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Martín-Nieves V, Fàbrega C, Guasch M, Fernández S, Sanghvi YS, Ferrero M, Eritja R. Oligonucleotides Containing 1-Aminomethyl or 1-Mercaptomethyl-2-deoxy-d-ribofuranoses: Synthesis, Purification, Characterization, and Conjugation with Fluorophores and Lipids. Bioconjug Chem 2021; 32:350-366. [PMID: 33543930 PMCID: PMC9122261 DOI: 10.1021/acs.bioconjchem.0c00717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Oligonucleotide conjugates are widely used as therapeutic drugs, gene analysis, and diagnostic tools. A critical step in the biologically relevant oligonucleotide conjugates is the design and synthesis of functional molecules that connect oligonucleotide with ligands. Here, we report the synthesis and application for oligonucleotide functionalization of novel tethers based on aminomethyl and mercaptomethyl sugar derivatives. Starting from a common cyano sugar precursor, three novel phosphoramidites have been prepared in the two α- and β-anomeric forms. The mercaptomethyl sugar was protected with the S-acetyl group, while two different protecting groups have been developed for the aminomethyl sugar. These two protecting groups are orthogonal, as they can be removed independently using photolysis or ammonolysis. This combination allowed the introduction of two different ligands in a single oligonucleotide.
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Affiliation(s)
- Virginia Martín-Nieves
- Departamento de Química Orgánica e Inorgánica, Universidad de Oviedo, 33006-Oviedo, Asturias, Spain
| | - Carme Fàbrega
- Department of Chemical and Biomolecular Nanotechnology, Institute for Advanced Chemistry of Catalonia (IQAC, CSIC), 08034-Barcelona, Spain.,CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, 08034-Barcelona, Spain
| | - Marc Guasch
- Department of Chemical and Biomolecular Nanotechnology, Institute for Advanced Chemistry of Catalonia (IQAC, CSIC), 08034-Barcelona, Spain.,CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, 08034-Barcelona, Spain
| | - Susana Fernández
- Departamento de Química Orgánica e Inorgánica, Universidad de Oviedo, 33006-Oviedo, Asturias, Spain
| | - Yogesh S Sanghvi
- Rasayan Inc., 2802 Crystal Ridge Road, Encinitas, California 92024-6615, United States
| | - Miguel Ferrero
- Departamento de Química Orgánica e Inorgánica, Universidad de Oviedo, 33006-Oviedo, Asturias, Spain
| | - Ramon Eritja
- Department of Chemical and Biomolecular Nanotechnology, Institute for Advanced Chemistry of Catalonia (IQAC, CSIC), 08034-Barcelona, Spain.,CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, 08034-Barcelona, Spain
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2
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Abstract
The development of the clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system has become a revolutionary step for genome engineering because it enables modification of target genomes. However, many biological applications with the CRISPR/Cas9 system are impeded by off-target effects and loci-dependent nuclease activity with various sgRNAs. Commonly used label-strategy-based CRISPR/Cas9 assays often suffer from possible disturbances to Cas9 activity and a time-consuming labeling procedure. Herein, we for the first time propose a DNA-templated CuNPs-based label-free CRISPR/Cas9 assay, with a low LOD of 0.13 nM and rapid detection in 35 min after CRISPR/Cas9 cleavage. Additionally, the site specificity of the DNA substrate was demonstrated. Through the proposed label-free strategy, a single-base change at a specific loci could lead to a significant reduction of the Cas9 cleavage effect, while the other common genetic modifications might be accepted by the CRIPR/Cas9 system. Therefore, the proposed label-free Cas9 assay may provide a new paradigm for the a priori in vitro CRISPR/Cas9 assay and exploration for in vivo biological applications.
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Affiliation(s)
- Jianyu Hu
- College of Architecture and Environment , Sichuan University , Chengdu 610064 , China
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry , Sichuan University , Chengdu 610064 , China
| | - Min Jiang
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry , Sichuan University , Chengdu 610064 , China
| | - Rui Liu
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry , Sichuan University , Chengdu 610064 , China
| | - Yi Lv
- Analytical and Testing Center , Sichuan University , Chengdu 610064 , China
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3
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de Rochambeau D, Sun Y, Barlog M, Bazzi HS, Sleiman HF. Modular Strategy To Expand the Chemical Diversity of DNA and Sequence-Controlled Polymers. J Org Chem 2018; 83:9774-9786. [DOI: 10.1021/acs.joc.8b01184] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Donatien de Rochambeau
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montréal, Québec H3A 0B8, Canada
| | - Yuanye Sun
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montréal, Québec H3A 0B8, Canada
| | - Maciej Barlog
- Department of Chemistry, Texas A&M University at Qatar, P.O. Box 23874, Doha, Qatar
| | - Hassan S. Bazzi
- Department of Chemistry, Texas A&M University at Qatar, P.O. Box 23874, Doha, Qatar
| | - Hanadi F. Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montréal, Québec H3A 0B8, Canada
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Yuen LH, Franzini RM. Stability of Oligonucleotide-Small Molecule Conjugates to DNA-Deprotection Conditions. Bioconjug Chem 2017; 28:1076-1083. [PMID: 28233987 DOI: 10.1021/acs.bioconjchem.7b00005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Oligonucleotide conjugates of small molecules are widely used in chemical biology and have found increasing interest in the context of DNA-encoded chemical libraries for drug discovery. Attachment of molecules to DNA bound to the solid support is an attractive small-molecule conjugation method that permits the use of organic solvents, rigorous reaction conditions, and simple workup. However, the conjugated structures must be resistant to the harsh DNA deprotection/cleavage conditions and the stabilities of building blocks under various deprotection conditions are mostly unexplored. In the present study, we analyzed the stability of 131 structurally diverse fragments that contain amides and amide-like elements during DNA deprotection protocols. Structural features susceptible to decomposition in DNA deprotection conditions were identified and a protocol that enabled the synthesis of DNA conjugates with labile fragments on solid support was identified.
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Affiliation(s)
- Lik Hang Yuen
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah , 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Raphael M Franzini
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah , 30 S 2000 E, Salt Lake City, Utah 84112, United States
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Kowata K, Kojima N, Komatsu Y. Development of a 3'-amino linker with high conjugation activity and its application to conveniently cross-link blunt ends of a duplex. Bioorg Med Chem 2016; 24:2108-13. [PMID: 27041396 DOI: 10.1016/j.bmc.2016.03.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 03/24/2016] [Accepted: 03/25/2016] [Indexed: 11/19/2022]
Abstract
The 2-aminoethyl carbamate linker (ssH linker) exhibits high activity in modifying the 5'-termini of oligonucleotides; however, the ssH linker is not appropriate for 3'-terminal modification because it undergoes intramolecular trans-acylation under heat-aqueous ammonia conditions. We developed an N-(2-aminoethyl)carbamate linker (revH linker), in which the carbamate is oriented in the reverse direction relative to that in 2-aminoethyl carbamate. The revH linker was tolerant to heat-alkaline conditions and retained its high reactivity in conjugation with exogenous molecules. The 3'-revH linker was efficiently linked with the 5'-ssH linker at the termini of complementary double strands with a bifunctional molecule, producing a synthetic loop structure. An anti-microRNA oligonucleotide (AMO) was prepared from the chemical ligation of three-stranded 2'-O-methyl RNAs, and the AMO with two alkyl loops exhibited high inhibition activity toward miRNA function. The revH linker is not only useful for 3'-terminal modification of oligonucleotides but also expands the utility range in combination with the 5'-ssH linker.
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Affiliation(s)
- Keiko Kowata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Naoshi Kojima
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Tsukuba Central 6, Higashi, Tsukuba-shi, Ibaraki 305-8566, Japan
| | - Yasuo Komatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan.
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Kupryushkin MS, Pyshnyi DV. Oligonucleotide derivatives in nucleic acid hybridization analysis. III. Synthesis and investigation of properties of oligonucleotides, bearing bifunctional non-nucleotide insertion. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2012. [DOI: 10.1134/s106816201206009x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Kayushin A, Demekhina A, Korosteleva M, Miroshnikov A, Azhayev A. Synthesis of biotin-containing phosphoramidite linker with polyether spacer arm. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2011; 30:490-502. [PMID: 21888541 DOI: 10.1080/15257770.2011.587702] [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
A phosphoramidite linker unit, based on glycerol backbone and containing a biotin residue attached through a tetraethylene glycol spacer arm, was synthesized. DMTr-Glycidol and tetraethylene glycol were used as starting materials. After conversion of one of hydroxy groups in tetraethylene glycol into an amino group, the epoxy cycle in DMTr-glycidol was opened by this amino alcohol, resulting in the corresponding ether and some quantity of secondary amine. After attaching of biotin residue to the ether followed by phosphitylation, the desirable linker was obtained. The structure of the linker was confirmed by (1)H-(1)H COSY, (1)H-(13)C HSQC, (1)H-(13)C HMBC, (1)H-(15)N HSQC, and (1)H-(15)N HMBC spectra. The resulted phosphoramidite linker unit is suitable for use in common DNA synthesizers. This approach can be used for preparation of various modifiers containing reporter groups attached to the primary amino function using conventional procedures.
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Affiliation(s)
- Alexey Kayushin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
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Kolganova NA, Florentiev VL, Chudinov AV, Zasedatelev AS, Timofeev EN. Simple and stereoselective preparation of an 4-(aminomethyl)-1,2,3-triazolyl nucleoside phosphoramidite. Chem Biodivers 2011; 8:568-76. [PMID: 21480503 DOI: 10.1002/cbdv.201000047] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A simple and stereoselective synthesis of a protected 4-(aminomethyl)-1-(2-deoxy-β-D-ribofuranosyl)-1,2,3-triazole cyanoethyl phosphoramidite was developed for the modification of synthetic oligonucleotides. The configuration of the 1,2,3-triazolyl moiety with respect to the deoxyribose was unambiguously determined in ROESY experiments. The aminomethyl group of the triazolyl nucleotide was fully functional in labelling reactions. Furthermore, the hybridization behavior of 5' triazole-terminated oligonucleotide was similar to that of 5' aminohexyl-terminated oligomer with the same sequence. Internal modifications of the oligonucleotide strands resulted in significant decrease of duplex stability.
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Affiliation(s)
- Natalia A Kolganova
- Engelhardt Institute of Molecular Biology, 32 Vavilov St., Moscow 119991, Russia
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10
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Pfleiderer W, Maier T. Nucleotides Part: LXXVII. New Types of Fluorescence Labeling of 2’-Deoxyguanosine. HETEROCYCLES 2010. [DOI: 10.3987/com-10-s(e)54] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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11
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Misiura K, Durrant I, Evans MR, Gait MJ. A New Multiple Labelling Method for Synthetic Oligonucleotides and Increased Sensitivity in DNA Detection. ACTA ACUST UNITED AC 2007. [DOI: 10.1080/07328319108046568] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Konrad Misiura
- a MRC Laboratory of Molecular Biology , Hills Road, Cambridge , CB2 2QH , UK
| | - Ian Durrant
- b Amersham International plc, Pollards Wood Laboratories , Nightingales Lane, Chalfont St Giles, Buckinghamshire , HP8 4SP , UK
| | - Michael R. Evans
- b Amersham International plc, Pollards Wood Laboratories , Nightingales Lane, Chalfont St Giles, Buckinghamshire , HP8 4SP , UK
| | - Michael J. Gait
- a MRC Laboratory of Molecular Biology , Hills Road, Cambridge , CB2 2QH , UK
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De Vos MJ, Elsen AV, Bollen A. New Non Nucleosidic Phosphoramidites for the Solid Phase Multi-Labelling of Oligonucleotides: Comb- and Multifork-Like Structures. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/15257779408013219] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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13
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Miller GP, Kool ET. Versatile 5'-functionalization of oligonucleotides on solid support: amines, azides, thiols, and thioethers via phosphorus chemistry. J Org Chem 2004; 69:2404-10. [PMID: 15049637 DOI: 10.1021/jo035765e] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although the preparation of conjugates of oligonucleotides is by now commonplace, existing methods (usually utilizing thiols or primary amines) are generally expensive, and often require postsynthetic reaction with the DNA followed by a separate purification. Here we describe simple procedures for a broad set of direct 5'-end (5'-terminal carbon) functionalizations of DNA oligonucleotides while they remain on the synthesizer column. 5'-Iodinated oligonucleotides (prepared by an automated cycle as previously reported) are converted directly to 5'-azides, 5'-thiocarbamates, and alkyl and aryl 5'-thioethers in high yields. Further, we demonstrate high-yielding conversions of DNA-azides to 5'-amines, and of thiocarbamates to 5'-thiols. Finally, we report a new, one-pot conversion of naturally substituted 5'-OH oligonucleotides (again on the solid support) to 5'-amino-oligonucleotides. All of the above reactions are demonstrated in multiple sequence contexts. Most of the procedures are automatable.
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Affiliation(s)
- Gregory P Miller
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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Siroky J, Zluvova J, Riha K, Shippen DE, Vyskot B. Rearrangements of ribosomal DNA clusters in late generation telomerase-deficient Arabidopsis. Chromosoma 2003; 112:116-23. [PMID: 14579127 DOI: 10.1007/s00412-003-0251-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2003] [Accepted: 07/07/2003] [Indexed: 10/26/2022]
Abstract
The ends of eukaryotic chromosomes are capped with special nucleoprotein structures called telomeres. Telomere shortening due to telomerase inactivation may result in fusion of homologous or heterologous chromosomes, leading to their successive breakage during anaphase movement, followed by fusion of broken ends in the next cell cycle, i.e. the breakage-fusion-bridge (BFB) cycle. Using fluorescence in situ hybridization (FISH) with 25S rDNA and specific bacterial artificial chromosome (BAC) probes we demonstrate participation of chromosomes 2 and 4 of Arabidopsis thaliana AtTERT null plants in the formation of anaphase bridges. Both homologous and non-homologous chromosomes formed transient anaphase bridges whose breakage and unequal separation led to genome rearrangement, including non-reciprocal translocations and aneuploidy. The 45S rDNA regions located at the ends of chromosomes 2 and 4 were observed in chromosome bridges at a frequency approximately ten times higher than expected in the case of random fusion events. This outcome could result from a functional association of rDNA repeats at nucleoli. We also describe increased variation in the number of nucleoli in some interphase cells with supernumerary rDNA FISH signals. These data indicate that dysfunctional telomeres in Arabidopsis lead to massive genome instability, which is induced by multiple rounds of the BFB mechanism.
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Affiliation(s)
- Jiri Siroky
- Laboratory of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
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Virta P, Katajisto J, Niittymäki T, Lönnberg H. Solid-supported synthesis of oligomeric bioconjugates. Tetrahedron 2003. [DOI: 10.1016/s0040-4020(03)00704-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Forget D, Renaudet O, Boturyn D, Defrancq E, Dumy P. 3′-Oligonucleotides conjugation via chemoselective oxime bond formation. Tetrahedron Lett 2001. [DOI: 10.1016/s0040-4039(01)02017-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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17
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Lengerova M, Vyskot B. Sex chromatin and nucleolar analyses in Rumex acetosa L. PROTOPLASMA 2001; 217:147-153. [PMID: 11732306 DOI: 10.1007/bf01283395] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Rumex acetosa (sorrel) is a dioecious plant with a XX/XY1Y2 sex chromosome system. Both the Y chromosomes are nearly entirely heterochromatic and it has been hypothesised that they can persist as chromocenters in male interphase nuclei. Using specific antibodies against 5-methylcytosine and histone H4 acetylated at terminal lysine 5, global levels of DNA methylation and histone acetylation were studied on the sex chromosomes and autosomes of both sexes. The heterochromatic Y chromosomes did not display a higher methylation level compared to the autosomes. The only prominent hypermethylation signals were found at two nucleolar organising regions located on the autosome pair V, as confirmed by in situ hybridisation with 25S rDNA probe and staining. Immuno-analysis of DNA methylation on female and male interphase nuclei neither revealed any sex-specific differences. Two active (silver-positive) nucleoli and two likely inactive nucleolar organising regions (displaying prominent methylation signals) were found in both sexes. In a fraction of nuclei isolated from leaf cells, two peripheral bodies strongly positive for 4',6-diamidino-2-phenylindole were observed only in males, never in females. These heterochromatin regions were depleted in histone H4 acetylation at terminal lysine 5 and corresponded, according to in situ hybridisation with a Y-chromosome-specific repetitive probe, to the two Y chromosomes. We conclude that the peripheral condensed bodies observed exclusively in male nuclei represent the constitutive heterochromatin of the Y chromosomes which is characterised by a substantial histone H4 underacetylation.
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Affiliation(s)
- M Lengerova
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
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18
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Yager TD, Baron L, Batra R, Bouevitch A, Chan D, Chan K, Darasch S, Gilchrist R, Izmailov A, Lacroix JM, Marchelleta K, Renfrew J, Renfrew J, Rushlow D, Steinbach E, Ton C, Waterhouse P, Zaleski H, Dunn JM, Stevens J. High performance DNA sequencing, and the detection of mutations and polymorphisms, on the Clipper sequencer. Electrophoresis 1999; 20:1280-300. [PMID: 10380769 DOI: 10.1002/(sici)1522-2683(19990101)20:6<1280::aid-elps1280>3.0.co;2-#] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The Visible Genetics Clipper sequencer is a new platform for automated DNA sequencing which employs disposable MicroCel cassettes and 50 microm thick polyacrylamide gels. Two DNA ladders can be analyzed simultaneously in each of 16 lanes on a gel, after labeling with far-red absorbing dyes such as Cy5 and Cy5.5. This allows a simultaneous bidirectional sequencing of four templates. We have evaluated the Clipper sequencer, by cycle-sequencing of an M13 single-stranded DNA standard, and by coupled amplification and sequencing (CLIP) of reverse-transcribed human immunodeficiency virus (HIV-1) RNA standards and clinical patient samples. (i) Limitations of instrument. We have examined basic instrument parameters such as detector stability, background, digital sampling rate, and gain. With proper usage, the optical and electronic subsystems of the Clipper sequencer do not limit the data collection or sequence-determination processes. (ii) Limitations of gel performance. We have also examined the physics of DNA band separation on 50 microm thick MicroCel gels. We routinely obtain well-resolved sequence which can be base-called with 98.5% accuracy to position approximately 450 on an 11 cm gel, and to position approximately 900 on a 25 cm gel. Resolution on 5 and 11 cm gels ultimately is limited by a sharp decrease in spacing between adjacent bands, in the biased reptation separation regime. Fick's (thermal) diffusion appears to be of minor importance on 6 cm or 11 cm gels, but becomes an additional resolution-limiting factor on 25 cm gels. (iii) Limitations of enzymology. Template quality, primer nesting, choice of DNA polymerase, and choice between dye primers and dye terminators are key determinants of the ability to detect mutations and polymorphisms on the Clipper sequencer, as on other DNA sequencers. When CLIP is used with dye-labeled primers and a DNA polymerase of the F667Y, delta(5'--> 3' exo) class, we can routinely detect single-nucleotide mutations and polymorphisms over the 0.35-0.65 heterozygosity range. We present an example of detecting therapeutically relevant mutations in a clinical HIV-1 RNA isolate.
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Affiliation(s)
- T D Yager
- Visible Genetics, Toronto, ON, Canada.
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McMinn DL, Greenberg MM. Postsynthetic Conjugation of Protected Oligonucleotides Containing 3‘-Alkylamines. J Am Chem Soc 1998. [DOI: 10.1021/ja9740834] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Nelson PS, Muthini S, Kent MA, Smith TH. 3′-Terminal Modification of Oligonucleotides Using a Universal Solid Support. ACTA ACUST UNITED AC 1997. [DOI: 10.1080/07328319708002546] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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21
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Smith TH, Kent MA, Muthini S, Boone SJ, Nelson PS. Oligonucleotide Labeling Methods 4. Direct Labeling Reagents with a Novel, Non-Nucleosidic, Chirally Defined 2-Deoxy-β-D-Ribosyl Backbone. ACTA ACUST UNITED AC 1996. [DOI: 10.1080/07328319608002458] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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22
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Abstract
The simple use of nonisotopic hybridization probes to detect complementary sequences provides valuable information in a large number of research and commercial applications. In hybridization assays, the four "S's (speed, simplicity, sensitivity, and specificity) are important criteria for determining the choice of probe and label. The direct chemical combination of synthetic oligonucleotide probes and enzyme labels offer advantages unmatched by other approaches, with the oligonucleotide providing rapid hybridization and high specificity, and the direct enzyme label providing simple and sensitive detection. Such oligonucleotide-enzyme conjugates ("oligozymes") can be used in a variety of hybridization and detection formats, including dot blots, Southern/northern blots, in situ, and solution hybridization/capture schemes. The practical synthesis and use of such oligozymes are summarized.
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Affiliation(s)
- J L Ruth
- US Fish and Wildlife Forensics Laboratory, Ashland, OR 97520, USA
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Kumar P, Sharma AK, Gupta KC. Base-Labile Group Protected Biotinphosphoramidite Reagents for Solid Phase Biotinylation of Oligonucleotides. ACTA ACUST UNITED AC 1996. [DOI: 10.1080/07328319608002428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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24
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Novel solid phase synthesis supports for the preparation of oligonucleotides containing 3′-alkyl amines. Tetrahedron 1996. [DOI: 10.1016/s0040-4020(96)00053-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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25
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Guy-Caffey JK, Bodepudi V, Bishop JS, Jayaraman K, Chaudhary N. Novel polyaminolipids enhance the cellular uptake of oligonucleotides. J Biol Chem 1995; 270:31391-6. [PMID: 8537413 DOI: 10.1074/jbc.270.52.31391] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Two new polyaminolipids have been synthesized for the purpose of improving cellular uptake of oligonucleotides. The amphipathic compounds are conjugates of spermidine or spermine linked through a carbamate bond to cholesterol. The polyaminolipids are relatively nontoxic to mammalian cells. In tissue culture assays, using fluorescent-tagged or radiolabeled triple helix-forming oligonucleotides, spermine-cholesterol and spermidine-cholesterol significantly enhance cellular uptake of the oligomers in the presence of serum. Spermine-cholesterol is comparable with DOTMA/DOPE (a 1:1 (w/w) formulation of the cationic lipid N-[1-(2,3-dioleyloxy)-propyl]-N,N,N-trimethylammonium chloride (DOTMA) and the neutral lipid dioleylphosphatidylethanolamine (DOPE)) in increasing cellular uptake of oligonucleotides, while spermidine-cholesterol is more efficient. The internalized oligonucleotides are routed to the nucleus as early as 20 min after treatment, suggesting that the polyaminolipids increase the permeability of cellular membranes to oligonucleotides. At later times, much of the incoming oligonucleotides are sequestered within punctate cytoplasmic granules, presumably compartments of endosomal origin. Coadministration with polyaminolipids markedly improves the cellular stability of the oligonucleotides; more than 80% of the material can be recovered intact up to 24 h after addition to cells. In the absence of the polyaminolipids, nearly all of the material is degraded within 6 h. These data suggest that the new polyaminolipids may be useful for the delivery of nucleic acid-based therapeutics into cells.
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Affiliation(s)
- J K Guy-Caffey
- Aronex Pharmaceuticals, Inc., The Woodlands, Texas 77381, USA
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26
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A novel phosphoramidite for the site-selective introduction of functional groups into oligonucleotides via versatile tethers. Tetrahedron Lett 1994. [DOI: 10.1016/s0040-4039(00)78208-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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27
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Kumar P, Bhatia D, Garg B, Gupta K. An improved method for synthesis of biotin phosphoramidites for solid phase biotinylation of oligonucleotides. Bioorg Med Chem Lett 1994. [DOI: 10.1016/s0960-894x(00)80376-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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28
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Abstract
An overview on non-radioactive bioanalytical indicator systems is presented. The nature of labels being important for direct as well as indirect systems is discussed. This is followed by the description of enzymatic, photochemical and chemical methods for labeling nucleic acids, proteins and glycans. These methods can be applied either for direct labeling of these biomolecules or for labeling of respective probes (DNA, RNA, oligonucleotides, antibodies, lectins). In the second part, various optical, luminescent and fluorescent detection approaches are described. The possibility to enhance the sensitivity by coupled amplification reactions (signal amplification, target-specific signal amplification, target amplification) is shown in a separate section. Finally, the wide variety of qualitative and quantitative reaction formats related to different applications is collected.
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Affiliation(s)
- C Kessler
- Abt. Molekularbiologie, Boehringer Mannheim GmbH, Penzberg, Germany
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29
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Orson FM, Kinsey BM, McShan WM. Linkage structures strongly influence the binding cooperativity of DNA intercalators conjugated to triplex forming oligonucleotides. Nucleic Acids Res 1994; 22:479-84. [PMID: 8127688 PMCID: PMC523607 DOI: 10.1093/nar/22.3.479] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Conjugation of DNA intercalators to triple helix forming oligodeoxynucleotides (ODN's) can enhance ODN binding properties and consequently their potential ability to modulate gene expression. To test the hypothesis that linkage structure could strongly influence the binding enhancement of intercalator conjugation with triplex forming ODN's, we have used a model system to investigate binding avidity of short oligomers conjugated to DNA intercalators through various linkages. Using a dA10.T10 target sequence imbedded in a 20 bp duplex, binding avidities of a T10 ODN joined to the DNA intercalator 6,9-diamino, 3-methoxy acridine (DAMA) by 8 different 5' linkages were measured using an electrophoretic mobility shift assay. Although unmodified T10 has a very limited capacity for stable binding under these conditions (apparent Kd > 250 microM at 4 degrees C), conjugation to DAMA using flexible linkers of certain lengths and chemical compositions greatly enhanced binding (Kd of 1 microM at 4 degrees C). Other linkers, however, modestly enhanced binding or had no effect on binding at all. Thus, the length, flexibility, and chemical composition of linker structures all substantially influence intercalator conjugated oligodeoxynucleotide binding avidity.
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Affiliation(s)
- F M Orson
- Veterans Affairs Medical Center, Research Center on AIDS and HIV Infections, Houston, TX 77030
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30
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Agrawal S. Functionalization of oligonucleotides with amino groups and attachment of amino specific reporter groups. Methods Mol Biol 1994; 26:93-120. [PMID: 8313010 DOI: 10.1007/978-1-59259-513-6_3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- S Agrawal
- Worcester Foundation for Experimental Biology, Shrewsbury, MA
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31
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Affiliation(s)
- J L Ruth
- US Fish and Wildlife Forensics Laboratory, Ashland, OR
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32
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Hovinen J, Guzaev A, Azhayev A, Lönnberg H. Novel non-nucleosidic phosphoramidite building blocks for versatile functionalization of oligonucleotides at primary hydroxy groups. ACTA ACUST UNITED AC 1994. [DOI: 10.1039/p19940002745] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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33
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Ebbinghaus SW, Gee JE, Rodu B, Mayfield CA, Sanders G, Miller DM. Triplex formation inhibits HER-2/neu transcription in vitro. J Clin Invest 1993; 92:2433-9. [PMID: 7901237 PMCID: PMC288427 DOI: 10.1172/jci116850] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Triplex-forming oligonucleotides (TFOs) have been shown to bind to target DNA sequences in several human gene promoters such as the c-myc oncogene, the epidermal growth factor receptor, and the dihydrofolate reductase genes. TFOs have been shown to inhibit transcription in vitro and gene expression in cell culture of the c-myc and other genes. The HER-2/neu oncogene, which is overexpressed in breast cancer and other human malignancies, contains a purine-rich sequence in its promoter, which is favorable for purine:purine:pyrimidine (R:R:Y) triplex formation. Although its function in the HER-2/neu promoter is unknown, this purine-rich site is homologous to a protein-binding sequence in the promoter of the epidermal growth factor receptor that is necessary for efficient transcription of this gene. We have shown that this sequence is a site for nuclear protein binding by incubation with a crude nuclear extract. We describe the formation of an interstrand triplex using a purine-rich oligonucleotide antiparallel to this purine-rich target sequence of the HER-2/neu promoter. Triplex formation by the oligonucleotide prevents protein binding to the target site in the HER-2/neu promoter in vitro. We have shown that this oligonucleotide is a potent and specific inhibitor of HER-2/neu transcription in an in vitro assay. The triplex target site contains a single pyrimidine base that does not conform to the R:R:Y triplex motif. In an attempt to abrogate the potentially destabilizing effects of this pyrimidine base on triplex formation, we have substituted an abasic linker for the pyrimidine residue in the triplex forming oligonucleotide. Triplex formation with the modified oligonucleotide appears to occur with approximately equivalent binding affinity. Triplex formation in the HER-2/neu oncogene promoter prevents transcription in vitro and may represent a future modality for specific inhibition of this gene in vivo.
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Affiliation(s)
- S W Ebbinghaus
- Department of Medicine, University of Alabama at Birmingham
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34
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Grzybowski J, Will DW, Randall RE, Smith CA, Brown T. Synthesis and antibody-mediated detection of oligonucleotides containing multiple 2,4-dinitrophenyl reporter groups. Nucleic Acids Res 1993; 21:1705-12. [PMID: 8493087 PMCID: PMC309404 DOI: 10.1093/nar/21.8.1705] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A series of non-nucleoside-based 2,4-dinitrophenyl (DNP) phosphoramidites have been prepared and used in the multiple labelling of oligonucleotides during solid-phase synthesis. The length of spacer arm between the DNP label and the oligonucleotide phosphate backbone, and the number of attached DNP groups have both been varied in order to determine the optimum conditions for anti-DNP antibody binding. Detection using enzyme-linked colorimetric techniques showed sensitivity equivalent to that obtainable using biotinylated oligonucleotides.
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Affiliation(s)
- J Grzybowski
- Edinburgh Centre for Molecular Recognition, Department of Chemistry, University of Edinburgh, UK
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35
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Makrigiorgos GM, Baranowska-Kortylewicz J, Bump E, Sahu SK, Berman RM, Kassis AI. A method for detection of hydroxyl radicals in the vicinity of biomolecules using radiation-induced fluorescence of coumarin. Int J Radiat Biol 1993; 63:445-58. [PMID: 8096857 DOI: 10.1080/09553009314550601] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A novel method is described to quantitate radiation-induced hydroxyl radicals in the vicinity of biomolecules in aqueous solutions. Coumarin-3-carboxylic acid (CCA) is a non-fluorescent molecule that, upon interaction with radiation in aqueous solution, produces fluorescent products. CCA was derivatized to its succinimidyl ester (SECCA) and coupled to free primary amines of albumin, avidin, histone-H1, polylysine, and an oligonucleotide. When SECCA-biomolecule conjugates were irradiated, the relationship between induced fluorescence and dose was linear in the dose range examined (0.01-10 Gy). The fluorescence excitation spectrum of irradiated SECCA-biomolecule conjugates was very similar to that of 7-hydroxy-SECCA-biomolecule conjugates, indicating the conversion of SECCA to 7-hydroxy-SECCA following irradiation. Control studies in environments that excluded certain radiation-induced water radicals for both the conjugated and unconjugated forms of irradiated SECCA demonstrated that: (1) the induction of fluorescence is mediated by the hydroxyl radical; (2) the presence of oxygen enhances induced fluorescence by a factor of about 1.4, and (3) other primary water radicals and secondary radicals caused by interaction of primary water radicals with biomolecules do not significantly influence the induced fluorescence. The data indicate that the induction of fluorescence on SECCA-biomolecule conjugates records specifically the presence of the hydroxyl radical in the immediate vicinity of the irradiated biomolecule. The method is rapid and sensitive, uses standard instrumentation, and the sample remains available for further studies.
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Affiliation(s)
- G M Makrigiorgos
- Department of Radiation Oncology, Harvard Medical School, Boston, MA 02115
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36
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37
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Temsamani J, Tang JY, Padmapriya A, Kubert M, Agrawal S. Pharmacokinetics, biodistribution, and stability of capped oligodeoxynucleotide phosphorothioates in mice. ANTISENSE RESEARCH AND DEVELOPMENT 1993; 3:277-84. [PMID: 8286928 DOI: 10.1089/ard.1993.3.277] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Several end-modified oligodeoxynucleotide phosphorothioates (S-oligonucleotides) were studied for their pharmacokinetics, biodistribution, excretion, and metabolic stability in vivo after intravenous administration in mice. The overall tissue distribution and excretion patterns of these S-oligonucleotides were found to be independent of 5' or 3' end modification studied. However, the 3' end modification proved to be of considerable importance with respect to metabolic stability of the oligonucleotide. In the case of uncapped and 5'-capped S-oligonucleotide, only 50% of intact oligonucleotide was recovered out of the total bioavailable concentration in liver and kidney. In contrast, in the case of 3'-capped oligonucleotides almost all bioavailable concentrations of 3'-capped oligonucleotide was found to be intact in kidney and liver at 24 hr after administration. These results demonstrate that superior pharmaceutical potential can be created by 3'-end modification of oligonucleotide phosphorothioates.
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Affiliation(s)
- J Temsamani
- Hybridon, Inc., Worcester, Massachusetts 01605
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38
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Nelson PS, Kent M, Muthini S. Oligonucleotide labeling methods. 3. Direct labeling of oligonucleotides employing a novel, non-nucleosidic, 2-aminobutyl-1,3-propanediol backbone. Nucleic Acids Res 1992; 20:6253-9. [PMID: 1475185 PMCID: PMC334513 DOI: 10.1093/nar/20.23.6253] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Novel CE-phosphoramidite (7a-e) and CPG (8a, c, d, e) reagents have been prepared from a unique 2-aminobutyl-1,3-propanediol backbone. The reagents have been used to directly label oligonucleotides with fluorescein, acridine, and biotin via automated DNA synthesis. The versatile 2-aminobutyl-1,3-propanediol backbone allows for labeling at any position (5', internal, and 3') during solid phase oligonucleotide synthesis. Multiple labels can be achieved by repetitive coupling cycles. Furthermore, the 3-carbon atom internucleotide phosphate distance is retained when inserted internally. Using this method, individual oligonucleotides possessing two and three different reporter molecules have been prepared.
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Affiliation(s)
- P S Nelson
- Nucleic Acids Chemistry Division, Clontech Laboratories, Inc., Palo Alto, CA 94303
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39
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Abstract
A method which allows discrete nucleic acid sequences to be detected with differently colored hybridization signals on the same blot involving only a single hybridization step is described. Nucleic acid probes labeled with digoxigenin, fluorescein, or biotin are hybridized simultaneously to immobilized target nucleic acids. Differential colorimetric detection is carried out in consecutive alkaline phosphatase-based immunoassays with one of three 3-hydroxy-2-naphthoic acid anilide phosphate/diazonium salt combinations as substrate. Each label is visualized by a different color precipitate (green, red, and blue) directly on the membrane. We demonstrate the use of this method in multicolor plasmid mapping, detection of different genomic sequences on a single Southern blot, discrimination of transcription levels in a Northern blot, and colony screening. Advantages and limitations of the method, as well as further applications, are discussed.
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Affiliation(s)
- H J Hoeltke
- Department of Molecular Biology, Boehringer-Mannheim GmbH, Penzberg, Germany
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40
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41
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Zendegui JG, Vasquez KM, Tinsley JH, Kessler DJ, Hogan ME. In vivo stability and kinetics of absorption and disposition of 3' phosphopropyl amine oligonucleotides. Nucleic Acids Res 1992; 20:307-14. [PMID: 1741256 PMCID: PMC310371 DOI: 10.1093/nar/20.2.307] [Citation(s) in RCA: 99] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Development of oligonucleotide derivatives as therapeutic agents requires an understanding of their pharmacokinetic behavior. The in vivo disposition and stability of a prototype of such compounds are reported here. The compound studied, a relatively G-rich 38 base 3' phosphopropyl amine oligonucleotide (TFO-1), was cleared from the circulation with a half-life of approximately 10 minutes, displaying distribution kinetics consistent with a two compartment model. TFO-1 was also readily absorbed into circulation from the peritoneal cavity. All tissues examined except brain accumulated the compound reaching concentrations calculated to be in the micromolar range. TFO-1 was found to be stable in circulation and in tissues in that a large fraction of intact material was detected 8 hours after injection, as assessed by gel electrophoresis. Approximately 20-30% of the injected dose was excreted in the urine over an 8 hour period. These results suggest that G-rich oligonucleotides, minimally modified at the 3' end, are relatively stable in vivo and have distribution kinetics favorable to use as therapeutic agents.
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Affiliation(s)
- J G Zendegui
- Triplex Pharmaceutical Corporation, The Woodlands, TX 77380
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42
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Asseline U, Bonfils E, Kurfürst R, Chassignol M, Roig V, Thuong NT. Solid-phase preparation of 5′,3′-heterobifunctional oligodeoxyribonucleotides using modified solid supports. Tetrahedron 1992. [DOI: 10.1016/s0040-4020(01)90786-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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43
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Lin KY, Matteucci M. Hybridization properties of deoxyoligonucleotides containing anthraquinone pseudonucleosides. Nucleic Acids Res 1991; 19:3111-4. [PMID: 1711680 PMCID: PMC328278 DOI: 10.1093/nar/19.11.3111] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Achiral pseudonucleosides bearing an anthraquinone moiety have been incorporated into deoxyoligonucleotides in internal, 3' and 5' positions. The ability of these modified deoxyoligonucleotides to hybridize to complementary RNA and DNA was investigated using Tm measurements. The anthraquinone was shown to enhance binding to a complementary RNA when linked to the 3' and 5' end. Pseudonucleoside substitutions on the 3' end of an oligonucleotide are also shown to confer serum stability to the oligonucleotide.
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Affiliation(s)
- K Y Lin
- Gilead Sciences, Foster City, CA 94404
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44
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Kessler C. The digoxigenin:anti-digoxigenin (DIG) technology--a survey on the concept and realization of a novel bioanalytical indicator system. Mol Cell Probes 1991; 5:161-205. [PMID: 1870582 DOI: 10.1016/0890-8508(91)90041-h] [Citation(s) in RCA: 85] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A review is given on the novel non-radioactive digoxigenin:anti-digoxigenin (DIG) bioanalytical indicator system. After a general introduction on direct and indirect indicator systems based on previous non-radioactive indicator reactions as well as in vitro and in vivo amplification procedures the principle of the new digoxigenin:anti-digoxigenin technology is demonstrated. The novel system is based on the specific high-affinity interaction between the cardenolide digoxigenin from Digitalis plants and a digoxigenin-specific antibody coupled with a reporter group. A variety of methods for digoxigenin modification of nucleic acids, proteins and glycans are presented. In addition, various applications of the novel non-radioactive indicator system in a variety of direct or indirect detection approaches with either insoluble or soluble substrates are described. It is also shown that with these applications alternative reaction formats are used which are partly characterized by additional amplification steps.
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Affiliation(s)
- C Kessler
- Boehringer Mannheim GmbH, Biochemical Research Center, Department of Genetics, Penzberg, F.R.G
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45
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Abstract
Reliable methods of machine-aided RNA synthesis have been established to complement those for DNA assembly. Oligonucleotides containing thio-modified backbones and 2'-O-alkyl sugars head the list of many newly available analogues. Biotin, fluorescent agents and many reporter groups can be conveniently introduced into oligonucleotides in multiples by phosphoramidite or H-phosphonate chemistry.
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Affiliation(s)
- M J Gait
- Medical Research Council, Cambridge, UK
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46
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Morgan RL, Celebuski JE. Large-scale purification of haptenated oligonucleotides using high-performance liquid chromatography. J Chromatogr A 1991. [DOI: 10.1016/s0021-9673(01)89238-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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47
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Tang JY, Agrawal S. Incorporation of multiple reporter groups on synthetic oligonucleotides. Nucleic Acids Res 1990; 18:6461. [PMID: 2243811 PMCID: PMC332580 DOI: 10.1093/nar/18.21.6461] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- J Y Tang
- Worcester Foundation for Experimental Biology, Shrewsbury, MA 01545
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48
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Misiura K, Durrant I, Evans MR, Gait MJ. Biotinyl and phosphotyrosinyl phosphoramidite derivatives useful in the incorporation of multiple reporter groups on synthetic oligonucleotides. Nucleic Acids Res 1990; 18:4345-54. [PMID: 1697061 PMCID: PMC331250 DOI: 10.1093/nar/18.15.4345] [Citation(s) in RCA: 65] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Non-nucleosidic phosphoramidite linker units suitable for use on commercial DNA synthesis machines have been designed for the direct incorporation of biotin and a new reporter group, phosphotyrosine, at multiple sites on synthetic oligonucleotides. The units are based on a 3-carbon glyceryl backbone where the reporter group is attached to the 2-O-position through a 3-aminopropyl spacer. 17-mer oligonucleotides were synthesized carrying at the 5'-end 1, 2, 4 or 8 biotinyl units or 1, 2, 4 or 8 phosphotyrosinyl units respectively and used for the detection of DNA on nitrocellulose filters by hybridization. Subsequent incubation of the filters with a monoclonal antibody to the reporter group followed by secondary detection using enhanced chemiluminescence (ECL) resulted in amplification of signal strengths as the number of reporter groups was increased. The results were quantitated by use of a charge couple device (CCD) camera. Spacing of biotin moieties by thymidyl residues resulted in further improvements in signal strengths, whereas similar spacing of phosphotyrosinyl units did not.
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Affiliation(s)
- K Misiura
- MRC Laboratory of Molecular Biology, Cambridge, UK
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49
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Nelson PS, Frye RA, Liu E. Bifunctional oligonucleotide probes synthesized using a novel CPG support are able to detect single base pair mutations. Nucleic Acids Res 1989; 17:7187-94. [PMID: 2677994 PMCID: PMC334798 DOI: 10.1093/nar/17.18.7187] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
A novel multifunctional controlled pore glass, MF-CPG (Fig. 1), has been synthesized and used to incorporate 3' terminal primary aliphatic amines into synthetic oligonucleotides. MF-CPG consists of a unique succinic acid linking arm which possesses both a masked primary amine for label attachment and a dimethoxytrityl protected hydroxyl for nucleotide chain elongation. Using MF-CPG, we have devised a simple and convenient technique to attach non-radioactive labels to the 3' terminus of oligonucleotides. Bifunctional probes can then be constructed by 32P labeling the 5' terminus with T4 kinase and gamma 32P-ATP. Using such bifunctional oligonucleotide probes in conjunction with polymerase chain reaction (PCR) amplification, we were able to detect single base substitutions in a target segment of the human H-ras protooncogene employing either functionality. Our technique thus expands the potential applications for oligonucleotides as hybridization probes.
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Affiliation(s)
- P S Nelson
- Diagnostic Chemistry Division, Clontech Laboratories, Inc., Palo Alto, CA 94303
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