1
|
Evéquoz D, Verhaart IEC, van de Vijver D, Renner W, Aartsma-Rus A, Leumann CJ. 7',5'-alpha-bicyclo-DNA: new chemistry for oligonucleotide exon splicing modulation therapy. Nucleic Acids Res 2021; 49:12089-12105. [PMID: 34850138 PMCID: PMC8643641 DOI: 10.1093/nar/gkab1097] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 10/12/2021] [Accepted: 10/25/2021] [Indexed: 01/16/2023] Open
Abstract
Antisense oligonucleotides are small pieces of modified DNA or RNA, which offer therapeutic potential for many diseases. We report on the synthesis of 7′,5′-α-bc-DNA phosphoramidite building blocks, bearing the A, G, T and MeC nucleobases. Solid-phase synthesis was performed to construct five oligodeoxyribonucleotides containing modified thymidine residues, as well as five fully modified oligonucleotides. Incorporations of the modification inside natural duplexes resulted in strong destabilizing effects. However, fully modified strands formed very stable duplexes with parallel RNA complements. In its own series, 7′,5′-α-bc-DNA formed duplexes with a surprising high thermal stability. CD spectroscopy and extensive molecular modeling indicated the adoption by the homo-duplex of a ladder-like structure, while hetero-duplexes with DNA or RNA still form helical structure. The biological properties of this new modification were investigated in animal models for Duchenne muscular dystrophy and spinal muscular atrophy, where exon splicing modulation can restore production of functional proteins. It was found that the 7′,5′-α-bc-DNA scaffold confers a high biostability and a good exon splicing modulation activity in vitro and in vivo.
Collapse
Affiliation(s)
- Damien Evéquoz
- Alpha Anomeric, 140 Bis, Rue de Rennes, 75006 Paris, France
| | - Ingrid E C Verhaart
- Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Davy van de Vijver
- Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | | | - Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Christian J Leumann
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| |
Collapse
|
2
|
Ni G, Du Y, Tang F, Liu J, Zhao H, Chen Q. Review of α-nucleosides: from discovery, synthesis to properties and potential applications. RSC Adv 2019; 9:14302-14320. [PMID: 35519323 PMCID: PMC9064229 DOI: 10.1039/c9ra01399g] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 04/29/2019] [Indexed: 02/05/2023] Open
Abstract
Nucleic acids play an important role in the genetic process of organisms; nucleosides, the building block of nucleic acids, typically exist in nature in a β configuration. As an anomer of β-nucleoside, α-nucleoside is extremely rare in nature. Because of their unique and interesting properties such as high stability, specific parallel double-stranded structure and some other biochemical properties, α-nucleosides have attracted wide attention. Various methods including but not limited to the mercuri procedure, fusion reaction and Vorbrüggen glycosylation have been used to synthesize α-nucleosides and their derivatives. However, to the best of our knowledge, there is no review that has summarized these works. Therefore, we systematically review the discovery, synthesis, properties, and potential applications of α-nucleosides in this article and look to provide a reference for subsequent studies in the coming years.
Collapse
Affiliation(s)
- Guangcheng Ni
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University Chengdu Sichuan 610041 P. R. China
| | - Yuqi Du
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University Chengdu Sichuan 610041 P. R. China
| | - Fan Tang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University Chengdu Sichuan 610041 P. R. China
| | - Jiang Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University Chengdu Sichuan 610041 P. R. China
| | - Hang Zhao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University Chengdu Sichuan 610041 P. R. China
| | - Qianming Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University Chengdu Sichuan 610041 P. R. China
| |
Collapse
|
3
|
Chatelain G, Meyer A, Morvan F, Vasseur JJ, Chaix C. Electrochemical detection of nucleic acids using pentaferrocenyl phosphoramidate α-oligonucleotides. NEW J CHEM 2011. [DOI: 10.1039/c0nj00902d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
4
|
Morvan F, Debart F, Vasseur JJ. From anionic to cationic alpha-anomeric oligodeoxynucleotides. Chem Biodivers 2010; 7:494-535. [PMID: 20232324 DOI: 10.1002/cbdv.200900220] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- François Morvan
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS, Université Montpellier 1 and Université Montpellier 2, Place Eugène Bataillon, CC1704, FR-34095 Montpellier cedex 5, France
| | | | | |
Collapse
|
5
|
Shaikh KI, Kumar S, Lundhus L, Bond AD, Sharma PK, Nielsen P. Synthesis of bicyclic 2'-deoxynucleosides with alpha-L-ribo- and beta-D-xylo-configurations and restricted S- and N-type conformations. J Org Chem 2009; 74:1557-66. [PMID: 19154130 DOI: 10.1021/jo8023472] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two bicyclic 2'-deoxynucleoside analogues are synthesized in 12 steps each from thymidine. With a six-membered ring fused to the C3'-C4' bond and an alpha-L-ribo- and a beta-D-xylo-configuration, these are conformationally restricted in an S- and an N-type conformation, respectively. The constitutions were proven by X-ray crystallography. The beta-D-xylo-configured analogue is successfully converted to a 3'-phosphoramidite and incorporated into oligodeoxynucleotides, which are found to hybridize to DNA and RNA complements with decreased affinity.
Collapse
Affiliation(s)
- Khalil I Shaikh
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, 5230 Odense M, Denmark
| | | | | | | | | | | |
Collapse
|
6
|
|
7
|
Zenkova MA, Karpova GG. Imperfectly matched nucleic acid complexes and their biochemical manifestation. RUSSIAN CHEMICAL REVIEWS 2007. [DOI: 10.1070/rc1993v062n04abeh000023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
8
|
Maury G, Rayner B, Imbach JL, Müller B, Restle T, Goody RS. Studies on the Interaction between HIV-1 Reverse Transcriptase and Templateoligo α-Thymidylate Duplexes. ACTA ACUST UNITED AC 2007. [DOI: 10.1080/07328319108046471] [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]
Affiliation(s)
- Georges Maury
- a Université de Montpellier II, Labomtoire de Chimie Bioorganique , Place Eugéne Bataillon, 34095 , Montpellier Cedex 5 , France
| | - Bernard Rayner
- a Université de Montpellier II, Labomtoire de Chimie Bioorganique , Place Eugéne Bataillon, 34095 , Montpellier Cedex 5 , France
| | - Jean-Louis Imbach
- a Université de Montpellier II, Labomtoire de Chimie Bioorganique , Place Eugéne Bataillon, 34095 , Montpellier Cedex 5 , France
| | - Barbara Müller
- b Abteilung Biophysik, Max-Planck-lnstitut für medizinische Forschung , Jahnstrß 29, 6900 , Heidelberg , F.R.G
| | - Tobias Restle
- b Abteilung Biophysik, Max-Planck-lnstitut für medizinische Forschung , Jahnstrß 29, 6900 , Heidelberg , F.R.G
| | - Roger S. Goody
- b Abteilung Biophysik, Max-Planck-lnstitut für medizinische Forschung , Jahnstrß 29, 6900 , Heidelberg , F.R.G
| |
Collapse
|
9
|
Sharma PK, Petersen M, Nielsen P. An α-d-Configured Bicyclic Nucleoside Restricted in an E-type Conformation: Synthesis and Parallel RNA Recognition. J Org Chem 2005; 70:4918-28. [PMID: 15960489 DOI: 10.1021/jo0500380] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An alpha-D-arabino configured bicyclic nucleoside strongly restricted in an E-type conformation by a 2'-3'-fused oxetane ring is synthesized. Several synthetic strategies toward the target compound are described, and the successful preparation from a D-xylose derivative is based on a ruthenium-mediated cleavage of a double bond, an S(N)2-inversion at the 2-position to give an arabino-configuration, nucleobase coupling, and finally ring closure to give the oxetane ring. The E-type conformation is confirmed by molecular modeling and NMR. The nucleoside is incorporated into short alpha-DNA sequences. In a mixed pyrimidine context, these recognize complementary parallel RNA-sequences with mainly increased affinity and complementary parallel DNA-sequences with decreased affinity. The present bicyclic analogue represents the first conformationally restricted alpha-DNA-analogue to improve nucleic acid recognition in mixmers with alpha-DNA monomers.
Collapse
Affiliation(s)
- Pawan K Sharma
- Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, 5230 Odense M, Denmark
| | | | | |
Collapse
|
10
|
Michel T, Martinand-Mari C, Debart F, Lebleu B, Robbins I, Vasseur JJ. Cationic phosphoramidate alpha-oligonucleotides efficiently target single-stranded DNA and RNA and inhibit hepatitis C virus IRES-mediated translation. Nucleic Acids Res 2003; 31:5282-90. [PMID: 12954764 PMCID: PMC203318 DOI: 10.1093/nar/gkg733] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2003] [Revised: 07/24/2003] [Accepted: 07/24/2003] [Indexed: 12/29/2022] Open
Abstract
A potential means to improve the efficacy of steric-blocking antisense oligonucleotides (ON) is to increase their affinity for a target RNA. The grafting of cationic amino groups to the backbone of the ON is one way to achieve this, as it reduces the electrostatic repulsion between the ON and its target. We have examined the duplex stabilising effects of introducing cationic phosphoramidate internucleoside linkages into ON with a non-natural alpha-anomeric configuration. Cationic alpha-ON bound with high affinity to single-stranded DNA and RNA targets. Duplex stabilisation was proportional to the number of cationic modifications, with fully cationic ON having particularly high thermal stability. The average stabilisation was greatly increased at low ionic strength. The duplex formed between cationic alpha-ON and their RNA targets were not substrates for RNase H. The penalty in T(m) inflicted by a single mismatch, however, was high; suggesting that they are well suited as sequence-specific, steric-blocking, antisense agents. Using a well-described target sequence in the internal ribosome entry site of the human hepatitis C virus, we have confirmed this potential in a cell-free translation assay as well as in a whole cell assay. Interestingly, no vectorisation was necessary for the cationic alpha-ON in cell culture.
Collapse
Affiliation(s)
- Thibaut Michel
- Laboratoire de Chimie Organique Biomoléculaire de Synthèse, UMR 5625 CNRS-UMII, CC 008, Université Montpellier II, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
| | | | | | | | | | | |
Collapse
|
11
|
Sørensen MD, Kvaernø L, Bryld T, Håkansson AE, Verbeure B, Gaubert G, Herdewijn P, Wengel J. alpha-L-ribo-configured locked nucleic acid (alpha-L-LNA): synthesis and properties. J Am Chem Soc 2002; 124:2164-76. [PMID: 11878970 DOI: 10.1021/ja0168763] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The syntheses of monomeric nucleosides and 3'-O-phosphoramidite building blocks en route to alpha-L-ribo-configured locked nucleic acids (alpha-L-LNA), composed entirely of alpha-L-LNA monomers (alpha-L-ribo configuration) or of a mixture of alpha-L-LNA and DNA monomers (beta-D-ribo configuration), are described and the alpha-L-LNA oligomers are studied. Bicyclic 5-methylcytosin-1-yl and adenine-9-yl nucleoside derivatives have been prepared and the phosphoramidite approach has been used for the automated oligomerization leading to alpha-L-LNA oligomers. Binding studies revealed very efficient recognition of single-stranded DNA and RNA target oligonucleotide strands. Thus, stereoirregular alpha-L-LNA 11-mers containing a mixture of alpha-L-LNA monomers and DNA monomers ("mix-mer alpha-L-LNA") were shown to display DeltaT(m) values of +1 to +3 degrees C per modification toward DNA and +4 to +5 degrees C toward RNA when compared with the corresponding unmodified DNA x DNA and DNA x RNA reference duplexes. The corresponding DeltaT(m) values per modification for the stereoregular fully modified alpha-L-LNA were determined to be +4 degrees C (against DNA) and +5 degrees C (against RNA). 11-Mer alpha-L-LNAs (mix-mer alpha- L-LNA or fully modified alpha- L-LNA) were shown in vitro to be significantly stabilized toward 3'-exonucleolytic degradation. A duplex formed between RNA and either mix-mer alpha-L-LNA or fully modified alpha-L-LNA induced in vitro Escherichia coli RNase H-mediated cleavage, albeit very slow, of the RNA targets at high enzyme concentrations.
Collapse
Affiliation(s)
- Mads D Sørensen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | | | | | | | | | | | | | | |
Collapse
|
12
|
Nielsen P, Christensen NK, Dalskov JK. Alpha-LNA (locked nucleic acid with alpha-D-configuration): synthesis and selective parallel recognition of RNA. Chemistry 2002; 8:712-22. [PMID: 11855719 DOI: 10.1002/1521-3765(20020201)8:3<712::aid-chem712>3.0.co;2-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Alpha-LNA is presented as a stereoisomer of LNA (locked nucleic acid) with alpha-D-configuration. Three different approaches towards the thymine alpha-LNA monomer as well as the 5-methylcytosine alpha-LNA monomer are presented. Different alpha-LNA sequences have been synthesised and their hybridisation with complementary DNA and RNA has been evaluated by means of thermal stability experiments and circular dichroism spectroscopy. In a mixed pyrimidine sequence, alpha-LNA displays unprecedented parallel-stranded and selective RNA binding. Furthermore, a remarkable selectivity for hybridisation with RNA over DNA is indicated.
Collapse
Affiliation(s)
- Poul Nielsen
- Department of Chemistry, University of Southern Denmark, Odense M.
| | | | | |
Collapse
|
13
|
Froeyen M, Lescrinier E, Kerremans L, Rosemeyer H, Seela F, Verbeure B, Lagoja I, Rozenski J, Van Aerschot A, Busson R, Herdewijn P. Alpha-homo-DNA and RNA form a parallel oriented non-A, non-B-type double helical structure. Chemistry 2001; 7:5183-94. [PMID: 11775692 DOI: 10.1002/1521-3765(20011203)7:23<5183::aid-chem5183>3.0.co;2-h] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cross-talking between nucleic acids is a prerequisite for information transfer. The absence of observed base pairing interactions between pyranose and furanose nucleic acids has excluded considering the former type as a (potential) direct precursor of contemporary RNA and DNA. We observed that alpha-pyranose oligonucleotides (alpha-homo-DNA) are able to hybridize with RNA and that both nucleic acid strands are parallel oriented. Hybrids between alpha-homo-DNA and DNA are less stable. During the synthesis of alpha-homo-DNA we observed extensive conversion of N6-benzoyl-5-methylcytosine into thymine under the usual deprotection conditions of oligonucleotide synthesis. Alpha-homo-DNA:RNA represents the first hybridization system between pyranose and furanose nucleic acids. The duplex formed between alpha-homo-DNA and RNA was investigated using CD, NMR spectroscopy, and molecular modeling. The general rule that orthogonal orientation of base pairs prevents hybridization is infringed. NMR experiments demonstrate that the base moieties of alpha-homo-DNA in its complex with RNA, are equatorially oriented and that the base moieties of the parallel RNA strand are pseudoaxially oriented. Modeling experiments demonstrate that the duplex formed is different from the classical A- or B-type double stranded DNA. We observed 15 base pairs in a full helical turn. The average interphosphate distance in the RNA strand is 6.2 A and in the alpha-homo-DNA strand is 6.9 A. The interstrand P-P distance is much larger than found in the typical A- and B-DNA. Most helical parameters are different from those of natural duplexes.
Collapse
Affiliation(s)
- M Froeyen
- Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Leuven, Belgium
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Affiliation(s)
- D J Hill
- Department of Chemistry and Materials Science & Engineering, The Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | | | | | | | | |
Collapse
|
15
|
Zamaratski E, Pradeepkumar PI, Chattopadhyaya J. A critical survey of the structure-function of the antisense oligo/RNA heteroduplex as substrate for RNase H. JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL METHODS 2001; 48:189-208. [PMID: 11384757 DOI: 10.1016/s0165-022x(01)00149-x] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The aim of this review is to draw a correlation between the structure of the DNA/RNA hybrid and its properties as a substrate for the RNase H, as well as to point the crucial structural requirements for the modified AONs to preserve their RNase H potency. The review is divided into the following parts: (1) mechanistic considerations, (2) target RNA folding-AON folding-RNase H assistance in AON/RNA hybrid formation, (3) carbohydrate modifications, (4) backbone modifications, (5) base modifications, (6) conjugated AONs, (7) importance of the tethered chromophore in AON for the AON/RNA hybrid interactions with the RNase H. The structural changes in the AON/RNA hybrid duplexes brought by different modifications of the sugar, backbone or base in the antisense strand, and the effect of these changes on the RNase H recognition of the modified substrates have been addressed. Only those AON modifications and the corresponding AON/RNA hybrids, which have been structurally characterized by spectroscopic means and functionally analyzed by their ability to elicit RNase H potency in comparison with the native counterpart have been presented here.
Collapse
Affiliation(s)
- E Zamaratski
- Department of Bioorganic Chemistry, Box 581, Biomedical Center, University of Uppsala, S-75123, Uppsala, Sweden
| | | | | |
Collapse
|
16
|
Vorobjev PE, Pyshnaya IA, Pyshnyi DV, Venyaminova AG, Ivanova EM, Zarytova VF, Bonora GM, Scalfi-Happ C, Seliger H. Nuclease resistance and RNase H sensitivity of oligonucleotides bridged by oligomethylenediol and oligoethylene glycol linkers. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 2001; 11:77-85. [PMID: 11334143 DOI: 10.1089/108729001750171290] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The properties of new chimeric oligodeoxynucleotides made of short sequences (tetramers, pentamers, octamers, and decamers) bridged by hexamethylenediol and hexaethylene glycol linkers have been investigated. These chimeric oligonucleotides showed an improved resistance toward snake venom 3'-phosphodiesterase, with an increased stability when a terminal 3'-3'-internucleotide phosphodiester bond is present. It also has been demonstrated that the hybrid complexes formed by bridged oligonucleotides and a complementary 20-mer RNA are able to elicit the activity of ribonuclease H (RNase H) from Escherichia coli. The substrate properties of chimeric oligonucleotides depend on the length of the oligonucleotide fragments bridged by linkers. Introduction of a nonnucleotide spacer into the native oligonucleotide only slightly hampers the extent of the RNA hydrolysis in the hybrid complexes, whereas a modification of the site of reaction is observed as a possible consequence of the steric disturbance due to the aliphatic linkers. Hence, these new chimeric oligonucleotides, namely, short oligonucleotide fragments bridged by nonnucleotide linkers, demonstrate a favorable combination of exonuclease resistance and high substrate activity toward RNase H. As a consequence, these chimeric oligonucleotides could be proposed as new, promising analogs to be used in the antisense strategy.
Collapse
Affiliation(s)
- P E Vorobjev
- Institute of Bioorganic Chemistry, Siberian Division of Russian Academy of Sciences, Novosibirsk
| | | | | | | | | | | | | | | | | |
Collapse
|
17
|
The 3′-modified antisense oligos promote faster hydrolysis of the target RNA by RNase H than the natural counterpart. Tetrahedron 2001. [DOI: 10.1016/s0040-4020(00)01029-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
18
|
Robbins I, Lebleu B. Vesicular stomatitis virus as model system for studies of antisense oligonucleotide translation arrest. Methods Enzymol 2000; 313:189-203. [PMID: 10595357 DOI: 10.1016/s0076-6879(00)13013-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Affiliation(s)
- I Robbins
- Institut de Génétique Moléculaire de Montpellier, UMR5535, CNRS, France
| | | |
Collapse
|
19
|
Affiliation(s)
- S T Crooke
- ISIS Pharmaceuticals, Inc., Carlsbad, California 92008, USA
| |
Collapse
|
20
|
Abstract
Given the progress reported during the past decade, a wide range of chemical modifications may be incorporated into potential antisense drugs. These modifications may influence all the properties of these molecules, including mechanism of action. DNA-like antisense drugs have been shown to serve as substrates when bound to target RNAs for RNase Hs. These enzymes cleave the RNA in RNA/DNA duplexes and now the human enzymes have been cloned and characterized. A number of mechanisms other than RNase H have also been reported for non-DNA-like antisense drugs. For example, activation of splicing, inhibition of 5'-cap formation, translation arrest and activation of double strand RNases have all been shown to be potential mechanisms. Thus, there is a growing repertoire of potential mechanisms of action from which to choose, and a range of modified oligonucleotides to match to the desired mechanism. Further, we are beginning to understand the various mechanisms in more detail. These insights, coupled with the ability to rapidly evaluate activities of antisense drugs under well-controlled rapid throughput systems, suggest that we will make more rapid progress in identifying new mechanisms, developing detailed understanding of each mechanism and creating oligonucleotides that better predict what sites in an RNA are most amenable to antisense drugs of various chemical classes.
Collapse
Affiliation(s)
- S T Crooke
- Isis Pharmaceuticals Inc, Carlsbad, CA 92008, USA
| |
Collapse
|
21
|
Seitz O. Chemisch modifizierte Antisense-Oligonucleotide: neue Fortschritte auf dem Gebiet der Bindung von RNA und der Aktivierung der Ribonuclease H. Angew Chem Int Ed Engl 1999. [DOI: 10.1002/(sici)1521-3757(19991203)111:23<3674::aid-ange3674>3.0.co;2-n] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
22
|
The 3rd Annual NIH Symposium on Therapeutic Oligonucleotides. Bethesda, Maryland, USA. December 4, 1998. Abstracts. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 1999; 9:359-431. [PMID: 10498436 DOI: 10.1089/oli.1.1999.9.359] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
23
|
Robbins I, Mitta G, Vichier-Guerre S, Sobol R, Ubysz A, Rayner B, Lebleu B. Selective mRNA degradation by antisense oligonucleotide-2,5A chimeras: involvement of RNase H and RNase L. Biochimie 1998; 80:711-20. [PMID: 9865493 DOI: 10.1016/s0300-9084(99)80024-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Antisense oligonucleotides (ON) allow the specific control of gene expression and phosphorothioate derivatives are currently being evaluated for possible clinical applications. Numerous second generation ON analogues with improved pharmacological properties have been described. Most of them, however, do not recruit RNase H, which is known to increase ON potency by eliciting the specific degradation of the target RNA. Silverman, Torrence and colleagues have conjugated 2,5A to natural antisense ON and demonstrated the preferential cleavage of a target RNA in cell-free and intact cell experiments. We have established for the first time that RNase H-incompetent ON, viz. alpha-anomeric ON analogues, can be converted into sequence-specific nucleases upon conjugation to 2,5A. The use of alpha-ON- and beta-ON-2,5A chimeras has allowed us to delineate the part played by RNase H and RNase L in target RNA degradation and translation arrest. Finally, the present studies have revealed limitations which are encountered in the choice of a suitable target for such ON-2,5A chimeras.
Collapse
Affiliation(s)
- I Robbins
- Institut de Génétique Moléculaire de Montpellier, CNRS, UMR 5535, Université de Montpellier II, France
| | | | | | | | | | | | | |
Collapse
|
24
|
Le Tinévez R, Mishra RK, Toulmé JJ. Selective inhibition of cell-free translation by oligonucleotides targeted to a mRNA hairpin structure. Nucleic Acids Res 1998; 26:2273-8. [PMID: 9580674 PMCID: PMC147550 DOI: 10.1093/nar/26.10.2273] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Using an in vitro selection approach we have previously isolated oligodeoxy aptamers that can bind to a DNA hairpin structure without disrupting the double-stranded stem. We report here that these oligomers can bind to the RNA version of this hairpin, mostly through pairing with a designed 6 nt anchor. The part of the aptamer selected against the DNA hairpin did not increase stability of the RNA-aptamer complex. However, it contributed to the binding site for Escherichia coli RNase H, leading to very efficient cleavage of the target RNA. In addition, a 2'- O -methyloligoribonucleotide analogue of one selected sequence selectively blocked in vitro translation of luciferase in wheat germ extract by binding to the hairpin region inserted upstream of the initiation codon of the reporter gene. Therefore, non-complementary oligomers can exhibit antisense properties following hybridization with the target RNA. Our study also suggests that in vitro selection might provide a means to extend the repertoire of sequences that can be targetted by antisense oligonucleotides to structured RNA motifs of biological importance.
Collapse
Affiliation(s)
- R Le Tinévez
- INSERM U 386, IFR Pathologies Infectieuses, Université Victor Segalen, 146 rue Léo Saignat, 33076 Bordeaux cédex, France
| | | | | |
Collapse
|
25
|
Keller C, Ali-Osman F. Translational inhibition of messenger RNA of the human pi class glutathione S-transferase by antisense oligodeoxyribonucleotides. Chem Biol Interact 1998; 111-112:307-23. [PMID: 9679562 DOI: 10.1016/s0009-2797(97)00168-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In this study, a T7 plasmid expression vector containing the cDNA of a variant human GST-pi gene, hGSTP1*C, was used to examine the translational inhibition of the GST-pi mRNA with antisense deoxyribonucleotides (AS-ONs), and to investigate the dependency of the inhibition on ribonuclease (RNAse) H, AS-ON and target mRNA sequence specificity and AS-ON back bone modification. Translational inhibition of hGSTP1*C mRNA showed significant AS-ON concentration-dependency and was both target mRNA and AS-ON sequence specific. Fully modified phosphoromonthioate AS-ONs were less inhibitory than their partial phosphoromonthioate analogs; unmodified AS-ONs were inactive. RNAse H enhanced the translational inhibition by AS-ON specific to the translation initiation region mRNA, and was associated with cleavage of the target mRNA at the site of AS-ON:mRNA hybridization. AS-ONs directed to the A-->G and C-->T transitions, unique to hGSTP1*C, were more RNAse H-dependent than AS-ONs directed against the translation initiation site, indicating a greater involvement of RNAse H-dependent mRNA cleavage in the mechanism of translational inhibition by AS-ON at the polymorphic site. These data suggest that AS-ONs provide a potentially effective means of specific down-regulation of the human GST-pi gene, and demonstrate that the sites of GST-pi gene allelo-polymorphism can be targeted to translationally down-regulate the different GST-pi gene variants, specifically and differentially targeted.
Collapse
Affiliation(s)
- C Keller
- Department of Experimental Pediatrics, University of Texas, M.D. Anderson Cancer Center, Houston 77030, USA
| | | |
Collapse
|
26
|
Tan TM, Kalisch BW, van de Sande JH, Ting RC, Tan YH. Biologic activity of oligonucleotides with polarity and anomeric center reversal. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 1998; 8:95-101. [PMID: 9593047 DOI: 10.1089/oli.1.1998.8.95] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Human papillomavirus (HPV) type 16 E6 and E7 inactivate the tumor suppressors p53 and pRB, respectively. Both viral oncoproteins play important roles in maintaining the transformed phenotype of cells. In this study, we examine the effects of antisense oligodeoxynucleotides with polarity and anomeric center reversal (alpha/beta-ODNs). ODNs of the general structure 5'alphaN3'3'NNN5'5'alphaN3'3'NNNN5'5'alphaN3+ ++'3'N5' were synthesized using phosphoramidite DNA chemistry. These alpha/beta-ODNs were complementary in sequence to regions flanking the start codons of HPV type 16 E6 and E7 genes. The anti-HPV type 16 alpha/beta-ODNs were able to form stable duplexes with their complementary RNA, which then serve as substrates for RNase H hydrolysis. Anti-HPV type 16 alpha/beta-ODNs also specifically inhibited the growth of two cervical carcinoma cell lines, CaSki and SiHa, both of which harbor HPV type 16 DNA. A decrease in E7 protein expression was also observed. Injection of nude mice with SiHa cells induces tumors. Treatment of these tumor-bearing mice with anti-HPV type 16 alpha/beta-ODNs led to substantially smaller tumors. These results show that alpha/beta-ODNs can exert antisense activities both in vitro and in vivo on the E6 and E7 genes of HPV type 16.
Collapse
MESH Headings
- Animals
- Carcinoma/pathology
- Carcinoma/therapy
- Cell Division/drug effects
- Codon/genetics
- DNA, Complementary/genetics
- DNA, Viral/genetics
- Female
- Gene Expression Regulation, Viral/drug effects
- Genes, Viral
- Humans
- Mice
- Mice, Inbred BALB C
- Mice, Nude
- Neoplasm Transplantation
- Nucleic Acid Hybridization
- Oligonucleotides, Antisense/chemistry
- Oligonucleotides, Antisense/pharmacology
- Oligonucleotides, Antisense/therapeutic use
- Oncogene Proteins, Viral/biosynthesis
- Oncogene Proteins, Viral/genetics
- Oncogenes
- Papillomaviridae/genetics
- Papillomavirus E7 Proteins
- Papillomavirus Infections/pathology
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Repressor Proteins
- Ribonuclease H/metabolism
- Structure-Activity Relationship
- Tumor Cells, Cultured
- Tumor Virus Infections/pathology
- Uterine Cervical Neoplasms/pathology
- Viral Structural Proteins/genetics
Collapse
Affiliation(s)
- T M Tan
- Institute of Molecular and Cell Biology, National University of Singapore, Singapore
| | | | | | | | | |
Collapse
|
27
|
Gee JE, Robbins I, van der Laan AC, van Boom JH, Colombier C, Leng M, Raible AM, Nelson JS, Lebleu B. Assessment of high-affinity hybridization, RNase H cleavage, and covalent linkage in translation arrest by antisense oligonucleotides. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 1998; 8:103-11. [PMID: 9593048 DOI: 10.1089/oli.1.1998.8.103] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Antisense oligonucleotides (ONs) are designed to hybridize target mRNA in a sequence-specific manner and inhibit gene expression by preventing translation, either by activation of RNase H or steric blockage of the ribosome complex. Second-generation ONs, which possess greater binding affinity for target RNA relative to the isosequential phosphodiester (PO) ONs, have been developed and include, among others, peptide nucleic acids (PNA) and N3' P5' phosphoramidate oligonucleotides (npONs). In the present study, PNA and npON derivatives were targeted to the coding portion of the complementary mRNA of the N protein of the vesicular stomatitis virus (VSV) in order to evaluate their ability to arrest translation in an in vitro rabbit reticulocyte lysate system. High-affinity hybridization of ONs lacking RNase H activity was not sufficient to block translation in this test system. Only antisense ONs acting via an RNase H mechanism or by steric hindrance through covalent attachment (via transplatin modification) to the target mRNA were found to definitively arrest translation in this study.
Collapse
Affiliation(s)
- J E Gee
- Institut de Génétique Moléculaire de Montpellier, CNRS, France
| | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Crooke ST. Advances in understanding the pharmacological properties of antisense oligonucleotides. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 1997; 40:1-49. [PMID: 9217922 DOI: 10.1016/s1054-3589(08)60136-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- S T Crooke
- Isis Pharmaceuticals, Inc., Carlsbad, California 92008, USA
| |
Collapse
|
29
|
Hendrix C, Rosemeyer H, Verheggen I, Van Aerschot A, Seela F, Herdewijn P. 1′, 5′ -Anhydrohexitol Oligonucleotides: Synthesis, Base Pairing and Recognition by Regular Oligodeoxyribonucleotides and Oligoribonucleotides. Chemistry 1997. [DOI: 10.1002/chem.19970030118] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
30
|
Vidalin O, Major ME, Rayner B, Imbach JL, Trépo C, Inchauspé G. In vitro inhibition of hepatitis C virus gene expression by chemically modified antisense oligodeoxynucleotides. Antimicrob Agents Chemother 1996; 40:2337-44. [PMID: 8891141 PMCID: PMC163531 DOI: 10.1128/aac.40.10.2337] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
We have explored different domains within the hepatitis C virus (HCV) 5' noncoding region as potential targets for inhibition of HCV translation by antisense oligodeoxynucleotides (ODNs). Inhibition assays were performed with two different cell-free systems, rabbit reticulocyte lysate and wheat germ extract, and three types of chemical structures for the ODNs were evaluated: natural phosphodiesters (beta-PO), alpha-anomer phosphodiesters (alpha-PO), and phosphorothioates (PS). A total of six original ODNs, displaying sequence-specific inhibition ranging from 62 to 96%, that mapped in the pyrimidine-rich tract (nucleotides [nt] 104 to 127) and in the initiator AUG codon (nt 338 to 357) were identified. Two ODNs, which were targeted at the initiatory AUG (nt 341 to 367 and 351 to 377) and which had been previously described as active against genotype 1b and 2a sequences, were shown to exhibit inhibition of expression (> 95%) of a type 1a sequence. Control experiments with the irrelevant chloramphenicol acetyltransferase sequence as a marker and randomized ODNs demonstrated that levels of inhibition associated with the use of PS compounds (of as much as 94%) were mainly due to nonspecific effects. Both alpha- and beta-PO ODNs were found equally active, and no difference could be seen in the activity of beta-PO when it was tested in either rabbit reticulocyte lysate or wheat germ extract, suggesting that RNase H-independent mechanisms may be involved in the inhibitions observed. However, specific RNA cleavage products generated from beta-PO inhibition experiments could be identified, indicating that, with these compounds, control of translation also involves RNase H-dependent mechanisms. This study further delimits the existence of favorable target sequences for the action of ODNs within the HCV 5' noncoding region and indicates the possibility of using nuclease-resistant alpha-PO compounds in cellular studies.
Collapse
Affiliation(s)
- O Vidalin
- Institut National de la Santé et de la Recherche Médicale U271, Lyon, France
| | | | | | | | | | | |
Collapse
|
31
|
Gotfredsen CH, Jacobsen JP, Wengel J. Synthesis and properties of alpha- and beta-oligodeoxynucleotides containing alpha- and beta-1-(2-O-methyl-D-arabino-furanosyl)thymine. Bioorg Med Chem 1996; 4:1217-25. [PMID: 8879543 DOI: 10.1016/0968-0896(96)00117-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Synthesis of the alpha- and beta-anomer of 2'-OMe-araT (alpha- and beta-1-(2-O-methyl-D-arabinofuranosyl)thymine) and their incorporation into oligodeoxynucleotide (ODN) analogues is described. Condensation of the key arabinofuranose derivative with silylated thymine afforded the alpha-anomer and the beta-anomer which were converted into the respective phosphoramidite building blocks. Automated synthesis of beta-ODNs containing beta-2'-OMe-araT (by use of standard beta-amidites and phosphoramidite building block 9b) and alpha-ODNs containing alpha-2'-OMe-araT (by use of alpha-T-amidite and phosphoramidite building block 9a) allowed evaluation of their properties. With regard to 3'-exonucleolytic degradation, 3'-end incorporation of either beta- or alpha-2'-OMe-araT resulted in considerable stabilization compared to unmodified beta-ODNs. Thermal stabilities of duplexes formed between modified ODNs and both unmodified DNA and RNA were evaluated and compared to unmodified controls. In all experiments stable duplexes were formed, but whereas beta-ODNs containing beta-2'-OMe-araT showed moderately lowered thermal stabilities towards both DNA and RNA, alpha-ODNs containing alpha-2'-OMe-araT exhibited significantly increased melting points (compared to beta-ODN controls) when complexed with RNA. These results illustrate the potential of using arabino-configurated nucleosides as modified monomers in biologically active ODN-analogues, either as, e.g., 2'-O-alkylated or 2'-O-functionalized derivatives.
Collapse
|
32
|
Affiliation(s)
- S T Crooke
- Isis Pharmaceuticals, Inc., Carlsbad, California 92008, USA
| |
Collapse
|
33
|
|
34
|
Abstract
Rapid advances in cancer gene therapy are driven by an explosive development of gene transfer technology and a strong demand for seeking alternatives to unsatisfactory conventional cancer therapies. Discovery of the genetic basis of cancer has indicated that cancer is a disease of genes. Among a variety of approaches to gene therapy of cancer, antisense oncogene and tumor suppressor gene therapy of cancer are the two strategies that aim at correcting genetic disorders of cancer through suppression of the abnormal expression of the proliferative genes. The potential effectiveness of these approaches is promised by their precise targeting at the mechanisms of the disease. Examples of several preclinical studies of these types of approaches that led to the approval of clinical trials are reviewed. Limitation and future development of these approaches are also discussed.
Collapse
Affiliation(s)
- W W Zhang
- Gene Therapy Unit, Biotech Group, Baxter Healthcare Corporation, Round Lake, IL 60073-0490, USA
| |
Collapse
|
35
|
Seela F, Leonard P. N7-DNA: Synthesis and Base Pairing of Oligonucleotides ContainingN7-(2-Deoxy-?-D-erythro-pentofuranosyl)guanine (N7Gd). Helv Chim Acta 1996. [DOI: 10.1002/hlca.19960790215] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
36
|
Bolli M, Lubini P, Leumann C. Nucleic-Acid Analogs with Restricted Conformational Flexibility in the Sugar-Phosphate Backbone (?Bicyclo-DNA?). Part 5. Synthesis, Characterization, and Pairing Properties of Oligo-?-D-(bicyclodeoxynucleotides) of the Bases Adenine and Thymine (?-Bicyclo-DNA). Helv Chim Acta 1995. [DOI: 10.1002/hlca.19950780816] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
37
|
|
38
|
Abstract
This review is aimed at biochemists and molecular biologists, and covers the chemistry and key features involved in the solid-phase synthesis of a variety of the better known DNA and RNA analogues by the phosphoramidite and H-phosphonate methods. A wide spectrum of biological applications such as inhibition of gene expression, translation arrest, RNA processing, affinity purification of RNA-protein complexes, in situ hybridization, and synthetic ribozymes are then discussed in some detail, enabling the molecular biologist to get an idea of what is possible using the current technology.
Collapse
|
39
|
|
40
|
Abdel Aleem AAH, Larsen E, Pedersen EB. Synthesis of carboxamide linked dimers, αT*αT and αUCl*αT. — duplex and triplex stabilities of the corresponding α oligodeoxynucleotides. Tetrahedron 1995. [DOI: 10.1016/0040-4020(95)00404-v] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
41
|
Zhang WW, Fang X. Section Review—Oncologic, Endocrine & Metabolic: Gene Therapy Strategies for Cancer. Expert Opin Investig Drugs 1995. [DOI: 10.1517/13543784.4.6.487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
42
|
Peters JM, Duncan JR, Wiley LM, Rucker RB, Keen CL. Effect of a metallothionein antisense oligonucleotide on embryo development. Reprod Toxicol 1995; 9:123-30. [PMID: 7795322 DOI: 10.1016/0890-6238(94)00062-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The effect of a metallothionein (MT) antisense oligodeoxynucleotide (ODN) on mouse preimplantation embryo development was investigated. Preimplantation embryos were cultured for 72 h and examined following exposure to either an MT antisense or sense ODN. Blastocyst formation (cavitation) and embryo cell number were lower in embryos exposed to the MT antisense ODN than in controls or in embryos exposed to the MT sense ODN. In embryos cultured in medium containing free nucleotides, cavitation frequency was not affected, although mean embryo cell number was lower than in controls. Combined, this work shows that an antisense ODN against MT can significantly affect blastocyst formation of preimplantation embryos; some, but not all, of the observed effects on embryo cell number may have been due to nucleotide toxicity.
Collapse
Affiliation(s)
- J M Peters
- Department of Obstetrics and Gynecology, University of California, Davis 95616, USA
| | | | | | | | | |
Collapse
|
43
|
|
44
|
Zhang WW, Fujiwara T, Grimm EA, Roth JA. Advances in cancer gene therapy. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 1995; 32:289-341. [PMID: 7748797 DOI: 10.1016/s1054-3589(08)61016-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- W W Zhang
- Department of Thoracic and Cardiovascular Surgery, University of Texas M. D. Anderson Cancer Center, Houston 77030, USA
| | | | | | | |
Collapse
|
45
|
Zelphati O, Imbach JL, Signoret N, Zon G, Rayner B, Leserman L. Antisense oligonucleotides in solution or encapsulated in immunoliposomes inhibit replication of HIV-1 by several different mechanisms. Nucleic Acids Res 1994; 22:4307-14. [PMID: 7524038 PMCID: PMC331952 DOI: 10.1093/nar/22.20.4307] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Phosphodiester and phosphorothioate oligonucleotides in alpha and beta configurations directed against the initiation codon region of the HIV-1 rev gene were evaluated for their ability to inhibit HIV-1 replication in acutely and chronically infected human CEM cells. Encapsulation in antibody-targeted liposomes (immunoliposomes) permitted intracellular delivery and distinction between oligonucleotide-mediated inhibition of viral entry and intracellular effects on viral RNA. Our results are consistent with four mechanisms of antiviral activity for these antisense oligonucleotides: (i) interference with virus-mediated cell fusion by free but not liposome-encapsulated phosphorothioate oligonucleotides of any sequence; (ii) interference with reverse transcription in a sequence non-specific manner by phosphorothioate oligonucleotides in alpha and beta configurations; (iii) interference with viral reverse transcription in a sequence-specific and RNase-H-independent manner by alpha and beta phosphodiester oligonucleotides; (iv) interference with viral mRNA in a sequence-specific and RNase-H-dependent manner by beta-phosphorothioate oligonucleotides.
Collapse
Affiliation(s)
- O Zelphati
- Centre d'Immunologie, Institut National de la Santé et de la Recherche Médicale-Centre National de la Recherche Scientifique de Marseille-Luminy Case 906, France
| | | | | | | | | | | |
Collapse
|
46
|
Ramazeilles C, Mishra RK, Moreau S, Pascolo E, Toulmé JJ. Antisense phosphorothioate oligonucleotides: selective killing of the intracellular parasite Leishmania amazonensis. Proc Natl Acad Sci U S A 1994; 91:7859-63. [PMID: 8058724 PMCID: PMC44503 DOI: 10.1073/pnas.91.17.7859] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
We targeted the mini-exon sequence, present at the 5' end of every mRNA of the protozoan parasite Leishmania amazonensis, by phosphorothioate oligonucleotides. A complementary 16-mer (16PS) was able to kill amastigotes--the intracellular stage of the parasite--in murine macrophages in culture. After 24 hr of incubation with 10 microM 16PS, about 30% infected macrophages were cured. The oligomer 16PS acted through antisense hybridization in a sequence-dependent way; no effect on parasites was observed with noncomplementary phosphorothioate oligonucleotides. The antisense oligonucleotide 16PS was a selective killer of the protozoans without any detrimental effect to the host macrophage. Using 16PS linked to a palmitate chain, which enabled it to complex with low density lipoproteins, improved the leishmanicidal efficiency on intracellular amastigotes, probably due to increased endocytosis. Phosphorothioate oligonucleotides complementary to the intron part of the mini-exon pre-RNA were also effective, suggesting that antisense oligomers could prevent trans-splicing in these parasites.
Collapse
Affiliation(s)
- C Ramazeilles
- Laboratoire de Biophysique Moléculaire Institut National de la Santé et de la Recherche Médicale Unité 386, Université de Bordeaux II, France
| | | | | | | | | |
Collapse
|
47
|
Cros P, Kurfürst R, Allibert P, Battail N, Piga N, Roig V, Thuong NT, Mandrand B, Hélène C. Monoclonal antibodies targeted to alpha-oligonucleotides. Characterisation and application in nucleic acid detection. Nucleic Acids Res 1994; 22:2951-7. [PMID: 7520567 PMCID: PMC310260 DOI: 10.1093/nar/22.15.2951] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The aim of the present study was to test the antigenicity of alpha-deoxyribonucleotides in order to develop a new tool for the detection of nucleic acid sequences for use in diagnostic applications. We describe four monoclonal antibodies (Mabs) which recognize alpha-deoxyribonucleotides. Two were raised against a poly(alpha-dT) sequence and specifically recognized the alpha-dT nucleotide. Two were raised against a sequence containing all four common nucleotides as alpha-nucleotides and, surprisingly, only recognized the alpha-dG nucleotide. For all four Mabs, no cross reactivity was observed with beta-oligonucleotides. These Mabs were reactive with alpha-oligonucleotide sequences whether these sequences were single-stranded or hybridized to DNA or RNA. The four Mabs were tested in a sandwich hybridization assay that consisted of an alpha-oligonucleotide (for target sequence recognition), one of the four Mabs (for recognition of the hybridized alpha-oligonucleotide), and goat anti-mouse antibody conjugated to horse radish peroxidase (HRP) (for detection). One of the monoclonal antibodies, Mab 2E11D7, was directly conjugated to HRP and used in sandwich hybridization to detect PCR fragments of HPV 18 DNA. The sensitivity of this reaction was 1 pg of plasmid DNA containing the HPV 18 fragment. The specificity of the detection was demonstrated using HPV 6/11 and 16 DNA sequences.
Collapse
Affiliation(s)
- P Cros
- Laboratoire des Sondes Nucléiques, bioMérieux, ENS, Lyon, France
| | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Tanaka H, Vickart P, Bertrand JR, Rayner B, Morvan F, Imbach JL, Paulin D, Malvy C. Sequence-specific interaction of alpha-beta-anomeric double-stranded DNA with the p50 subunit of NF kappa B: application to the decoy approach. Nucleic Acids Res 1994; 22:3069-74. [PMID: 8065920 PMCID: PMC310277 DOI: 10.1093/nar/22.15.3069] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The potential use of alpha-beta-anomeric duplex oligonucleotides to inhibit transcription factor activity by the decoy approach is investigated in this report. Indeed, several alpha-beta-anomeric heteroduplexes display a sequence-specific interaction with the p50 subunit of the transcription factor NF kappa B. Used in a decoy approach, these duplexes interact strongly enough with this transcription factor to modulate the expression of a reporter gene, under the control of NF kappa B. However, all the alpha-beta-anomeric heteroduplexes do not interact with the p50 subunit; the sequence of the chirally natural beta-anomeric strand may explain the different recognition properties of the protein. The analysis of the appropriate beta-anomeric sequences is consistent with a preferential interaction of the p50 subunit with one strand of double-stranded DNA.
Collapse
Affiliation(s)
- H Tanaka
- Laboratoire de Biochimie-Enzymologie, INSERM U140, CNRS URA147, Institut Gustave Roussy, Villejuif, France
| | | | | | | | | | | | | | | |
Collapse
|
49
|
Seela F, Winter H. N7-DNA: Synthesis and Base Pairing of Oligonucleotides containing 7-(2-Deoxy-? -D-erythro-pentofuranosyl)adenine (N7Ad). Helv Chim Acta 1994. [DOI: 10.1002/hlca.19940770302] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
50
|
Janardhanam S, Nambiar KP. Investigation of stereoselectivities in the coupling reactions of 1-O-methyl-3, 5-di-O-p-toluoyl-2-deoxyribofuranoside with purines and pyrimidines. Tetrahedron Lett 1994. [DOI: 10.1016/s0040-4039(00)73064-4] [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]
|