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Novikova D, Sagaidak A, Vorona S, Tribulovich V. A Visual Compendium of Principal Modifications within the Nucleic Acid Sugar Phosphate Backbone. Molecules 2024; 29:3025. [PMID: 38998973 PMCID: PMC11243533 DOI: 10.3390/molecules29133025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/21/2024] [Accepted: 06/24/2024] [Indexed: 07/14/2024] Open
Abstract
Nucleic acid chemistry is a huge research area that has received new impetus due to the recent explosive success of oligonucleotide therapy. In order for an oligonucleotide to become clinically effective, its monomeric parts are subjected to modifications. Although a large number of redesigned natural nucleic acids have been proposed in recent years, the vast majority of them are combinations of simple modifications proposed over the past 50 years. This review is devoted to the main modifications of the sugar phosphate backbone of natural nucleic acids known to date. Here, we propose a systematization of existing knowledge about modifications of nucleic acid monomers and an acceptable classification from the point of view of chemical logic. The visual representation is intended to inspire researchers to create a new type of modification or an original combination of known modifications that will produce unique oligonucleotides with valuable characteristics.
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Affiliation(s)
- Daria Novikova
- Laboratory of Molecular Pharmacology, St. Petersburg State Institute of Technology, St. Petersburg 190013, Russia
| | - Aleksandra Sagaidak
- Laboratory of Molecular Pharmacology, St. Petersburg State Institute of Technology, St. Petersburg 190013, Russia
| | - Svetlana Vorona
- Laboratory of Molecular Pharmacology, St. Petersburg State Institute of Technology, St. Petersburg 190013, Russia
| | - Vyacheslav Tribulovich
- Laboratory of Molecular Pharmacology, St. Petersburg State Institute of Technology, St. Petersburg 190013, Russia
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2
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Zharkov TD, Mironova EM, Markov OV, Zhukov SA, Khodyreva SN, Kupryushkin MS. Fork- and Comb-like Lipophilic Structures: Different Chemical Approaches to the Synthesis of Oligonucleotides with Multiple Dodecyl Residues. Int J Mol Sci 2023; 24:14637. [PMID: 37834092 PMCID: PMC10572690 DOI: 10.3390/ijms241914637] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
Lipophilic oligonucleotide conjugates represent a powerful tool for nucleic acid cellular delivery, and many methods for their synthesis have been developed over the past few decades. In the present study, a number of chemical approaches for the synthesis of different fork- and comb-like dodecyl-containing oligonucleotide structures were performed, including use of non-nucleotide units and different types of phosphate modifications such as alkyl phosphoramidate, phosphoryl guanidine, and triazinyl phosphoramidate. The influence of the number of introduced lipophilic residues, their mutual arrangement, and the type of formed modification backbone on cell penetration was evaluated. The results obtained indicate great potential in the developed chemical approaches, not only for the synthesis of complex oligonucleotide structures but also for the fine-tuning of their properties.
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Affiliation(s)
| | | | | | | | | | - Maxim S. Kupryushkin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of RAS, Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (T.D.Z.); (E.M.M.); (O.V.M.); (S.A.Z.); (S.N.K.)
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3
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Hansen RA, Märcher A, Pedersen KN, Gothelf KV. Insertion of Chemical Handles into the Backbone of DNA during Solid-Phase Synthesis by Oxidative Coupling of Amines to Phosphites. Angew Chem Int Ed Engl 2023; 62:e202305373. [PMID: 37119479 DOI: 10.1002/anie.202305373] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 05/01/2023]
Abstract
Conjugation of molecules or proteins to oligonucleotides can improve their functional and therapeutic capacity. However, such modifications are often limited to the 5' and 3' end of oligonucleotides. Herein, we report the development of an inexpensive and simple method that allows for the insertion of chemical handles into the backbone of oligonucleotides. This method is compatible with standardized automated solid-phase oligonucleotide synthesis, and relies on formation of phosphoramidates. A unique phosphoramidite is incorporated into a growing oligonucleotide, and oxidized to the desired phosphoramidate using iodine and an amine of choice. Azides, alkynes, amines, and alkanes have been linked to oligonucleotides via internally positioned phosphoramidates with oxidative coupling yields above 80 %. We show the design of phosphoramidates from secondary amines that specifically hydrolyze to the phosphate only at decreased pH. Finally, we show the synthesis of an antibody-DNA conjugate, where the oligonucleotide can be selectively released in a pH 5.5 buffer.
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Affiliation(s)
- Rikke A Hansen
- sDepartment of Chemistry and Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus, Denmark
| | - Anders Märcher
- sDepartment of Chemistry and Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus, Denmark
| | - Kristian Nørgaard Pedersen
- sDepartment of Chemistry and Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus, Denmark
| | - Kurt V Gothelf
- sDepartment of Chemistry and Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus, Denmark
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4
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Dovydenko IS, Kupryushkin MS, Pyshnyi DV, Apartsin EK. A convenient solid phase approach to obtain lipophilic 5'-phosphoramidate derivatives of DNA and RNA oligonucleotides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2018; 37:102-111. [PMID: 29424633 DOI: 10.1080/15257770.2017.1421765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
This paper explores the potential of a modified phosphotriester approach to the synthesis of 5'-phosphoramidate derivatives of DNA and RNA oligonucleotides. The modification of 5'-deprotected support-bound oligonucleotides is done in two steps: i) conversion of the 5'-OH group of an oligonucleotide into an activated phosphodiester, and ii) treatment of the activated phosphodiester with an aminocompound. The approach is efficient and compatible with conventional solid phase oligonucleotide synthesis. It can be used for the conjugation of therapeutically relevant oligonucleotides with functional moieties or carrier constructions, which are to be removed after endocytosis.
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Affiliation(s)
- Ilya S Dovydenko
- a Institute of Chemical Biology and Fundamental Medicine SB RAS , Novosibirsk , Russia
| | - Maxim S Kupryushkin
- a Institute of Chemical Biology and Fundamental Medicine SB RAS , Novosibirsk , Russia
| | - Dmitrii V Pyshnyi
- a Institute of Chemical Biology and Fundamental Medicine SB RAS , Novosibirsk , Russia
| | - Evgeny K Apartsin
- a Institute of Chemical Biology and Fundamental Medicine SB RAS , Novosibirsk , Russia
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5
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Paul S, Roy S, Monfregola L, Shang S, Shoemaker R, Caruthers MH. Oxidative substitution of boranephosphonate diesters as a route to post-synthetically modified DNA. J Am Chem Soc 2015; 137:3253-64. [PMID: 25679520 DOI: 10.1021/ja511145h] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The introduction of modifications into oligonucleotides is important for a large number of applications in the nucleic acids field. However, the method of solid-phase DNA synthesis presents significant challenges for incorporating many useful modifications that are unstable to the conditions for preparing synthetic DNA. Here we report that boranephosphonate diesters undergo facile nucleophilic substitution in a stereospecific manner upon activation by iodine. We have subsequently used this reactivity to post-synthetically introduce modifications including azides and fluorophores into DNA by first synthesizing boranephosphonate-linked 2'-deoxyoligonucleotides and then treating these oligomers with iodine and various nucleophiles. In addition, we show that this reaction is an attractive method for preparing stereodefined phosphorus-modified oligonucleotides. We have also examined the mechanism of this reaction and show that it proceeds via an iodophosphate intermediate. Beyond nucleic acids synthesis, due to the ubiquity of phosphate derivatives in natural compounds and therapeutics, this stereospecific reaction has many potential applications in organophosphorus chemistry.
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Affiliation(s)
- Sibasish Paul
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, Colorado 80303, United States
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6
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WITHDRAWN: Efficient transformation of nitroarenes into dialkyl N-arylphosphoramidates in one step under microwave conditions. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.10.006] [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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7
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Dohno C, Shibata T, Okazaki M, Makishi S, Nakatani K. Amphiphilic DNA Duplex Stabilized by a Hydrophobic Zipper. European J Org Chem 2012. [DOI: 10.1002/ejoc.201200540] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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8
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Veeneman GH, van der Marel GA, van den Elst H, van Boom JH. Synthesis of oligodeoxynucleotides containing thymidines linked via an internucleosidic-(3′-5′)-methylene bond. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19901090712] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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9
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Böhrsch V, Serwa R, Majkut P, Krause E, Hackenberger CPR. Site-specific functionalisation of proteins by a Staudinger-type reaction using unsymmetrical phosphites. Chem Commun (Camb) 2010; 46:3176-8. [DOI: 10.1039/b926818a] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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10
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Haggam R, Conrad J, Beifuss U. Practical and reliable synthesis of dialkyl N-arylphosphoramidates with nitroarenes as substrates. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2009.09.037] [Citation(s) in RCA: 21] [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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11
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12
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Peyrottes S, Vasseur JJ, Imbach JL, Rayner B. Synthesis, Base Pairing Properties and Nuclease Resistance of Oligothymidylate Analogs Containing Methoxyphosphoramidate Internucleoside Linkages. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/15257779408013213] [Citation(s) in RCA: 3] [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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13
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Rohr K, Vogel S. Polyaza Crown Ethers as Non-Nucleosidic Building Blocks in DNA Conjugates: Synthesis and Remarkable Stabilization of dsDNA. Chembiochem 2006; 7:463-70. [PMID: 16508997 DOI: 10.1002/cbic.200500392] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The synthesis of amphiphilic polyaza crown ether monomers X (benzyl-substituted), Y (palmityl-substituted) and Z (cholesteryl-substituted) and their incorporation into oligonucleotides are described. Their effects on thermal duplex stability were investigated by UV melting curve analysis in different alkaline metal buffer solutions. Thermal-denaturation experiments showed remarkable stabilization of dsDNA by polyaza crown ether monomers when incorporated in opposite positions. The series of polyaza crown ether monomers (X, Y and Z) with different overall lipophilicities showed a trend of increased stability of the corresponding dsDNA with increasing lipophilicity of the polyaza crown ether monomer. Multiple incorporations of benzyl-substituted polyaza crown ether monomer X as dangling ends on both sides of dsDNA resulted in strongly increased stability of the corresponding duplex.
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Affiliation(s)
- Katja Rohr
- Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
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14
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Ruozi B, Battini R, Tosi G, Forni F, Vandelli MA. Liposome-oligonucleotides interaction for in vitro uptake by COS I and HaCaT cells. J Drug Target 2005; 13:295-304. [PMID: 16199373 DOI: 10.1080/10611860500215014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Liposomes are considered very promising delivery systems for antisense therapeutic approach, offering drug protection and facilitating oligonucleotide cell internalization. The present study was aimed to investigate the influence of phospholipid composition of the liposomal systems both on the encapsulation and on the oligonucleotide carrier capacity in vitro. Liposomes composed of neutral (phosphatidylcholine, cholesterol and dioleoylphosphatidylethanolamine) and/or cationic lipids (N-(1-(2,3-dioleoyloxy)propyl)-N,N,N-trimethylammonium chloride salt, DOTAP) with different molar ratios were complexed with 5' fluorescein conjugated 29-mer phosphorothioate oligonucleotide (PS-ODN). The interaction was evaluated using atomic force microscopy (AFM), gel electrophoresis and HPLC analysis. Cytofluorimetric analysis and fluorescence microscopy were applied to evaluate the uptake and intracellular distribution of fluorescently labelled PS-ODN after transfection in two cell lines, COS I (fibroblast cell) and HaCaT (immortalized keratinocyte cell). The AFM studies reveal that the liposome/PS-ODN interaction leads the formation of a new irregular structure that completely hides the PS-ODN. Gel electrophoresis experiments and HPLC analysis have clearly demonstrated that also neutral liposomes are able to keep a little amount of PS-ODN but without strain to the complexation; the interaction was weak and rapidly destabilized when the complex was added to the cells. Transfection experiments performed with different incubation times show that DOTAP liposomes increase the rate of cellular uptake of PS-ODN and seem to influence its intracellular distribution in COS I cells where the oligonucleotide looks localized in nucleoli. Similar behaviour, at a lesser extent, is exhibited in HaCaT cells.
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Affiliation(s)
- Barbara Ruozi
- University of Modena and Reggio Emilia, Department of Pharmaceutical Sciences, Via Campi 183, 41100, Modena, Italy
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15
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16
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Challa H, Bruice TC. Incorporation of positively charged deoxynucleic S-methylthiourea linkages into oligodeoxyribonucleotides. Bioorg Med Chem Lett 2001; 11:2423-7. [PMID: 11549438 DOI: 10.1016/s0960-894x(01)00455-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Oligodeoxyribonucleic acids (15- and 18-mers) containing both negatively charged phosphate and positively charged S-methyl thiourea internucleoside linkages (DNmt/DNA chimera) have been synthesized. DNA binding characteristics and nuclease resistance of DNmt/DNA chimera have been evaluated.
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Affiliation(s)
- H Challa
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, 93106, USA
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17
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Laurent A, Naval M, Debart F, Vasseur JJ, Rayner B. Chiral and steric effects in the efficient binding of alpha-anomeric deoxyoligonucleoside N-alkylphosphoramidates to ssDNA and RNA. Nucleic Acids Res 1999; 27:4151-9. [PMID: 10518605 PMCID: PMC148688 DOI: 10.1093/nar/27.21.4151] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We report hybridization properties of new phosphate-modified alpha-oligonucleoside analogs with non-ionic or cationic internucleotide linkages such as methoxy-ethylphosphoramidate (PNHME), phosphoromorpholi-date (PMOR) and dimethylaminopropylphosphor-amidate (PNHDMAP). First we evaluated the chirality effect of the phosphorus atom on the affinity of alpha- or beta-dodecanucleoside phosphodiesters containing one chirally enriched N -alkylphosphoramidate linkage located in the middle of the sequence d(TCTT-AA*CCCACA). As for P-substituted beta-oligonucleo-tides, a difference in binding behavior between the two diastereoisomers (difference in Delta T (m)) exists in the hybridization properties of alpha-analogs when DNA was the target but this effect was not detrimental to duplex stability. This effect was considerably reduced when RNA was the target. Secondly we studied the effect of steric hindrance around phosphorus on the affinity of fully modified beta- and alpha-oligonucleoside N -alkylphosphoramidates for their DNA and RNA targets. This effect was very weak with alpha-analogs whereas it was more pronounced with beta-oligos. PNHME-modified alpha-oligonucleosides formed more stable duplexes with DNA (Delta T (m)+9.6 degrees C) and RNA (Delta T (m)+1.4 degrees C) targets than the 'parent' phosphodiester. Finally, base pairing specificity of these alpha-oligonucleo-side N -alkylphosphoramidates for their targets was found to be as high as for natural oligonucleoside phosphodiesters.
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Affiliation(s)
- A Laurent
- Laboratoire de Chimie Organique Biomoléculaire de Synthèse, UMR 5625 CNRS-UM II, CC 008, Université Montpellier II, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
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18
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Davis PW, Osgood SA. A new method for introducing amidate linkages in oligonucleotides using phosphoramidite chemistry. Bioorg Med Chem Lett 1999; 9:2691-2. [PMID: 10509917 DOI: 10.1016/s0960-894x(99)00467-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Cyanoethyl-protected phosphotriester links in oligonucleotides made with standard pophosporamidite chemistry were converted to pbosphoramidate linkages during oligonucleotide synthesis on solid support. The cyanoethyl group was removed with piperidine, and the resulting phosphodiester was activated with p-tosyl chloride. An amine nucleophile displaced the tosyl to yield a phosphoramidate linkage.
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Affiliation(s)
- P W Davis
- Isis Pharmaceuticals, Inc., Carlsbad, CA 92008, USA
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19
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Synthesis and triple helix-forming ability of oligonucleotides with N,N-dimethylaminoethyl phosphoramidate linkages. Tetrahedron Lett 1999. [DOI: 10.1016/s0040-4039(99)01478-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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20
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Baraniak J, Korczyński D, Kaczmarek R, Wasilewska E. New Approach to the Solid Phase Synthesis of N3′→P5′ Phosphoramidate Oligonucleotides. ACTA ACUST UNITED AC 1998. [DOI: 10.1080/07328319808003473] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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21
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Fresta M, Chillemi R, Spampinato S, Sciuto S, Puglisi G. Liposomal delivery of a 30-mer antisense oligodeoxynucleotide to inhibit proopiomelanocortin expression. J Pharm Sci 1998; 87:616-25. [PMID: 9572914 DOI: 10.1021/js9702978] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
An oligodeoxynucleic sequence of 30 bases (30-mer ODN), complementary to a region of beta-endorphin mRNA, was synthesized to have an antisense effect with regard to the expression of this oligopeptide. Following the solid-phase synthesis of the oligodeoxynucleotide, the 30-mer ODN was encapsulated within liposomes to provide a higher resistance against DNases and an improved entrance into cells. The most suitable liposome formulation as a 30-mer ODN carrier consisted of small unilamellar vesicles (50 nm) with an encapsulation capacity of 4.76 microL/micromol. The liposomal formulations containing dipalmitoyl-DL-alpha-phosphatidyl-L-serine presented fusogenic properties, which are of great importance for the delivery of antisense compounds. The antisense activity of 30-mer ODN-loaded liposomes was evaluated by the determination of beta-endorphin levels in AtT-20 cells. The free 30-mer ODN did not provide any lowering of the beta-endorphin production, whereas the liposomally entrapped compound elicited a concentration-dependent inhibition. The inhibition was determined by a sequence-specific binding of the 30-mer ODN with the target mRNA.
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Affiliation(s)
- M Fresta
- Dipartimento di Scienze Farmaceutiche, Facoltà di Farmacia, Università di Catania, Viale Andrea Doria 6, I-95125 Catania, Italy
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22
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Saison-Behmoaras TE, Duroux I, Nguyen TT, Asseline U, Hélène C. Antisense properties of end-modified oligonucleotides targeted to Ha-ras oncogene. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 1997; 7:361-8. [PMID: 9303188 DOI: 10.1089/oli.1.1997.7.361] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Phosphodiester oligodeoxyribonucleotides linked to an intercalating agent or a dodecanol tail or both complementary to the 12th codon region of Ha-ras mRNA were compared with the unmodified oligonucleotides of the same size and sequence with respect to their ability to induce RNaseH cleavage and antisense activity in cell culture. The hydrophobic tail not only protected the oligonucleotide from nucleases but also enhanced RNase H cleavage of the target. Oligonucleotides carrying both an acridine and a dodecanol substituent inhibited the proliferation of HBL100ras1 cells (human mammary cells stably transformed with the T24 Ha-ras gene carrying a G-->T point mutation in codon 12) at a 20-fold to 30-fold lower concentration than unmodified ones. Therefore, these modified oligonucleotides may prove useful for antisense applications.
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23
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Laurent A, Debart F, Rayner B. A new route to oligodeoxynucleoside phosphoramidates (PNH2). Tetrahedron Lett 1997. [DOI: 10.1016/s0040-4039(97)01153-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
Antisense oligonucleotides represent a novel class of potential drugs for highly selective blocking of genes. The basic concept of antisense strategy is simple: an antisense molecule recognizes a complementary mRNA (or DNA) by sequence-specific base pairing, and hence prevents translation (or transcription), resulting in a selective inhibition of protein synthesis. Because of these properties, antisense oligonucleotides have great potential as therapeutic agents in several human diseases, such as viral diseases, malignancies and dominant hereditary diseases. However, technical difficulties have slowed down their use as drugs: structural modifications are needed to increase the stability and potency of synthetic oligonucleotides, specific delivery systems are required to facilitate their entry into target cells, and more information is needed to their mechanism of action. Much of the current research on antisense oligonucleotides takes place at the interface of chemistry and biomedical sciences, a multidisciplinary field where finding a common language is sometimes difficult. The aim of this review is to present an overview of the antisense strategy in terms which should be understandable for chemists, biologists and physicians.
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Affiliation(s)
- H Lönnberg
- Department of Chemistry Turku University, Finland
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26
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Wiederholt K, Rajur SB, Giuliano J, O'Donnel MJ, McLaughlin LW. DNA-Tethered Hoechst Groove-Binding Agents: Duplex Stabilization and Fluorescence Characteristics. J Am Chem Soc 1996. [DOI: 10.1021/ja960948m] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kristin Wiederholt
- Contribution from the Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02167
| | - Sharanabasava B. Rajur
- Contribution from the Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02167
| | - John Giuliano
- Contribution from the Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02167
| | - Maryanne J. O'Donnel
- Contribution from the Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02167
| | - Larry W. McLaughlin
- Contribution from the Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02167
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27
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Chaturvedi S, Horn T, Letsinger RL. Stabilization of triple-stranded oligonucleotide complexes: use of probes containing alternating phosphodiester and stereo-uniform cationic phosphoramidate linkages. Nucleic Acids Res 1996; 24:2318-23. [PMID: 8710502 PMCID: PMC145931 DOI: 10.1093/nar/24.12.2318] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Pyrimidine oligonucleotides containing alternating anionic and stereo-uniform cationic N-(dimethylamino-propyl)phosphoramidate linkages [e.g. d(T+T-)7T, d(T+T-)2(T+C-)5T and (U'+U'-)7dT, where U' is 2'-O-methyluridine)] are shown to bind to complementary double-stranded DNA segments in 0.1 M NaCl at pH 7 to form triple-stranded complexes with the pyrimidine.purine.pyrimidine motif. For each of the sequences investigated, one stereoisomer bound with higher affinity, and the other stereoisomer with lower affinity, than the corresponding all-phosphodiester oligonucleotide. The stereoisomer of d(T+T-)7T that interacted weakly with a dT.dA target in 0.1 M NaCl formed a novel dA.dA.dT triple-stranded complex with poly(dA) or d(Al5C4A15) in 1 M NaCl; in contrast, the stereoisomer that bound strongly to the dT.dA target failed to form a dA.dA.dT triple-stranded complex.
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Affiliation(s)
- S Chaturvedi
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
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28
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Switzer C, Prakash TP, Ahn Y. Synthesis and characterization of an oligonucleotide containing the bifurcated nucleobase ω-adenylpropyl uracil. Bioorg Med Chem Lett 1996. [DOI: 10.1016/0960-894x(96)00112-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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29
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Endo M, Komiyama M. Novel Phosphoramidite Monomer for the Site-Selective Incorporation of a Diastereochemically Pure Phosphoramidate to Oligonucleotide. J Org Chem 1996. [DOI: 10.1021/jo951621r] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Masayuki Endo
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113, Japan
| | - Makoto Komiyama
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113, Japan
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Oligonucleotides with alternating anionic and cationic phosphoramidate linkages: Synthesis and hybridization of stereo-uniform isomers. Tetrahedron Lett 1996. [DOI: 10.1016/0040-4039(95)02309-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Ikeda H, Fuji K, Tanaka K. Preparation, characterization and DNA photocleavage of diazapyrene-tethered oligothymidylates. Bioorg Med Chem Lett 1996. [DOI: 10.1016/0960-894x(95)00567-d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Li H, Porter K, Huang F, Shaw BR. Boron-containing oligodeoxyribonucleotide 14mer duplexes: enzymatic synthesis and melting studies. Nucleic Acids Res 1995; 23:4495-501. [PMID: 7501475 PMCID: PMC307409 DOI: 10.1093/nar/23.21.4495] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
A set of three 14mer oligodeoxyribonucleotides of sequence d(5'-CTATGGCCTCAG*CT-3'/3'-GATACCGGAGTCGA-5') containing G* variants either as 2'-deoxyguanosine phosphate (unmodified), N7-cyanoborane 2'-deoxyguanosine phosphate (base-modified) or 2'-deoxyguanosine boranophosphate (backbone-modified) were synthesized by template-directed primer extension. Both the N7-cyanoborane 2'-deoxyguanosine triphosphate and 2'-deoxyguanosine alpha-boranotriphosphate nucleotides are good substrates for Sequenase. We infer that a single Sp boranophosphate linkage (which has a stereochemistry equivalent to the corresponding Rp thiophosphate analog) is formed in the backbone-modified 14mer. Thermally induced helix-coil transitions were monitored for the hybridized duplexes using UV and circular dichroism (CD) spectroscopy. The CD spectra of the two types of boron-modified hybrids closely resemble the unmodified parent duplex, forming B-type helices in 150 mM NaCl, 1 mM EDTA, 10 mM phosphate, pH 7.4, buffer. UV melting results indicate that both hybrids have stabilities comparable with the parent duplex as measured by Tm or delta G degree 25. These studies indicate that singly modified base- or backbone-boronated DNA are good analogs of normal DNA.
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Affiliation(s)
- H Li
- Department of Chemistry, Duke University, Durham, NC 27708-0346, USA
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Jørgensen PN, Svendsen ML, Scheuer-Larsen C, Wengel J. Incorporation of 3′-C-(Hydroxymethyl)thymidine into novel oligodeoxynucleotide analogues. Tetrahedron 1995. [DOI: 10.1016/0040-4020(94)01089-i] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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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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O'Donnel MJ, Herbert N, McLaughlin LW. The stereospecific introduction of reporter groups to oligodeoxynucleotides by the labeling of individual phosphorus diastereomers. Bioorg Med Chem Lett 1994. [DOI: 10.1016/s0960-894x(01)80670-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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37
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Manoharan M, Johnson LK, Bennett C, Vickers TA, Ecker DJ, Cowsert LM, Freier SM, Dan Cook P. Cholic acid-oligonucleotide conjugates for antisense applications. Bioorg Med Chem Lett 1994. [DOI: 10.1016/s0960-894x(01)80680-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Pantopoulos K, Johansson HE, Hentze MW. The role of the 5' untranslated region of eukaryotic messenger RNAs in translation and its investigation using antisense technologies. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1994; 48:181-238. [PMID: 7938549 PMCID: PMC7133200 DOI: 10.1016/s0079-6603(08)60856-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
This chapter discusses the recent advances in the field of translational control and the possibility of applying the powerful antisense technology to investigate some of the unanswered questions, especially those pertaining to the role of the 5’untranslated region ( UTR) on translation initiation. Translational regulation is predominantly exerted during the initiation phase that is considered to be the rate-limiting step. Two types of translational regulation can be distinguished: global, in which the initiation rate of (nearly) all cellular messenger RNA (mRNA) is controlled and selective, in which the translation rate of specific mRNAs varies in response to the biological stimuli. In most cases of global regulation, control is exerted via the phosphorylation state of certain initiation factors, whereas only a few examples of selective regulation have been characterized well enough to define the underlying molecular events. Interestingly, cis-acting regulatory sequences, affecting translation initiation, have been found not only in the 5’UTRs of selectively regulated mRNAs, but also in the 3’UTRs. Thus, in addition to the protein encoding open reading frames, both the 5’ and 3’UTRs of mRNAs must be considered for their effect on translation.
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Key Words
- alas, 5-aminolevulinate synthase
- bfgf, basic fibroblast growth factor
- bip, immunoglobulin-binding protein
- cat, chloramphenicol acetyltransferase
- dai, double-stranded rna-activated inhibitor
- ealas, erythroid-specific form of alas
- frp, ferritin repressor protein
- gcd, general control derepressible
- gcn, general control nonderepressible
- gef, guanine-nucleotide exchange factor
- grp, glucose-regulated protein
- hgh, human growth hormone
- icam, intracellular adhesion molecule
- ire, iron-responsive element
- ire-bp, iron-responsive element-binding protein
- ires, internal ribosomal entry site
- irf, iron regulatory factor
- irp, iron regulatory protein
- la, lupus erythematosus antigen
- lap, liver-enriched activating protein
- lip, liver-enriched inhibitory protein
- mep, methyl phosphonate
- pa, phosphoramidate
- pdgf, platelet-derived growth factor
- pest, phosphotriester
- pll, poly(1-lysine)
- po, phosphodiester
- ps, phosphorothioate
- ps2, phosphorodithioate
- ssl, suppressor of stem-loop
- tce, translational control element
- tgf, transforming growth factor
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Affiliation(s)
- K Pantopoulos
- Gene Expression Programme, European Molecular Biology Laboratory, Heidelberg, Germany
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Affiliation(s)
- J W Jaroszewski
- Department of Organic Chemistry, Royal Danish School of Pharmacy, Copenhagen
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Fidanza JA, Ozaki H, McLaughlin LW. Functionalization of oligonucleotides by the incorporation of thio-specific reporter groups. Methods Mol Biol 1994; 26:121-43. [PMID: 8313000 DOI: 10.1007/978-1-59259-513-6_4] [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: 01/29/2023]
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41
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Beaucage SL, Iyer RP. The synthesis of modified oligonucleotides by the phosphoramidite approach and their applications. Tetrahedron 1993. [DOI: 10.1016/s0040-4020(01)87958-8] [Citation(s) in RCA: 277] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Bevan C, Mutton I, Pipe A. Resolution of diastereomeric phosphoramidate bridged unnatural oligonucleotides by micellar electrokinetic chromatography. J Chromatogr A 1993. [DOI: 10.1016/0021-9673(93)80063-e] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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43
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Ozaki H, McLaughlin LW. The estimation of distances between specific backbone-labeled sites in DNA using fluorescence resonance energy transfer. Nucleic Acids Res 1992; 20:5205-14. [PMID: 1408835 PMCID: PMC334306 DOI: 10.1093/nar/20.19.5205] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A series DNA helices of twenty-four base pairs has been prepared for the study of fluorescence resonance energy transfer. Each of the DNA helices contains two phosphorothioate diesters (one in each strand) at pre-selected sites for introduction of the desired donor and acceptor fluorophores. The phosphorothioate-containing oligodeoxynucleotides have been prepared as pure Rp or Sp derivatives or as deastereomeric mixtures. Fluorescein and eosin are employed as the respective donor and acceptor fluorophores. A series of donor-acceptor pairs was generated by labeling of the appropriate phosphorothioate diester with the desired fluorophore and annealing the two complementary DNA strands (one containing the acceptor and one containing the donor fluorophore) to form the double-stranded helix. The 24-mer helices containing two covalently attached fluorophores exhibited some thermal destabilization and the extent of this destabilization was dependent upon the stereochemical orientation of the fluorophore. The Sp derivatives direct the fluorophore out, away from the the DNA helix, while the Rp derivatives direct the fluorophore toward the major groove. As expected, the Sp labeled duplexes were more stable than the corresponding Rp labeled sequences. However, all of the duplex structures formed were stable under the conditions used to measure energy transfer. Energy transfer could be observed with these complexes from the quenching of the donor fluorescence in the presence of the acceptor fluorophore. Using Förster's theories, distances separating the fluorophores could be calculated that were generally in reasonable agreement with the distances expected in an idealized B-form DNA helix. However anomalous results were obtained for one donor/acceptor pair where the expected distance was less than 20 A. Fluorescence anisotropy values determined in solutions of varying viscosity were quite high suggesting that the fluorophores did not experience complete freedom of movement when attached to the DNA helix.
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Affiliation(s)
- H Ozaki
- Department of Chemistry, Boston College, Chestnut Hill, MA 02167
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45
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Sun JS, Lavery R. Strand orientation of [alpha]-oligodeoxynucleotides in triple helix structures: dependence on nucleotide sequence. J Mol Recognit 1992; 5:93-8. [PMID: 1298305 DOI: 10.1002/jmr.300050304] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The aims of the present theoretical study of the conformations of [alpha]-oligodeoxynucleotides forming triple helices with DNA duplexes are to understand the structural and energetic factors involved in [alpha]-triple helix formation by means of energy minimization, and to explain the experimentally observed dependence of strand orientation on the nucleotide sequence. It is found that the energetically preferred orientation of the [alpha]-oligonucleotide with respect to the homopurine strand depends on the sequence of the homopurine.homopyrimidine tracts. This is a consequence of the structural heteromorphism of base triplets in the intrinsically more stable reverse Hoogsteen hydrogen bonding configuration. Practical rules are proposed for determining the orientation of the nuclease-resistant [alpha]-oligodeoxynucleotide strand which will form the most stable triple helix.
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Affiliation(s)
- J S Sun
- Laboratoire de Biophysique, Muséum National d'Histoire Naturelle, INSERM U201, CNRS UA481, Paris, France
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46
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MacKellar C, Graham D, Will DW, Burgess S, Brown T. Synthesis and physical properties of anti-HIV antisense oligonucleotides bearing terminal lipophilic groups. Nucleic Acids Res 1992; 20:3411-7. [PMID: 1630912 PMCID: PMC312497 DOI: 10.1093/nar/20.13.3411] [Citation(s) in RCA: 105] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
A number of phosphoramidite monomers have been prepared and used in the synthesis of antisense phosphorothioate oligonucleotides bearing 5'-polyalkyl and cholesterol moieties. Similar groups have also been attached to the 3'-end of oligonucleotides by means of functionalised CPG. Melting temperatures of duplexes formed between phosphorothioate oligonucleotides with lipophilic end-groups and complementary DNA strands were found to be identical to those formed by the equivalent unmodified phosphorothioates.
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Affiliation(s)
- C MacKellar
- Department of Chemistry, University of Edinburgh, UK
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47
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Iso Y, Yoneda F, Ikeda H, Tanaka K, Fuji K. Synthesis of viologen-tagged oligodeoxynucleotides. Tetrahedron Lett 1992. [DOI: 10.1016/s0040-4039(00)93980-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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48
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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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49
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Nagai K, Hecht S. Site-specific DNA cleavage by antisense oligonucleotides covalently linked to phenazine di-N-oxide. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)54382-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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50
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Sun JS, Giovannangeli C, François JC, Kurfurst R, Montenay-Garestier T, Asseline U, Saison-Behmoaras T, Thuong NT, Hélène C. Triple-helix formation by alpha oligodeoxynucleotides and alpha oligodeoxynucleotide-intercalator conjugates. Proc Natl Acad Sci U S A 1991; 88:6023-7. [PMID: 2068079 PMCID: PMC52014 DOI: 10.1073/pnas.88.14.6023] [Citation(s) in RCA: 83] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Base-pair sequences in double-stranded DNA can be recognized by homopyrimidine oligonucleotides that bind to the major groove at homopurine.homopyrimidine sequences thereby forming a local triple helix. To make oligodeoxynucleotides resistant to nucleases, we replaced the natural (beta) anomers of the nucleotide units by the synthetic (alpha) anomers. The 11-mer alpha oligodeoxynucleotide 5'-d(TCTCCTCCTTT)-3' binds to the major groove of DNA in an antiparallel orientation with respect to the homopurine strand, whereas a beta oligonucleotide adopts a parallel orientation. When an intercalating agent was attached to the 3' end of the alpha oligodeoxynucleotide, a strong stabilization of the triple helix was observed. A 16-base-pair homopurine.homopyrimidine sequence of human immunodeficiency virus proviral DNA was chosen as a target for a 16-mer homopyrimidine alpha oligodeoxynucleotide. A restriction enzyme that cleaves DNA at the junction of the homopurine.homopyrimidine sequence was inhibited by triple-helix formation. The 16-mer alpha oligodeoxynucleotide substituted by an intercalating agent was approximately 20 times more efficient than the unsubstituted oligomer. Nuclease-resistant alpha oligodeoxynucleotides offer additional possibilities to control gene expression at the DNA level.
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Affiliation(s)
- J S Sun
- Laboratoire de Biophysique, Muséum National d'Histoire Naturelle, Institut National de la Santé et de la Recherche Médicale, Paris, France
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