of Chemical and Biological Engineering , University of Colorado , UCB 596 , Boulder , Colorado 80309 , United States
| | - Liangcan He
- Department of Chemical and Biological Engineering , University of Colorado , UCB 596 , Boulder , Colorado 80309 , United States
| | - Heidi R Culver
- Department of Chemical and Biological Engineering , University of Colorado , UCB 596 , Boulder , Colorado 80309 , United States
| | - Xinpeng Zhang
- Department of Chemical and Biological Engineering , University of Colorado , UCB 596 , Boulder , Colorado 80309 , United States
| | - Jennifer N Cha
- Department of Chemical and Biological Engineering , University of Colorado , UCB 596 , Boulder , Colorado 80309 , United States
| | - Christopher N Bowman
- Department of Chemical and Biological Engineering , University of Colorado , UCB 596 , Boulder , Colorado 80309 , United States
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10
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Aparin IO, Proskurin GV, Golovin AV, Ustinov AV, Formanovsky AA, Zatsepin TS, Korshun VA. Fine Tuning of Pyrene Excimer Fluorescence in Molecular Beacons by Alteration of the Monomer Structure. J Org Chem 2017; 82:10015-10024. [PMID: 28856889 DOI: 10.1021/acs.joc.7b01451] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Oligonucleotide probes labeled with pyrene pairs that form excimers have a number of applications in hybridization analysis of nucleic acids. A long excited state lifetime, large Stokes shift, and chemical stability make pyrene excimer an attractive fluorescent label. Here we report synthesis of chiral phosphoramidite building blocks based on (R)-4-amino-2,2-dimethylbutane-1,3-diol, easily available from an inexpensive d-(-)-pantolactone. 1-Pyreneacetamide, 1-pyrenecarboxamide, and DABCYL derivatives have been used in preparation of molecular beacon (MB) probes labeled with one or two pyrenes/quenchers. We observed significant difference in the excimer emission maxima (475-510 nm; Stokes shifts 125-160 nm or 7520-8960 cm-1) and excimer/monomer ratio (from 0.5 to 5.9) in fluorescence spectra depending on the structure and position of monomers in the pyrene pair. The pyrene excimer formed by two rigid 1-pyrenecarboxamide residues showed the brightest emission. This is consistent with molecular dynamics data on excimer stability. Increase of the excimer fluorescence for MBs after hybridization with DNA was up to 24-fold.
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Affiliation(s)
- Ilya O Aparin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Gleb V Proskurin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Andrey V Golovin
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University , Leninskie gory 1-73, Moscow 119992, Russia
| | - Alexey V Ustinov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Andrey A Formanovsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Timofei S Zatsepin
- Skolkovo Institute of Science and Technology , 143026 Skolkovo, Russia
- Central Research Institute of Epidemiology , 111123 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University , Leninskie gory 1-73, 119992 Moscow, Russia
| | - Vladimir A Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Gause Institute of New Antibiotics , 119021 Moscow, Russia
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11
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Warminski M, Kowalska J, Jemielity J. Synthesis of RNA 5'-Azides from 2'-O-Pivaloyloxymethyl-Protected RNAs and Their Reactivity in Azide-Alkyne Cycloaddition Reactions. Org Lett 2017. [PMID: 28636394 DOI: 10.1021/acs.orglett.7b01591] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Commercially available 2'-O-pivaloyloxymethyl (PivOM) phosphoramidites were employed in an SPS protocol for RNA 5' azides. The utility of the N3-RNAs in CuAAC and SPAAC was demonstrated by RNA 5' labeling, chemical ligation including fragment joining and cyclization, and bioconjugation. As a result, several new RNA conjugates that may be valuable tools for studies on biological events such as innate immune response (cyclic dinucleotides), post-transcriptional gene regulation (circular RNAs), or mRNA turnover (m7G capped RNAs) were obtained.
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Affiliation(s)
- Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw , Pasteura 5, 02-093 Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw , Pasteura 5, 02-093 Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw , Banacha 2c, 02-097 Warsaw, Poland
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12
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Abstract
Oligonucleotides carrying a variety of chemical modifications including conjugates are finding increasing applications in therapeutics, diagnostics, functional genomics, proteomics, and as research tools in chemical and molecular biology. The successful synthesis of oligonucleotides primarily depends on the use of appropriately protected nucleoside building blocks including the exocyclic amino groups of the nucleobases, the hydroxyl groups at the 2'-, 3'-, and 5'-positions of the sugar moieties, and the internucleotide phospho-linkage. This unit is a thoroughly revised update of the previously published version and describes the recent development of various protecting groups that facilitate reliable oligonucleotide synthesis. In addition, various protecting groups for the imide/lactam function of thymine/uracil and guanine, respectively, are described to prevent irreversible nucleobase modifications that may occur in the presence of reagents used in oligonucleotide synthesis. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Geeta Meher
- Spring Bank Pharmaceuticals, Inc, Milford, Massachusetts
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13
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El-Faham A, El-Merghany A, Ghabbour HA. Crystal structure of N′-(2-phenylacetyl)thiophene-2-carbohydrazide monohydrate, C 13H 14N 2O 3S. Z KRIST-NEW CRYST ST 2017. [DOI: 10.1515/ncrs-2016-0152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
C13H14N2O3S, monoclinic, C2/c (no. 15), a = 27.9910(12) Å, b = 6.5721(3) Å, c = 14.2821(7) Å, β = 92.600(3)°, V = 2624.6(2) Å3, Z = 8, R
gt(F) = 0.042, wR
ref(F
2) = 0.105, T = 100 K.
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Affiliation(s)
- Ayman El-Faham
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
- Department of Chemistry, Faculty of Science, Alexandria University, P.O. Box 426, Ibrahimia, Alexandria 21321, Egypt
| | - Adel El-Merghany
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
- Department of Chemistry, Faculty of Science, Suez University, Suez, Egypt
| | - Hazem A. Ghabbour
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud, University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
- Department of Medicinal Chemistry, Faculty of Pharmacy, University of Mansoura, Mansoura 35516, Egypt
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14
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Slavíčková M, Pohl R, Hocek M. Additions of Thiols to 7-Vinyl-7-deazaadenine Nucleosides and Nucleotides. Synthesis of Hydrophobic Derivatives of 2'-Deoxyadenosine, dATP and DNA. J Org Chem 2016; 81:11115-11125. [PMID: 27709938 DOI: 10.1021/acs.joc.6b02098] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Additions of alkyl- or arylthiols to 7-vinyl-7-deaza-2'-deoxyadenosine gave a series of 7-[2-(alkyl- or arylsulfanyl)ethyl]-7-deaza-2'-deoxyadenosines in 45-85% yields. The nucleosides were converted to 5'-O-mono-(dASRMP) or triphosphates (dASRTP) by phosphorylation. The modified triphosphates were also prepared by thiol addition to 7-vinyl-7-deaza-dATP. The triphosphates dASRTP were good substrates for DNA polymerases useful in the enzymatic synthesis of base-modified oligonucleotides (ONs) or DNA containing flexibly linked hydrophobic substituents in the major groove. Primer extension was used for the synthesis of ONs with one or several modifications, PCR was used for the synthesis of heavily modified DNA, whereas terminal deoxynucleotidyl transferase was used for a single-nucleotide labeling of the 3'-end.
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Affiliation(s)
- Michaela Slavíčková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Gilead & IOCB Research Center, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Gilead & IOCB Research Center, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Gilead & IOCB Research Center, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague , Hlavova 8, Prague-2 12843, Czech Republic
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15
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Hassan EM, Willmore WG, DeRosa MC. Aptamers: Promising Tools for the Detection of Circulating Tumor Cells. Nucleic Acid Ther 2016; 26:335-347. [PMID: 27736306 DOI: 10.1089/nat.2016.0632] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Circulating tumor cells (CTCs) are cells that shed from a primary tumor and freely circulate in the blood, retaining the ability to initiate metastasis and form a secondary tumor in distant organs in the body. CTCs reflect the molecular profile of the primary tumor, therefore studying CTCs can allow for an understanding of the mechanism of metastasis, and an opportunity to monitor the prognosis of cancer. Unfortunately, the detection of CTCs is a considerable challenge due to their low abundance in the bloodstream and the lack of consistent markers present to recognize these cells. The aim of this review is to summarize some of the aptamer-based affinity methods for the detection of CTCs. The basic biological concept of how metastasis occurs and the role of CTCs in this process are presented. Some methods of CTC detection employing antibodies or peptides are mentioned here for comparison. The review of present literature suggests that aptamers are emerging as competitive technology in the detection of CTCs, especially due to their unique properties, but there still remain several challenges to be met, including the need to improve the throughput and sensitivity of such methods.
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Affiliation(s)
- Eman M Hassan
- 1 Institut National de la Recherche Scientifique-Energie, Materiaux Telecommunication , Quebec, Canada .,2 Department of Chemistry, Carleton University , Ottawa, Canada
| | | | - Maria C DeRosa
- 2 Department of Chemistry, Carleton University , Ottawa, Canada .,3 Institute of Biochemistry, Carleton University , Ottawa, Canada
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16
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Christmann M, Hu J, Kitamura M, Stoltz B. Tetrahedron reports on organic chemistry. Tetrahedron 2015. [DOI: 10.1016/s0040-4020(15)00744-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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17
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Gjonaj L, Roelfes G. Selective chemical modification of DNA with alkoxy- and benzyloxyamines. Org Biomol Chem 2015; 13:6059-65. [DOI: 10.1039/c5ob00595g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
DNA is modified selectively at cytosine with benzyloxyamine and -derivatives carrying handles for click reactions.
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Affiliation(s)
- Lorina Gjonaj
- Stratingh Institute for Chemistry
- University of Groningen
- 9747 AG Groningen
- The Netherlands
| | - Gerard Roelfes
- Stratingh Institute for Chemistry
- University of Groningen
- 9747 AG Groningen
- The Netherlands
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18
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Vybornyi M, Nussbaumer AL, Langenegger SM, Häner R. Assembling multiporphyrin stacks inside the DNA double helix. Bioconjug Chem 2014; 25:1785-93. [PMID: 25186936 DOI: 10.1021/bc500297e] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Double stranded DNA hybrids containing up to four consecutive, face-to-face stacked porphyrins are described. Non-nucleosidic, 5,15-bisphenyl-substituted porphyrin building blocks were incorporated into complementary oligonucleotide strands. Upon hybridization multiple porphyrins are well accommodated inside the DNA scaffold without disturbing the overall B-DNA structure. The formation of double strands containing up to four free base porphyrins is enabled without compromising duplex stability. UV/vis, fluorescence, and CD spectroscopy demonstrate the formation of porphyrins H-aggregates inside the DNA double helix and provide evidence for the existence of strong excitonic coupling between interstrand stacked porphyrins. H-aggregation results in considerable fluorescence quenching. Most intense CD effects are observed in stacks containing four porphyrins. The findings demonstrate the value of DNA for the controlled formation of molecularly defined porphyrin aggregates.
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Affiliation(s)
- Mykhailo Vybornyi
- Department of Chemistry and Biochemistry, University of Bern , Freiestrasse 3, CH-3012 Bern, Switzerland
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19
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Kupryushkin MS, Nekrasov MD, Stetsenko DA, Pyshnyi DV. Efficient functionalization of oligonucleotides by new achiral nonnucleosidic monomers. Org Lett 2014; 16:2842-5. [PMID: 24820262 DOI: 10.1021/ol500668n] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A novel synthetic strategy has been designed for preparation of achiral nonnucleosidic phosphoramidite monomers for automated solid-phase oligonucleotide synthesis. It is based on O-DMTr-protected 4-(2-hydroxyethyl)-morpholine-2,3-dione as the key compound and a family of building blocks obtained by its ring-opening by primary aliphatic amines. A series of nonnucleosidic phosphoramidites containing various side-chain functionalities was synthesized, and corresponding oligodeoxyribonucleotides incorporating modified units in single or multiple positions along the chain were prepared.
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Affiliation(s)
- Maxim S Kupryushkin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
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20
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Stoltz B, Motherwell W. Tetrahedron reports on organic chemistry. Tetrahedron 2013. [DOI: 10.1016/s0040-4020(13)01252-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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21
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Murray JI, Spivey AC, Woscholski R. Alternative synthetic tools to phospho-specific antibodies for phosphoproteome analysis: progress and prospects. J Chem Biol 2013; 6:175-84. [PMID: 24432133 DOI: 10.1007/s12154-013-0100-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 06/18/2013] [Indexed: 12/17/2022] Open
Abstract
Signal transduction cascades in living systems are often controlled via post-translational phosphorylation and dephosphorylation of proteins. These processes are catalyzed in vivo by kinase and phosphatase enzymes, which consequently play an important role in many disease states, including cancer and immune system disorders. Current techniques for studying the phosphoproteome (isotopic labeling, chromatographic techniques, and phosphospecific antibodies), although undoubtedly very powerful, have yet to provide a generic tool for phosphoproteomic analysis despite the widespread utility such a technique would have. The use of small molecule organic catalysts that can promote selective phosphate esterification could provide a useful alternative to current state-of-the-art techniques for use in, e.g., the labeling and pull-down of phosphorylated proteins. This report reviews current techniques used for phosphoproteomic analysis and the recent use of small molecule peptide-based catalysts in phosphorylation reactions, indicating possible future applications for this type of catalyst as synthetic alternatives to phosphospecific antibodies for phosphoproteome analysis.
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Affiliation(s)
- James I Murray
- Department of Chemistry, Imperial College London, London, SW7 2AZ UK
| | - Alan C Spivey
- Department of Chemistry, Imperial College London, London, SW7 2AZ UK
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22
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Guzaev AP. Solid-phase supports for oligonucleotide synthesis. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2013; Chapter 3:3.1.1-3.1.60. [PMID: 23775808 DOI: 10.1002/0471142700.nc0301s53] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
This unit attempts to provide a reasonably complete inventory of over 280 solid supports available to oligonucleotide chemists for preparation of natural and 3'-modified oligonucleotides. Emphasis is placed on non-nucleosidic solid supports. The relationship between the structural features of linkers and their behavior in oligonucleotide synthesis and deprotection is discussed wherever the relevant observations are available.
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23
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Cao L, Xi Z. Fast thiol–maleamic methyl ester addition for facile covalent cross-linking of oligonucleotides. Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2013.01.112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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24
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Dang AT, Johnson MA, Bundle DR. Synthesis of a Candida albicans tetrasaccharide spanning the β1,2-mannan phosphodiester α-mannan junction. Org Biomol Chem 2013; 10:8348-60. [PMID: 22996034 DOI: 10.1039/c2ob26355f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The cell wall phosphomannan of Candida species is a complex N-linked glycoprotein with a glycan chain containing predominantly an α-linked mannose backbone with α-mannose branches. A minor β-mannan component is attached to the branches either via a glycosidic bond (acid stable β-mannan) or a phosphodiester bond (acid-labile β-mannan). The α-mannan residues of the cell wall phosphomannan do not afford protective antibody, while the β-mannan portion is a protective antigen and has become an attractive target as the key epitope of a conjugate vaccine. We report the first synthesis of a tetrasaccharide 1 consisting of a β1,2-mannopyranosyl trisaccharide linked via a phosphodiester to methyl α-mannopyranoside. This encompasses the attachment site of the acid labile β-mannan to the α-mannan component of the cell wall phosphomannan. The trisaccharide was formed by an iterative process to first create a β-glucopyranoside linkage and then epimerize the C-2 center via an oxidation-reduction sequence. The phosphate diester linkage was accessed via an anomeric H-phosphonate. The binding of phosphomannan fragment 1 with the protective antibody C3.1 has been evaluated and compared with a β-mannotrioside in hapten inhibition experiments. The observed activities are rationalized with a model for docked in the binding site of C3.1.
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Affiliation(s)
- Anh-Thu Dang
- Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Canada
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25
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Challenges and opportunities for small molecule aptamer development. J Nucleic Acids 2012; 2012:748913. [PMID: 23150810 PMCID: PMC3488411 DOI: 10.1155/2012/748913] [Citation(s) in RCA: 286] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 09/08/2012] [Indexed: 12/14/2022] Open
Abstract
Aptamers are single-stranded oligonucleotides that bind to targets with high affinity and selectivity. Their use as molecular recognition elements has emerged as a viable approach for biosensing, diagnostics, and therapeutics. Despite this potential, relatively few aptamers exist that bind to small molecules. Small molecules are important targets for investigation due to their diverse biological functions as well as their clinical and commercial uses. Novel, effective molecular recognition probes for these compounds are therefore of great interest. This paper will highlight the technical challenges of aptamer development for small molecule targets, as well as the opportunities that exist for their application in biosensing and chemical biology.
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26
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Markova LI, Malinovskii VL, Patsenker LD, Häner R. Synthesis and properties of squaraine-modified DNA. Org Biomol Chem 2012; 10:8944-7. [PMID: 23076304 DOI: 10.1039/c2ob26787j] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The incorporation of squaraines into DNA via the phosphoramidite approach is described. High molar absorptivity, environment-sensitive fluorescence properties and intense CD effects render squaraines valuable building blocks for DNA-based optical probes and nanostructures.
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Affiliation(s)
- Larysa I Markova
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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27
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Pérez-Rentero S, Grijalvo S, Ferreira R, Eritja R. Synthesis of oligonucleotides carrying thiol groups using a simple reagent derived from threoninol. Molecules 2012; 17:10026-45. [PMID: 22922274 PMCID: PMC6268497 DOI: 10.3390/molecules170910026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 08/03/2012] [Accepted: 08/14/2012] [Indexed: 11/16/2022] Open
Abstract
Oligonucleotides carrying thiol groups are useful intermediates for a remarkable number of applications involving nucleic acids. In this study, DNA oligonucleotides carrying tert-butylsulfanyl protected thiol groups have been prepared. A building block derived from threoninol has been developed to introduce a thiol group at any predetemined position of an oligonucleotide. The resulting thiolated oligonucleotides have been used for the preparation of oligonucleotide conjugates and for the functionalization of gold nanoparticles using the reactivity of the thiol groups.
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Affiliation(s)
- Sonia Pérez-Rentero
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, E-08028 Barcelona, Spain; (S.P.-R.); (S.G.); (R.F.)
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Jordi Girona 18, E-08034 Barcelona, Spain
| | - Santiago Grijalvo
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, E-08028 Barcelona, Spain; (S.P.-R.); (S.G.); (R.F.)
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Jordi Girona 18, E-08034 Barcelona, Spain
| | - Rubén Ferreira
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, E-08028 Barcelona, Spain; (S.P.-R.); (S.G.); (R.F.)
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Jordi Girona 18, E-08034 Barcelona, Spain
| | - Ramon Eritja
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, E-08028 Barcelona, Spain; (S.P.-R.); (S.G.); (R.F.)
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Jordi Girona 18, E-08034 Barcelona, Spain
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28
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Kojima N, Komatsu Y. Synthesis and application of highly reactive amino linkers for functional oligonucleotides. ACTA ACUST UNITED AC 2012; Chapter 4:Unit 4.48.1-23. [PMID: 22395967 DOI: 10.1002/0471142700.nc0448s48] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Oligonucleotides are functionalized by conjugation with a variety of molecules, and aliphatic amino linkers have been frequently used as a tether for their modifications. This unit describes the syntheses and applications of novel amino linkers having a carbamate structure. Two major chemical properties of the primary amine are induced by the neighboring effect of the carbamate group, which are found to be optimum in an aminoethyl carbamate structure. First, the hydrophobic monomethoxytrityl group can be rapidly removed from the aminoethyl carbamate under very mild acidic conditions, while the deprotection is not completed in standard aliphatic amines even under high acid concentration. This significant feature enables the convenient purification of amino-modified oligonucleotides by using the hydrophobic interaction of the monomethoxytrityl group with a reverse-phase resin. Second, the introduction of the carbamate linkage reduces the pK(a) value of the neighboring primary amine, resulting in an increase in the conjugation yields with various functional molecules, such as those having active esters. The novel amino linkers that have an aminoethyl carbamate linkage indicate potent activity and are applicable for the preparation of various functional oligonucleotides.
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Affiliation(s)
- Naoshi Kojima
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo, Japan
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29
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Kaboudin B, Mostafalu R. Triethylphosphate/Phosphorus Pentoxide as an Efficient Reagent for the Phosphorylation of Phenols. PHOSPHORUS SULFUR 2012. [DOI: 10.1080/10426507.2011.639822] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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30
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Söderberg L, Lavén G, Kalek M, Stawinski J. 31P NMR and computational studies on stereochemistry of conversion of phosphoramidate diesters into the corresponding phosphotriesters. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2011; 30:552-64. [PMID: 21888546 DOI: 10.1080/15257770.2011.586009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
31P NMR spectroscopy was used to investigate a stereochemical course of a nitrite-promoted conversion of phosphoramidate diesters into the corresponding phosphotriesters. It was found that this reaction occurred with almost complete epimerization at the phosphorus center and at the C1 atom in the amine moiety. On the basis of the 31P NMR data, a plausible mechanism for the reaction was proposed. The density functional theory calculation of the key step of the reaction, i.e., breaking of the P-N bond and formation of the P-O bond, suggested a one-step S(N)2(P) process with retention of configuration at the phosphorus center.
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Affiliation(s)
- Linda Söderberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
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31
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Dubey L, Ryazanova O, Zozulya V, Fedoryak D, Dubey I. Postsynthetic modification of oligonucleotides with imidazophenazine dye and its effect on duplex stability. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2011; 30:585-96. [PMID: 21888549 DOI: 10.1080/15257770.2011.598489] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Carboxyalkyl derivative of the intercalating agent imidazo[4,5-b]phenazine was used for the postsynthetic oligonucleotide modification. Model pentadecathymidylate-imidazophenazine conjugate was prepared from 5'-aminoalkyl-modified (dT)(15) by using phosphonium coupling reagent BOP in the presence of 1-hydroxybenzotriazole. Spectral-fluorescent properties of the conjugate were studied. The attachment of the dye was found to increase the thermal stability of (dT)(15) duplex with poly(dA) by more than 4°C, probably by the intercalation mechanism.
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Affiliation(s)
- Larysa Dubey
- Institute of Molecular Biology and Genetics, National Academy of Sciences, Kyiv, Ukraine
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32
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Tanabe K, Ando Y, Nishimoto SI. Reversible modification of oligodeoxynucleotides: click reaction at phosphate group and alkali treatment. Tetrahedron Lett 2011. [DOI: 10.1016/j.tetlet.2011.10.109] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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33
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Stoltz B, Motherwell W. Tetrahedron reports on organic chemistry. Tetrahedron 2011. [DOI: 10.1016/s0040-4020(11)00770-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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34
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Meyer A, Pourceau G, Vasseur JJ, Morvan F. 5'-Bis-conjugation of oligonucleotides by amidative oxidation and click chemistry. J Org Chem 2011; 75:6689-92. [PMID: 20795720 DOI: 10.1021/jo101134z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A pent-4-ynyl tert-butyl N,N-diisopropyl phosphoramidite was coupled at the 5'-end of oligonucleotides to give a phosphite triester linkage, which forms an H-phosphonate diester linkage during treatment with dichloroacetic acid. Then an amidative oxidation with CCl(4) in the presence of an amine and a 1,3-dipolar cycloaddition with an azide under copper(I) catalysis afforded the bis-conjugated oligonucleotides with high efficiency. The introduction of a bromoalkyl group as a precursor of azidoalkyl by amidative oxidation allowed the performance of two selective 1,3-dipolar cycloadditions.
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Affiliation(s)
- Albert Meyer
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS Université Montpellier 1, Université Montpellier 2, CC1704, Place E. Bataillon, 34095 Montpellier Cedex 5, France
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35
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Stoltz B, Motherwell W. Tetrahedron reports on organic chemistry. Tetrahedron 2010. [DOI: 10.1016/s0040-4020(10)01735-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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36
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Solid-phase synthesis of oligodeoxynucleotides containing N4-[2-(t-butyldisulfanyl)ethyl]-5-methylcytosine moieties. Molecules 2010; 15:5692-707. [PMID: 20720521 PMCID: PMC6257692 DOI: 10.3390/molecules15085692] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Revised: 07/28/2010] [Accepted: 08/05/2010] [Indexed: 11/17/2022] Open
Abstract
An efficient route for the synthesis of the phosphoramidite derivative of 5-methylcytosine bearing a tert-butylsulfanyl group protected thiol is described. This building block is used for the preparation of oligonucleotides carrying a thiol group at the nucleobase at the internal position of a DNA sequence. The resulting thiolated oligonucleotides are useful intermediates to generate oligonucleotide conjugates carrying molecules of interest at internal positions of a DNA sequence.
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37
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Murugaiah V, Zedalis W, Lavine G, Charisse K, Manoharan M. Reversed-phase high-performance liquid chromatography method for simultaneous analysis of two liposome-formulated short interfering RNA duplexes. Anal Biochem 2010; 401:61-7. [DOI: 10.1016/j.ab.2010.02.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Revised: 02/05/2010] [Accepted: 02/09/2010] [Indexed: 12/24/2022]
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38
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Coughlin JE, Padmanabhan S, Zhang G, Kirk CJ, Govardhan CP, Korba BE, O'Loughlin K, Green CE, Mirsalis J, Morrey JD, Iyer RP. Orally bioavailable anti-HBV dinucleotide acyloxyalkyl prodrugs. Bioorg Med Chem Lett 2010; 20:1783-6. [PMID: 20117930 DOI: 10.1016/j.bmcl.2010.01.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Revised: 12/30/2009] [Accepted: 01/04/2010] [Indexed: 11/17/2022]
Abstract
The acyloxyalkyl derivatives of a model anti-HBV dinucleotide were synthesized and evaluated as orally bioavailable prodrugs. Our studies have led to the identification of the first orally bioavailable dinucleotide prodrugs for further therapeutic development against the hepatitis B virus (HBV).
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Affiliation(s)
- John E Coughlin
- Spring Bank Pharmaceuticals Inc., Milford, MA, United States
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39
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Pourceau G, Meyer A, Vasseur JJ, Morvan F. Azide solid support for 3'-conjugation of oligonucleotides and their circularization by click chemistry. J Org Chem 2009; 74:6837-42. [PMID: 19663415 DOI: 10.1021/jo9014563] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A solid support bearing an azido linker was used to synthesize a 3'-azido-alkyl-oligonucleotide by phosphoramidite chemistry. The resulting oligonucleotide was either conjugated by 1,3-dipolar cycloaddition on solid support or in solution with mannose-propargyl derivative and in solution with dansyl propargyl. Besides, after introduction of an alkyne function at the 5'-end, the resulting oligonucleotide bearing both 3'-azide and 5'-alkyne functions was circularized.
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Affiliation(s)
- Gwladys Pourceau
- 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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40
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Malinovskii VL, Wenger D, Häner R. Nucleic acid-guided assembly of aromatic chromophores. Chem Soc Rev 2009; 39:410-22. [PMID: 20111767 DOI: 10.1039/b910030j] [Citation(s) in RCA: 225] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The rational formation of aromatic chromophore arrays is an intriguing challenge since ordered collectives of chromophores possess properties that are largely different from those of the individual molecules. Therefore, nucleic acids are increasingly used as scaffolds for the construction of multi-chromophore arrays. This tutorial review provides an introduction to the field of nucleic acid-guided chromophore assemblies for non-specialists and a reference point for those familiar with the area by highlighting the recent developments and describing some of the spectroscopic methods used for the study of oligonucleotide-chromophore conjugates.
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Affiliation(s)
- Vladimir L Malinovskii
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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41
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Uno SN, Dohno C, Bittermann H, Malinovskii V, Häner R, Nakatani K. A Light-Driven Supramolecular Optical Switch. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200903251] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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42
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Uno SN, Dohno C, Bittermann H, Malinovskii V, Häner R, Nakatani K. A Light-Driven Supramolecular Optical Switch. Angew Chem Int Ed Engl 2009; 48:7362-5. [DOI: 10.1002/anie.200903251] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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43
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Dabkowski W, Kazimierczak Ł. O-Methyl-bis-O-(4-nitrophenyl)phosphite: a novel chemoselective O-phosphitylating reagent. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2009.06.102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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44
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Teo YN, Wilson JN, Kool ET. Polyfluorophores on a DNA backbone: a multicolor set of labels excited at one wavelength. J Am Chem Soc 2009; 131:3923-33. [PMID: 19254023 DOI: 10.1021/ja805502k] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We recently described the assembly of fluorescent deoxyriboside monomers ("fluorosides") into DNA-like phosphodiester oligomers (oligodeoxyfluorosides or ODFs) in which hydrocarbon and heterocyclic aromatic fluorophores interact both physically and electronically. Here we report the identification of a multicolor set of water-soluble ODF dyes that display emission colors across the visible spectrum, and all of which can be simultaneously excited by long-wavelength UV light at 340-380 nm. Multispectral dye candidates were chosen from a library of 4096 tetramer ODFs constructed on PEG-polystyrene beads using a simple long-pass filter to observe all visible colors at the same time. We resynthesized and characterized a set of 23 ODFs containing one to four individual chromophores and included 2-3 spacer monomers to increase aqueous solubility and minimize aggregation. Emission maxima of this set range from 376 to 633 nm, yielding apparent colors from violet to red, all of which can be visualized directly. The spectra of virtually all ODFs in this set varied considerably from the simple combination of monomer components, revealing extensive electronic interactions between the presumably stacked monomers. In addition, comparisons of anagrams in the set (isomers having the same components in a different sequence) reveal the importance of nearest-neighbor interactions in the emissive behavior. Preliminary experiments with human tumor (HeLa) cells, observing two ODFs by laser confocal microscopy, showed that they can penetrate the outer cellular membrane, yielding cytoplasmic localization. In addition, a set of four distinctly colored ODFs was incubated with live zebrafish embryos, showing tissue penetration, apparent biostability, and no apparent toxicity. The results suggest that ODF dyes may be broadly useful as labels in biological systems, allowing the simultaneous tracking of multiple species by color, and allowing visualization in moving systems where classical fluorophores fail.
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Affiliation(s)
- Yin Nah Teo
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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45
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Ahmadibeni Y, Parang K. Solid-supported reagents for synthesis of nucleoside monothiophosphates, dithiodiphosphates, and trithiotriphosphates. ACTA ACUST UNITED AC 2009; Chapter 13:Unit13.9. [PMID: 19319857 DOI: 10.1002/0471142700.nc1309s36] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This unit describes procedures for the selective synthesis of nucleoside monothiophosphates, dithiodiphosphates, and trithiotriphosphates from solid-supported phosphitylating reagents. Rigid and sterically hindered polymer-bound 1,3,2-oxathiaphospholane is reacted selectively with the 5'-hydroxyl group of nucleosides in the presence of 1H-tetrazole. Sulfurization in the presence of Beaucage's reagent (3H-1,2-benzodithiole-3-one 1,1-dioxide) followed by ring-opening with 3-hydroxypropionitrile and basic cleavage in the presence of 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) through the elimination of polymer-bound ethylene episulfide afford nucleoside monothiophosphates. Furthermore, reaction of polymer-bound diphosphitylating and triphosphitylating reagents, prepared from polymer-bound benzyl alcohol, with unprotected nucleosides, sulfurization with Beaucage's reagent, and acidic cleavage using trifluoroacetic acid cocktail produce nucleoside dithiodiphosphates and trithiotriphosphates in moderate yields.
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46
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Iwamoto N, Oka N, Sato T, Wada T. Stereocontrolled solid-phase synthesis of oligonucleoside H-phosphonates by an oxazaphospholidine approach. Angew Chem Int Ed Engl 2009; 48:496-9. [PMID: 18985643 DOI: 10.1002/anie.200804408] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Naoki Iwamoto
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bioscience Building 702, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
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Iwamoto N, Oka N, Sato T, Wada T. Stereocontrolled Solid-Phase Synthesis of Oligonucleoside H-Phosphonates by an Oxazaphospholidine Approach. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200804408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Michalski J, Dabkowski W. Unconventional Activators in the Synthesis of Oligonucleotides and Their Structural Analogues. HETEROCYCLES 2009. [DOI: 10.3987/rev-08-sr(d)10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Chidambaram N, Zhou L, Cohen JS. Targeting of Antisense: Synthesis of Steroid-Linked and Steroid-Bridged Oligodeoxynucleotides. Drug Deliv 2008. [DOI: 10.3109/10717549609031378] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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