1
|
Featherston AL, Kwon Y, Pompeo MM, Engl OD, Leahy DK, Miller SJ. Catalytic asymmetric and stereodivergent oligonucleotide synthesis. Science 2021; 371:702-707. [PMID: 33574208 DOI: 10.1126/science.abf4359] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 01/13/2021] [Indexed: 12/14/2022]
Abstract
We report the catalytic stereocontrolled synthesis of dinucleotides. We have demonstrated, for the first time to our knowledge, that chiral phosphoric acid (CPA) catalysts control the formation of stereogenic phosphorous centers during phosphoramidite transfer. Unprecedented levels of diastereodivergence have also been demonstrated, enabling access to either phosphite diastereomer. Two different CPA scaffolds have proven to be essential for achieving stereodivergence: peptide-embedded phosphothreonine-derived CPAs, which reinforce and amplify the inherent substrate preference, and C2-symmetric BINOL-derived CPAs, which completely overturn this stereochemical preference. The presently reported catalytic method does not require stoichiometric activators or chiral auxiliaries and enables asymmetric catalysis with readily available phosphoramidites. The method was applied to the stereocontrolled synthesis of diastereomeric dinucleotides as well as cyclic dinucleotides, which are of broad interest in immuno-oncology as agonists of the stimulator of interferon genes (STING) pathway.
Collapse
Affiliation(s)
| | - Yongseok Kwon
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Matthew M Pompeo
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Oliver D Engl
- Process Chemistry Development, Takeda Pharmaceuticals International Co., Cambridge, MA 02139, USA
| | - David K Leahy
- Process Chemistry Development, Takeda Pharmaceuticals International Co., Cambridge, MA 02139, USA.
| | - Scott J Miller
- Department of Chemistry, Yale University, New Haven, CT 06520, USA.
| |
Collapse
|
2
|
Yang X. Solid-Phase Synthesis of RNA Analogs Containing Phosphorodithioate Linkages. ACTA ACUST UNITED AC 2017; 70:4.77.1-4.77.13. [PMID: 28921494 DOI: 10.1002/cpnc.40] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The oligoribonucleotide phosphorodithioate (PS2-RNA) modification uses two sulfur atoms to replace two non-bridging oxygen atoms at an internucleotide phosphorodiester backbone linkage. Like a natural phosphodiester RNA backbone linkage, a PS2-modified backbone linkage is achiral at phosphorus. PS2-RNAs are highly stable to nucleases and several in vitro assays have demonstrated their biological activity. For example, PS2-RNAs silenced mRNA in vitro and bound to protein targets in the form of PS2-aptamers (thioaptamers). Thus, the interest in and promise of PS2-RNAs has drawn attention to synthesizing, isolating, and characterizing these compounds. RNA-thiophosphoramidite monomers are commercially available from AM Biotechnologies and this unit describes an effective methodology for solid-phase synthesis, deprotection, and purification of RNAs having PS2 internucleotide linkages. © 2017 by John Wiley & Sons, Inc.
Collapse
|
3
|
Thiviyanathan V, Gorenstein DG. Aptamers and the next generation of diagnostic reagents. Proteomics Clin Appl 2014; 6:563-73. [PMID: 23090891 DOI: 10.1002/prca.201200042] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 09/17/2012] [Accepted: 09/20/2012] [Indexed: 01/06/2023]
Abstract
Antibodies have been extensively used as capture and detection reagents in diagnostic applications of proteomics-based technologies. Proteomic assays need high sensitivity and specificity, a wide dynamic range for detection, and accurate, reproducible quantification with small confidence values. However, several inherent limitations of monoclonal antibodies in meeting the emerging challenges of proteomics led to the development of a new class of oligonucleotide-based reagents. Natural and derivatized nucleic acid aptamers are emerging as promising alternatives to monoclonal antibodies. Aptamers can be effectively used to simultaneously detect thousands of proteins in multiplex discovery platforms, where antibodies often fail due to cross-reactivity problems. Through chemical modification, vast range of additional functional groups can be added at any desired position in the oligonucleotide sequence, therefore the best features of small molecule drugs, proteins, and antibodies can be brought together into aptamers, making aptamers the most versatile reagent in proteomics. In this review, we discuss the recent developments in aptamer technology, including new selection methods and the aptamers' application in proteomics.
Collapse
Affiliation(s)
- Varatharasa Thiviyanathan
- Centers for Proteomics & Systems Biology, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX, USA
| | | |
Collapse
|
4
|
Pallan PS, Yang X, Sierant M, Abeydeera ND, Hassell T, Martinez C, Janicka M, Nawrot B, Egli M. Crystal structure, stability and Ago2 affinity of phosphorodithioate-modified RNAs. RSC Adv 2014. [DOI: 10.1039/c4ra10986d] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The high Ago2 affinity of siRNAs with combined 2′-O-methyl and phosphorodithioate backbone modifications (MePS2) in the 3′-terminal region of the sense strand is likely the result of enhanced hydrophobic interactions with the protein's PAZ domain.
Collapse
Affiliation(s)
- Pradeep S. Pallan
- Department of Biochemistry
- Vanderbilt University
- School of Medicine
- Nashville, USA
| | | | - Malgorzata Sierant
- Department of Bioorganic Chemistry
- Centre of Molecular and Macromolecular Studies
- Polish Academy of Sciences
- Lodz, Poland
| | | | | | | | - Magdalena Janicka
- Department of Bioorganic Chemistry
- Centre of Molecular and Macromolecular Studies
- Polish Academy of Sciences
- Lodz, Poland
| | - Barbara Nawrot
- Department of Bioorganic Chemistry
- Centre of Molecular and Macromolecular Studies
- Polish Academy of Sciences
- Lodz, Poland
| | - Martin Egli
- Department of Biochemistry
- Vanderbilt University
- School of Medicine
- Nashville, USA
| |
Collapse
|
5
|
Bats JW, Schell P, Engels JW. Biphenyl- and phenylnaphthalenyl-substituted 1H-imidazole-4,5-dicarbonitrile catalysts for the coupling reaction of nucleoside methyl phosphonamidites. Acta Crystallogr C 2013; 69:529-33. [PMID: 23629908 DOI: 10.1107/s0108270113009293] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 04/05/2013] [Indexed: 11/10/2022] Open
Abstract
Crystal structures are reported for three substituted 1H-imidazole-4,5-dicarbonitrile compounds used as catalysts for the coupling reaction of nucleoside methyl phosphonamidites, namely 2-(3',5'-dimethylbiphenyl-2-yl)-1H-imidazole-4,5-dicarbonitrile, C19H14N4, (I), 2-(2',4',6'-trimethylbiphenyl-2-yl)-1H-imidazole-4,5-dicarbonitrile, C20H16N4, (II), and 2-[8-(3,5-dimethylphenyl)naphthalen-1-yl]-1H-imidazole-4,5-dicarbonitrile, C23H16N4, (III). The asymmetric unit of (I) contains two independent molecules with similar conformations. There is steric repulsion between the imidazole group and the terminal phenyl group in all three compounds, resulting in the nonplanarity of the molecules. The naphthalene group of (III) shows significant deviation from planarity. The C-N bond lengths in the imidazole rings range from 1.325 (2) to 1.377 (2) Å. The molecules are connected into zigzag chains by intermolecular N-H···N(imidazole) [for (I)] or N-H····N(cyano) [for (II) and (III)] hydrogen bonds.
Collapse
Affiliation(s)
- Jan W Bats
- Institut für Organische Chemie und Chemische Biologie, Universität Frankfurt, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany.
| | | | | |
Collapse
|
6
|
Yang X, Sierant M, Janicka M, Peczek L, Martinez C, Hassell T, Li N, Li X, Wang T, Nawrot B. Gene silencing activity of siRNA molecules containing phosphorodithioate substitutions. ACS Chem Biol 2012; 7:1214-20. [PMID: 22512638 DOI: 10.1021/cb300078e] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Chemically synthesized small interfering RNAs (siRNAs) have been widely used to identify gene function and hold great potential in providing a new class of therapeutics. Chemical modifications are desired for therapeutic applications to improve siRNA efficacy. Appropriately protected ribonucleoside-3'-yl S-[β-(benzoylmercapto)ethyl]pyrrolidino-thiophosphoramidite monomers were prepared for the synthesis of siRNA containing phosphorodithioate (PS2) substitutions in which the two non-bridging oxygen atoms are replaced by sulfur atoms. A series of siRNAs containing PS2 substitutions have been strategically designed, synthesized, and evaluated for their gene silencing activities. These PS2-siRNA duplexes exhibit an A-form helical structure similar to unmodified siRNA. The effect of PS2 substitutions on gene silencing activity is position-dependent, with certain PS2-siRNAs showing activity significantly higher than that of unmodified siRNA. The relative gene silencing activities of siRNAs containing either PS2 or phosphoromonothioate (PS) linkages at identical positions are variable and depend on the sites of modification. 5'-Phosphorylation of PS2-siRNAs has little or no effect on gene silencing activity. Incorporation of PS2 substitutions into siRNA duplexes increases their serum stability. These results offer preliminary evidence of the potential value of PS2-modified siRNAs.
Collapse
Affiliation(s)
- Xianbin Yang
- AM Biotechnologies LLC, 12521 Gulf Freeway, Houston, Texas 77034, United
States
| | - Malgorzata Sierant
- Department of Bioorganic
Chemistry,
Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz, Poland
| | - Magdalena Janicka
- Department of Bioorganic
Chemistry,
Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz, Poland
| | - Lukasz Peczek
- Department of Bioorganic
Chemistry,
Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz, Poland
| | - Carlos Martinez
- Sigma Life Science, 9186 Six Pines, The Woodlands, Texas 77380, United States
| | - Tom Hassell
- Sigma Life Science, 9186 Six Pines, The Woodlands, Texas 77380, United States
| | - Na Li
- AM Biotechnologies LLC, 12521 Gulf Freeway, Houston, Texas 77034, United
States
| | - Xin Li
- AM Biotechnologies LLC, 12521 Gulf Freeway, Houston, Texas 77034, United
States
| | - Tianzhi Wang
- The Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Barbara Nawrot
- Department of Bioorganic
Chemistry,
Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz, Poland
| |
Collapse
|
7
|
Jain ML, Bruice PY, Szabó IE, Bruice TC. Incorporation of positively charged linkages into DNA and RNA backbones: a novel strategy for antigene and antisense agents. Chem Rev 2011; 112:1284-309. [PMID: 22074477 DOI: 10.1021/cr1004265] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Moti L Jain
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
| | | | | | | |
Collapse
|
8
|
Oka N, Wada T. Stereocontrolled synthesis of oligonucleotide analogs containing chiral internucleotidic phosphorus atoms. Chem Soc Rev 2011; 40:5829-43. [PMID: 21720637 DOI: 10.1039/c1cs15102a] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Oligonucleotides, in which one of the two nonbridging oxygen atoms of internucleotidic phosphates is replaced by a different type of atom or a substituent, are useful as therapeutic agents and probes to elucidate mechanisms of enzymatic reactions. The internucleotidic phosphorus atoms of these oligonucleotides are chiral, and the properties of these oligonucleotides are affected by the absolute configuration of the chiral phosphorus atoms. In order to address the issue of chirality, various methods have been developed to synthesize these P-chiral oligonucleotide analogs in a stereocontrolled manner. This critical review focuses on the recent progress in this field (123 references).
Collapse
Affiliation(s)
- Natsuhisa Oka
- Department of Chemistry, Faculty of Engineering, Gifu University, Gifu 501-1193, Japan
| | | |
Collapse
|
9
|
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]
|
10
|
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
|
11
|
Lebedev AV, Paul N, Yee J, Timoshchuk VA, Shum J, Miyagi K, Kellum J, Hogrefe RI, Zon G. Hot start PCR with heat-activatable primers: a novel approach for improved PCR performance. Nucleic Acids Res 2008; 36:e131. [PMID: 18796527 PMCID: PMC2582603 DOI: 10.1093/nar/gkn575] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The polymerase chain reaction (PCR) is widely used for applications which require a high level of specificity and reliability, such as genetic testing, clinical diagnostics, blood screening, forensics and biodefense. Great improvements to PCR performance have been achieved by the use of Hot Start activation strategies that aim to prevent DNA polymerase extension until more stringent, higher temperatures are reached. Herein we present a novel Hot Start activation approach in PCR where primers contain one or two thermolabile, 4-oxo-1-pentyl (OXP) phosphotriester (PTE) modification groups at 3′-terminal and 3′-penultimate internucleotide linkages. Studies demonstrated that the presence of one or more OXP PTE modifications impaired DNA polymerase primer extension at the lower temperatures that exist prior to PCR amplification. Furthermore, incubation of the OXP-modified primers at elevated temperatures was found to produce the corresponding unmodified phosphodiester (PDE) primer, which was then a suitable DNA polymerase substrate. The OXP-modified primers were tested in conventional PCR with endpoint detection, in one-step reverse transcription (RT)–PCR and in real-time PCR with SYBR Green I dye and Taqman® probe detection. When OXP-modified primers were used as substitutes for unmodified PDE primers in PCR, significant improvement was observed in the specificity and efficiency of nucleic acid target amplification.
Collapse
Affiliation(s)
- Alexandre V Lebedev
- Department of Research and Development, TriLink BioTechnologies, Inc., 9955 Mesa Rim Road, San Diego, CA 92121, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Sobkowski M, Stawinski J, Kraszewski A. A convenient stereochemical notation for p-chiral nucleotide analogs. ACTA ACUST UNITED AC 2008; Appendix 1:Appendix 1E. [PMID: 18428960 DOI: 10.1002/0471142700.nca01es28] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The D(P)/L(P) convention is a stereochemical notation for P-chiral nucleotide analogs and related compounds. In contrast to the absolute R(P)/S(P) notation, the D(P)/L(P) system is based on a geometrical relationship between substituents in a dinucleoside monophosphate skeleton. The D(P)/L(P) notation is a convenient alternative to the R(P)/S(P) notation for stereochemical correlation analysis of physical, chemical, and biological properties of nucleotide and oligonucleotide analogs bearing any type of tri- or tetra-coordinated phosphorus moiety.
Collapse
|
13
|
Rapireddy S, He G, Roy S, Armitage BA, Ly DH. Strand invasion of mixed-sequence B-DNA by acridine-linked, gamma-peptide nucleic acid (gamma-PNA). J Am Chem Soc 2007; 129:15596-600. [PMID: 18027941 DOI: 10.1021/ja074886j] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptide nucleic acid (PNA) is a synthetic mimic of DNA and RNA that can recognize double-stranded B-DNA through direct Watson-Crick base-pairing. Although promising, PNA recognition is presently limited to mostly purine- and pyrimidine-rich targets, because mixed-sequence PNA, in general, does not have sufficient binding free energy to invade B-DNA. In this Article, we show that conformationally preorganized gamma-peptide nucleic acid (gamma-PNA) containing an acridine moiety covalently linked at the C-terminus can invade mixed-sequence B-DNA in a sequence-specific manner. Recognition occurs through direct Watson-Crick base-pairing. This finding is significant because it demonstrates that the same principles that guide the recognition of single-stranded DNA and RNA can also be applied to double-stranded B-DNA.
Collapse
Affiliation(s)
- Srinivas Rapireddy
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, USA
| | | | | | | | | |
Collapse
|
14
|
Sobkowski M, Stawinski J, Kraszewski A. A proposal for a convenient notation for P-chiral nucleotide analogues. Part 2. Dinucleoside monophosphate analogues. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2007; 25:1363-75. [PMID: 17067958 DOI: 10.1080/15257770600918862] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
A configuration of ligands around a phosphorus atom in P-chiral dinucleoside monophosphate analogues can be described using DP/LP stereochemical notation, which allows immediate correlation between the notation of configuration and the actual spatial arrangement of the phosphorus ligands. The area of applications of this new stereochemical nomenclature covers dinucleoside units bridged by virtually any type of tri-and tetra-coordinated phosphorus moieties, that is, phosphorothioates, phosphoramidates, phosphoramidites, boranephosphates, methanephosphonates, H-phosphonates, and many others.
Collapse
Affiliation(s)
- Michal Sobkowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
| | | | | |
Collapse
|
15
|
Schell P, Laux WHG, Engels JW. Triarylmethyl Substituted 4,5-Dicyanoimidazoles as Activators for Rp-Diastereoselective Synthesis of TpN Dinucleoside Methylphosphonates. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319908044654] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
16
|
Laurent A, Debart F, Bologna JC, Vasseur JJ, Rayner B. High Affinity Of Backbone-Modified α-Anomeric Oligodeoxynucleottoes For Dna And Rna Targets. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319808004697] [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)
- A. Laurent
- a Laboratoire de Chimie Bio-organique, CC 008, UMR 5625 CNRS-UMII , Université Montpellier II , Place Eugene Bataillon, 34095 , Montpellier , Cedex 5, France
| | - F. Debart
- a Laboratoire de Chimie Bio-organique, CC 008, UMR 5625 CNRS-UMII , Université Montpellier II , Place Eugene Bataillon, 34095 , Montpellier , Cedex 5, France
| | - J.-C. Bologna
- a Laboratoire de Chimie Bio-organique, CC 008, UMR 5625 CNRS-UMII , Université Montpellier II , Place Eugene Bataillon, 34095 , Montpellier , Cedex 5, France
| | - J.-J. Vasseur
- a Laboratoire de Chimie Bio-organique, CC 008, UMR 5625 CNRS-UMII , Université Montpellier II , Place Eugene Bataillon, 34095 , Montpellier , Cedex 5, France
| | - B. Rayner
- a Laboratoire de Chimie Bio-organique, CC 008, UMR 5625 CNRS-UMII , Université Montpellier II , Place Eugene Bataillon, 34095 , Montpellier , Cedex 5, France
| |
Collapse
|
17
|
Schell P, Engels JW. 5-[2-(2-Methoxy)bornyl]tetrazole as Catalyst for Diastereoselective Synthesis of 2′-Deoxy Dinucleoside (3′, 5′)-Methylphosphonates. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319708002948] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Peter Schell
- a Institute of Organic Chemistry, Johann Wolfgang Goethe-University , Marie-Curie-Str. 11, D-60439, Frankfurt , Germany
| | - Joachim W. Engels
- a Institute of Organic Chemistry, Johann Wolfgang Goethe-University , Marie-Curie-Str. 11, D-60439, Frankfurt , Germany
| |
Collapse
|
18
|
Michel T, Debart F, Heitz F, Vasseur JJ. Highly stable DNA triplexes formed with cationic phosphoramidate pyrimidine alpha-oligonucleotides. Chembiochem 2005; 6:1254-62. [PMID: 15912553 DOI: 10.1002/cbic.200400436] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The ability of cationic phosphoramidate pyrimidine alpha-oligonucleotides (ONs) to form triplexes with DNA duplexes was investigated by UV melting experiments, circular dichroism spectroscopy and gel mobility shift experiments. Replacement of the phosphodiester linkages in alpha-ONs with positively charged phosphoramidate linkages results in more efficient triplex formation, the triplex stability increasing with the number of positive charges. At a neutral pH and in the absence of magnesium ions, it was found that a fully cationic phosphoramidate alpha-TFO (triplex-forming oligonucleotide) forms a highly stable triplex that melts at a higher temperature than the duplex target. No hysteresis between the annealing and melting curves was noticed; this indicates fast association. Moreover, the recognition of a DNA duplex with a cationic alpha-TFO through Hoogsteen base pairing is highly sequence-specific. To the best of our knowledge, this is the first report of stable triplexes in the pyrimidine motif formed by cationic alpha-oligonucleotides and duplex targets.
Collapse
Affiliation(s)
- Thibaut Michel
- LCOBS, UMR 5625 CNRS-UMII, CC 008, Université Montpellier II, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
| | | | | | | |
Collapse
|
19
|
Michel T, Mouls L, Debart F, Vasseur JJ. Imidazolethyl-phosphoramidate alpha-oligonucleotides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2003; 22:1263-5. [PMID: 14565395 DOI: 10.1081/ncn-120022942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Alpha-ODNs conjugated to imidazole groups via phosphoramidate internucleosidic linkages were synthesized. The presence of the imidazolethyl-phosphoramidate linkage improved the affinity of alpha-ODNs for their nucleic acid targets.
Collapse
Affiliation(s)
- T Michel
- Laboratoire de Chimie Organique Biomoléculaire de Synthèse, Université de Montpellier II, UMR 5625 CNRS-UMII, Montpellier, France
| | | | | | | |
Collapse
|
20
|
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.
Collapse
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
| | | | | | | | | |
Collapse
|
21
|
Sanghvi YS, Andrade M, Deshmukh RR, Holmberg L, Scozzari AN, Cole DL. Chemical Synthesis and Purification of Phosphorothioate Antisense Oligonucleotides. ACTA ACUST UNITED AC 1999. [DOI: 10.1007/978-1-4615-5067-9_1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
|
22
|
Schell P, Engels JW. Rp-Diastereoselective synthesis of dinucleoside methylphosphonates by the phosphoramidite approach. Tetrahedron Lett 1998. [DOI: 10.1016/s0040-4039(98)01972-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
23
|
Debart F, Meyer A, Vasseur JJ, Rayner B. Anomeric inversion (from beta to alpha) in methylphosphonate oligonucleosides enhances their affinity for DNA and RNA. Nucleic Acids Res 1998; 26:4551-6. [PMID: 9753720 PMCID: PMC147882 DOI: 10.1093/nar/26.20.4551] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Here we report that the poor binding of methylphosphonate oligodeoxynucleosides (MP-ODNs) to their nucleic acid targets can be improved by additional inversion of the anomeric configuration (from beta to alpha) in the sugar moieties to give a new class of analogs, MP alpha-oligonucleosides. MP alpha-dT12and MP 5' alpha-d(TCTTAACCCACA) 3' were synthesized and their ability to form hybrids with complementary single stranded (ss)DNA and ssRNA, as well as with double stranded (ds)DNA, was evaluated. The thermal stability of hybrids formed with MP alpha-analogs was compared with the affinity of phosphodiester (PO) and phosphorothioate (PS) beta- and alpha-oligomers for their targets. Non-ionic MP alpha-oligonucleosides bound to their complementary DNA and RNA strands more tightly than their homologues with natural beta-anomeric configuration did. With DNA target, MP alpha-oligomers formed duplexes more stable than the corresponding natural PO beta-oligomer did. MP alpha-heteropolymer hybridized to RNA target better than PS beta-oligonucleotide did but the hybrid was less stable (DeltaTm-0.5 degrees C per mod.) than the hybrid formed with the natural PO beta-oligomer. Only MP alpha-dT12 bound to dsDNA target at low salt concentration (0.1 M NaCl).
Collapse
Affiliation(s)
- F Debart
- Laboratoire de Chimie Bio-organique, CC008, UMR 5625 CNRS-UM II, Université Montpellier II, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France.
| | | | | | | |
Collapse
|
24
|
Stec WJ, Woźniak LA, Pyzowski J, Niewiarowski W. Novel cost-effective methanephosphonoanilidothioate approach to the stereoselective synthesis of dinucleoside (3',5')-methanephosphonates. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 1997; 7:381-95. [PMID: 9303190 DOI: 10.1089/oli.1.1997.7.381] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A new method of stereoselective preparation of di(2'-deoxy or 2'-OMe)ribonucleoside (3',5')-methanephosphonate 5 is presented. The DBU/LiCl-assisted reaction of 5'-O-DMT-(2'-deoxy or 2'-OMe)ribonucleoside 3'-O-(S-alkyl methanephosphonothioate) 9 with 5'-OH nucleosides proceeds with full stereospecificity, giving 5 in moderate to good yield. The conversion of 5'-O-DMT-(2'-deoxy or 2'-OMe) ribonucleoside 3'-methanephosphonoanilidothioates 8 and 3'-O-methanephosphonoanilidates 10 by means of NaH/CX2 (X = O,S) followed by S-alkylation leads to monomers 9, with the possibility of use of both separated diastereomers of 8 for the preparation of one selected diastereomer of 5. The relative configuration at the P atom in 2'-OMe and deoxynucleoside derivatives of compounds 9 was established by means of stereoselective degradation of nucleoside 3'-O-methanephosphonothioates 11 (precursors of 9) with nuclease P1.
Collapse
Affiliation(s)
- W J Stec
- Department of Bioorganic Chemistry, Polish Academy of Sciences, Lódź, Poland
| | | | | | | |
Collapse
|
25
|
Reynolds MA, Hogrefe RI, Jaeger JA, Schwartz DA, Riley TA, Marvin WB, Daily WJ, Vaghefi MM, Beck TA, Knowles SK, Klem RE, Arnold LJ. Synthesis and thermodynamics of oligonucleotides containing chirally pure R(P) methylphosphonate linkages. Nucleic Acids Res 1996; 24:4584-91. [PMID: 8948653 PMCID: PMC146287 DOI: 10.1093/nar/24.22.4584] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Methylphosphonate (MP) oligodeoxynucleotides (MPOs) are metabolically stable analogs of conventional DNA containing a methyl group in place of one of the non-bonding phosphoryl oxygens. All 16 possible chiral R(P) MP dinucleotides were synthesized and derivatized for automated oligonucleotide synthesis. These dimer synthons can be used to prepare (i) all-MP linked oligonucleotides having defined R(P) chirality at every other position (R(P) chirally enriched MPOs) or (ii) alternating R(P) MP/phosphodiester backbone oligonucleotides, depending on the composition of the 3'-coupling group. Chirally pure dimer synthons were also prepared with 2'-O-methyl sugar modifications. Oligonucleotides prepared with these R(P) chiral methylphosphonate linkage synthons bind RNA with significantly higher affinity than racemic MPOs.
Collapse
|