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Clavé G, Reverte M, Vasseur JJ, Smietana M. Modified internucleoside linkages for nuclease-resistant oligonucleotides. RSC Chem Biol 2021; 2:94-150. [PMID: 34458777 PMCID: PMC8341215 DOI: 10.1039/d0cb00136h] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/16/2020] [Indexed: 12/21/2022] Open
Abstract
In the past few years, several drugs derived from nucleic acids have been approved for commercialization and many more are in clinical trials. The sensitivity of these molecules to nuclease digestion in vivo implies the need to exploit resistant non-natural nucleotides. Among all the possible modifications, the one concerning the internucleoside linkage is of particular interest. Indeed minor changes to the natural phosphodiester may result in major modifications of the physico-chemical properties of nucleic acids. As this linkage is a key element of nucleic acids' chemical structures, its alteration can strongly modulate the plasma stability, binding properties, solubility, cell penetration and ultimately biological activity of nucleic acids. Over the past few decades, many research groups have provided knowledge about non-natural internucleoside linkage properties and participated in building biologically active nucleic acid derivatives. The recent renewing interest in nucleic acids as drugs, demonstrated by the emergence of new antisense, siRNA, aptamer and cyclic dinucleotide molecules, justifies the review of all these studies in order to provide new perspectives in this field. Thus, in this review we aim at providing the reader insights into modified internucleoside linkages that have been described over the years whose impact on annealing properties and resistance to nucleases have been evaluated in order to assess their potential for biological applications. The syntheses of modified nucleotides as well as the protocols developed for their incorporation within oligonucleotides are described. Given the intended biological applications, the modifications described in the literature that have not been tested for their resistance to nucleases are not reported.
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Affiliation(s)
| | - Maeva Reverte
- IBMM, Univ. Montpellier, CNRS, ENSCM Montpellier France
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2
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Matsuno Y, Shoji T, Kim S, Chiba K. Synthetic Method for Oligonucleotide Block by Using Alkyl-Chain-Soluble Support. Org Lett 2016; 18:800-3. [PMID: 26845521 DOI: 10.1021/acs.orglett.6b00077] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A straightforward method for the synthesis of oligonucleotide blocks using a Cbz-type alkyl-chain-soluble support (Z-ACSS) attached to the 3'-OH group of 3'-terminal nucleosides was developed. The Z-ACSS allowed for the preparation of fully protected deoxyribo- and ribo-oligonucleotides without chromatographic purification and released dimer- to tetramer-size oligonucleotide blocks via hydrogenation using a Pd/C catalyst without significant loss or migration of protective groups such as 5'-end 4,4'-dimethoxtrityl, 2-cyanoethyl on internucleotide bonds, or 2'-TBS.
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Affiliation(s)
- Yuki Matsuno
- Laboratory of Bio-organic Chemistry, Tokyo University of Agriculture and Technology , 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Takao Shoji
- Laboratory of Bio-organic Chemistry, Tokyo University of Agriculture and Technology , 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Shokaku Kim
- Laboratory of Bio-organic Chemistry, Tokyo University of Agriculture and Technology , 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Kazuhiro Chiba
- Laboratory of Bio-organic Chemistry, Tokyo University of Agriculture and Technology , 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
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Kan LS, Lin PY, Yano J. Syntheses and Characterization of Diastereoisomers of 2′-O-Methyladenylyl-3′,5′-2′-O-Methyladenosine Methyl Phosphonates and 2′-O-Methyladenylyl-3′,5′-2′-O-Methyladenosine Ethylphosphotriesters. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.199300099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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4
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Arunachalam TS, Wichert C, Appel B, Müller S. Mixed oligonucleotides for random mutagenesis: best way of making them. Org Biomol Chem 2012; 10:4641-50. [PMID: 22552713 DOI: 10.1039/c2ob25328c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The generation of proteins, especially enzymes, with pre-deliberated, novel properties is a big challenge in the field of protein engineering. This aim, over the years was critically facilitated by newly emerging methods of combinatorial and evolutionary techniques, such as combinatorial gene synthesis followed by functional screening of many structural variants generated in parallel (library). Libraries can be generated by a large number of available methods. Therein the use of mixtures of pre-formed trinucleotide blocks representing codons for the 20 canonical amino acids for oligonucleotide synthesis stands out as allowing fully controlled partial (or total) randomization individually at any number of arbitrarily chosen codon positions of a given gene. This has created substantial demand of fully protected trinucleotide synthons of good reactivity in standard oligonucleotide synthesis. We here review methods for the preparation of oligonucleotide mixtures with a strong focus on codon-specific trinucleotide blocks.
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Affiliation(s)
- Tamil Selvi Arunachalam
- Institut für Biochemie, Ernst Moritz Arndt Universität, Felix Hausdorff Strasse 4, Greifswald, D-17487, Germany
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Quaedflieg PJLM, Pikkemaat JA, van der Marel GA, Kuyl-Yeheskiely E, Altona C, van Boom JH. Synthesis and physicochemical properties of decanucleotides containing (3′→ 5′)-O-CH2-O-linkages at predetermined positions. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19931120104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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6
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Jones GDD, Le Pla RC, Farmer PB. Phosphotriester adducts (PTEs): DNA's overlooked lesion. Mutagenesis 2009; 25:3-16. [DOI: 10.1093/mutage/gep038] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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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.
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Affiliation(s)
- Alexandre V Lebedev
- Department of Research and Development, TriLink BioTechnologies, Inc., 9955 Mesa Rim Road, San Diego, CA 92121, USA
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8
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Nifantiev EE, Grachev MK. Trivalent phosphorus acids amides as phosphorylating agents for alcohols and amines. RUSSIAN CHEMICAL REVIEWS 2007. [DOI: 10.1070/rc1994v063n07abeh000106] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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9
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Ahmadibeni Y, Parang K. Synthesis and evaluation of modified oligodeoxynucleotides containing diphosphodiester internucleotide linkages. Angew Chem Int Ed Engl 2007; 46:4739-43. [PMID: 17497623 DOI: 10.1002/anie.200605029] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yousef Ahmadibeni
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, 41 Lower College Road, Kingston, RI 02881, USA
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Ahmadibeni Y, Parang K. Synthesis and Evaluation of Modified Oligodeoxynucleotides Containing Diphosphodiester Internucleotide Linkages. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200605029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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11
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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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12
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Yáñez J, Argüello M, Osuna J, Soberón X, Gaytán P. Combinatorial codon-based amino acid substitutions. Nucleic Acids Res 2004; 32:e158. [PMID: 15537836 PMCID: PMC534637 DOI: 10.1093/nar/gnh156] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2004] [Revised: 10/22/2004] [Accepted: 10/22/2004] [Indexed: 11/14/2022] Open
Abstract
Twenty Fmoc-protected trinucleotide phosphoramidites representing a complete set of codons for the natural amino acids were chemically synthesized for the first time. A pool of these reagents was incorporated into oligonucleotides at substoichiometric levels to generate two libraries of variants that randomly carry either few or many codon replacements on a region encoding nine amino acids of the bacterial enzyme TEM-1 beta-lactamase. Assembly of the libraries was performed in a completely automated mode through a simple modification of ordinary protocols. This technology eliminates codon redundancy, stop codons and enables complete exploration of sequence space for single, double and triple mutations throughout a protein region spanning several residues. Sequence analysis of many non-selected clones revealed a good incorporation of the trinucleotides, producing combinations of mutations quite different from those obtained using conventional degenerate oligonucleotides. Ceftazidime-selection experiments yielded several never before reported variants containing novel amino acid combinations in the beta-lactamase omega loop region.
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Affiliation(s)
- Jorge Yáñez
- Instituto de Biotecnología/UNAM, Ap. Postal 510-3 Cuernavaca, Morelos 62250, México
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Tsujikawa L, Weinfield M, Reha-Krantz LJ. Differences in replication of a DNA template containing an ethyl phosphotriester by T4 DNA polymerase and Escherichia coli DNA polymerase I. Nucleic Acids Res 2003; 31:4965-72. [PMID: 12930945 PMCID: PMC212818 DOI: 10.1093/nar/gkg722] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A DNA template containing a single ethyl phosphotriester was replicated in vitro by the bacteriophage T4 DNA polymerase and by Escherichia coli DNA polymerase I (DNA pol I). Escherichia coli DNA pol I bypassed the lesion efficiently, but partial inhibition was observed for T4 DNA polymerase. The replication block produced by the ethyl phosphotriester was increased at low dNTP concentrations and for a mutant T4 DNA polymerase with an antimutator phenotype, increased proofreading activity, and reduced ability to bind DNA in the polymerase active center. These observations support a model in which an ethyl phosphotriester impedes primer elongation by T4 DNA polymerase by decreasing formation of the ternary DNA polymerase-DNA-dNTP complex. When primer elongation is not possible, proofreading becomes the favored reaction. Apparent futile cycles of nucleotide incorporation and proofreading, the idling reaction, were observed at the site of the lesion. The replication block was overcome by higher dNTP concentrations. Thus, ethyl phosphotriesters may be tolerated in vivo by the up-regulation of dNTP biosynthesis that occurs during the cellular checkpoint response to blocked DNA replication forks.
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Affiliation(s)
- Laura Tsujikawa
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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Bowman KJ, Pla RL, Guichard Y, Farmer PB, Jones GD. Evaluation of phosphodiesterase I-based protocols for the detection of multiply damaged sites in DNA: the detection of abasic, oxidative and alkylative tandem damage in DNA oligonucleotides. Nucleic Acids Res 2001; 29:E101. [PMID: 11600720 PMCID: PMC60229 DOI: 10.1093/nar/29.20.e101] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
It has been proposed that DNA multiply damaged sites (MDS), where more than one moiety in a local region ( approximately 1 helical turn, 10 bp) of the DNA is damaged, are lesions of enhanced biological significance. However, other than indirect measures, there are few analytical techniques that allow direct detection of MDS in DNA. In the present study we demonstrate the potential of protocols incorporating an exonucleolytic snake venom phosphodiesterase (SVPD) digestion stage to permit the direct detection of certain tandem damage, in which two lesions are immediately adjacent to each other on the same DNA strand. A series of prepared oligonucleotides containing either single or pairs of tetrahydrofuran moieties (F), thymine glycol lesions (T(g)) or methylphosphotriester adducts (Me-PTE) were digested with SVPD and the digests examined by either (32)P-end-labelling or electrospray mass spectrometry. The unambiguous observation of SVPD-resistant 'trimer' species in the digests of oligonucleotides containing adjacent F, T(g) and Me-PTE demonstrates that the SVPD digestion strategy is capable of allowing direct detection of certain tandem damage. Furthermore, in studies to determine the specificity of SVPD in dealing with pairs of lesions on the same strand, it was found mandatory to have the two lesions immediately adjacent to each other in order to generate the trimer species; pairs of lesions separated by as few as one or two normal nucleotides behave principally as single lesions towards SVPD.
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Affiliation(s)
- K J Bowman
- Department of Oncology and Biomonitoring and Molecular Interactions Section, MRC Toxicology Unit, Hodgkin Building, University of Leicester, PO Box 138, Lancaster Road, Leicester LE1 9HN, UK
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Hayakawa Y. Toward an Ideal Synthesis of Oligonucleotides: Development of a Novel Phosphoramidite Method with High Capability. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2001. [DOI: 10.1246/bcsj.74.1547] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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16
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Hayakawa Y, Kawai R, Hirata A, Sugimoto JI, Kataoka M, Sakakura A, Hirose M, Noyori R. Acid/azole complexes as highly effective promoters in the synthesis of DNA and RNA oligomers via the phosphoramidite method. J Am Chem Soc 2001; 123:8165-76. [PMID: 11516266 DOI: 10.1021/ja010078v] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The utility of various kinds of acid salts of azole derivatives as promoters for the condensation of a nucleoside phosphoramidite and a nucleoside is investigated. Among the salts, N-(phenyl)imidazolium triflate, N-(p-acetylphenyl)imidazolium triflate, N-(methyl)benzimidazolium triflate, benzimidazolium triflate, and N-(phenyl)imidazolium perchlorate have shown extremely high reactivity in a liquid phase. These reagents serve as powerful activators of deoxyribonucleoside 3'-(allyl N,N-diisopropylphosphoramidite)s or 3'-(2-cyanoethyl N,N-diisopropylphosphoramidite)s employed in the preparation of deoxyribonucleotides, and 3'-O-(tert-butyldimethylsilyl)ribonucleoside 2'-(N,N-diisopropylphosphoramidite)s or 2'-O-(tert-butyldimethylsilyl)ribonucleoside 3'-(N,N-diisopropylphosphoramidite)s used for the formation of 2'-5' and 3'-5' internucleotide linkages between ribonucleosides, respectively. The azolium salt has allowed smooth and high-yield condensation of the nucleoside phosphoramidite and a 5'-O-free nucleoside, in which equimolar amounts of the reactants and the promoter are employed in the presence of powdery molecular sieves 3A in acetonitrile. It has been shown that some azolium salts serve as excellent promoters in the solid-phase synthesis of oligodeoxyribonucleotides and oligoribonucleotides. For example, benzimidazolium triflate and N-(phenyl)imidazolium triflate can be used as effective promoters in the synthesis of an oligodeoxyribonucleotide, (5')CGACACCCAATTCTGAAAAT(3') (20mer), via a method using O-allyl/N-allyloxycarbonyl-protected deoxyribonucleoside 3'-phosphoramidites or O-(2-cyanoethyl)/N-phenoxyacetyl-protected deoxyribonucleotide 3'-phosphoramidite as building blocks, respectively, on high-cross-linked polystyrene resins. Further, N-(phenyl)imidazolium triflate is useful for the solid-phase synthesis of oligoribonucleotides, such as (5')AGCUACGUGACUACUACUUU(3') (20mer), according to an allyl/allyloxycarbonyl-protected strategy. The utility of the azolium promoter has been also demonstrated in the liquid-phase synthesis of some biologically important substances, such as cytidine-5'-monophosphono-N-acetylneuraminic acid (CMP-Neu5Ac) and adenylyl(2'-5')adenylyl(2'-5')adenosine (2-5A core).
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Affiliation(s)
- Y Hayakawa
- Laboratory of Bioorganic Chemistry, Graduate School of Human Informatics, Nagoya University, Chikusa, Nagoya 464-8601, Japan.
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Nifantiev EE, Grachev MK, Burmistrov SY. Amides of trivalent phosphorus acids as phosphorylating reagents for proton-donating nucleophiles. Chem Rev 2000; 100:3755-800. [PMID: 11749327 DOI: 10.1021/cr9601371] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- E E Nifantiev
- V. I. Lenin Moscow State Pedagocical University, Chemistry Department, Nesvizhskii per., 3, 119021 Moscow, Russian Federation
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18
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Gaytán P, Yañez J, Sánchez F, Mackie H, Soberón X. Combination of DMT-mononucleotide and Fmoc-trinucleotide phosphoramidites in oligonucleotide synthesis affords an automatable codon-level mutagenesis method. CHEMISTRY & BIOLOGY 1998; 5:519-27. [PMID: 9751646 DOI: 10.1016/s1074-5521(98)90007-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Synthetic DNA has been used to introduce variability into protein-coding regions. In protocols that produce a few mutations per gene, the sampling of amino-acid sequence space is limited by the bias imposed by the genetic code. It has long been apparent that the incorporation of trinucleotides in the synthetic regime would circumvent this problem and significantly enhance the usefulness of the technique. RESULTS A new method is described for the creation of codon-level degenerate oligodeoxyribonucleotides that combines conventional dimethoxytrityl (DMT) mononucleoside phosphoramidite chemistry with 9-fluorenylmethoxycarbonyl (Fmoc) trinucleotide phosphoramidites (whose synthesis is reported in the paper). The substoichiometric use of these Fmoc-trinucleotides in an automatable, solid-phase synthesis procedure afforded DNA fragments comprising the wild-type sequence and a controllable distribution of mutants within two- and three-codon stretches of DNA, within the multiple cloning site of the conventional cloning vector pUC19. CONCLUSIONS DMT and Fmoc are compatible protecting groups in conventional oligonucleotide synthesis methods, resulting in controllable levels of codon-based mutagenesis.
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Affiliation(s)
- P Gaytán
- Department of Molecular Recognition and Biostructure, Instituto de Biotecnología/UNAM, Cuernavaca, Mor. México
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Vaughn JP, Stekler J, Demirdji S, Mills JK, Caruthers MH, Iglehart JD, Marks JR. Inhibition of the erbB-2 tyrosine kinase receptor in breast cancer cells by phosphoromonothioate and phosphorodithioate antisense oligonucleotides. Nucleic Acids Res 1996; 24:4558-64. [PMID: 8948649 PMCID: PMC146276 DOI: 10.1093/nar/24.22.4558] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Antisense activity against erbB-2 of a variety of sulfur-modified oligonucleotides was examined in a breast cancer cell line which overexpresses this oncogene. Using a 15 base anti-erbB-2 sequence previously shown to be effective, various backbone configurations containing phosphoromonothioate or phosphorodithioate linkages were evaluated for antisense activity by a two-color flow cytometric assay. This sequence was effective in inhibiting the production of erbB-2 protein when it was configured as a monothioate at each linkage and as an alternating dithioate/phosphodiester. Both of these compounds were also able to specifically inhibit erbB-2 mRNA expression, indicative of RNase H-mediated activity. The same sequence protected by either three dithioate or three monothioate linkages at each end was ineffective as an antisense reagent, suggesting that endonuclease activity is a significant determinant of the stability of oligonucleotides. Finally, the erbB-2 sequence target was shifted in an effort to improve antisense activity. A new lead sequence was identified that was significantly more effective in inhibiting erbB-2 protein levels and retained activity at lower concentrations.
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Affiliation(s)
- J P Vaughn
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
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21
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Thorogood H, Grasby JA, Connolly BA. Influence of the phosphate backbone on the recognition and hydrolysis of DNA by the EcoRV restriction endonuclease. A study using oligodeoxynucleotide phosphorothioates. J Biol Chem 1996; 271:8855-62. [PMID: 8621526 DOI: 10.1074/jbc.271.15.8855] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A set of phosphorothioate-containing oligonucleotides based on pGACGATATCGTC, a self-complementary dodecamer that contains the EcoRV recognition sequence (GATATC), has been prepared. The phosphorothioate group has been individually introduced at the central nine phosphate positions and the two diastereomers produced at each site separated and purified. The Km and Vmax values found for each of these modified DNA molecules with the EcoRV restriction endonuclease have been determined and compared with those seen for the unmodified all-phosphate-containing dodecamer. This has enabled an evaluation of the roles that both of the non-esterified oxygen atoms in the individual phosphates play in DNA binding and hydrolysis by the endonuclease. The results have also been compared with crystal structures of the EcoRV endonuclease, complexed with an oligodeoxynucleotide, to allow further definition of phosphate group function during substrate binding and turnover. For further study, see the related article "Probing the Indirect Readout of the Restriction Enzyme EcoRV: Mutational Analysis of Contacts to the DNA Backbone" (Wenz, A., Jeltsch, A., and Pingoud, A. (1996) J. Biol. Chem. 271, 5565-5573).
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Affiliation(s)
- H Thorogood
- Department of Biochemistry and Genetics, University of Newcastle, Newcastle upon Tyne NE2 4HH, United Kingdom
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22
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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.
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Fearon KL, Stults JT, Bergot BJ, Christensen LM, Raible AM. Investigation of the 'n-1' impurity in phosphorothioate oligodeoxynucleotides synthesized by the solid-phase beta-cyanoethyl phosphoramidite method using stepwise sulfurization. Nucleic Acids Res 1995; 23:2754-61. [PMID: 7651837 PMCID: PMC307101 DOI: 10.1093/nar/23.14.2754] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Electrospray ionization mass spectrometry (ESI-MS) of reversed-phase HPLC-purified phosphorothioate oligodeoxynucleotides (S-ODNs), and the single-('n - 1') and double-nucleotide deletion ('n - 2') impurities subsequently isolated from them by preparative polyacrylamide gel electrophoresis (PAGE), has provided direct analytical data for the identification of both S-ODN products and their major oligomeric impurities. The 'n - 1' impurity seen by PAGE consists of a mixture of all possible single deletion sequences relative to the parent S-ODN (n-mer) and results from repetitive, though minor, imperfections in the synthesis cycle, such as incomplete detritylation, or incomplete coupling followed by incomplete capping or incomplete sulfurization. Therefore each possible 'n - 1', 'n - 2', and other short-mer sequence is present only in very low abundance. The conversion of the gel-isolated 'n - 1' impurity from phosphorothioate to phosphodiester followed by base composition-dependent anion-exchange chromatography allowed for independent confirmation of its heterogeneity and quantitation of its various components. ESI-MS of both S-ODN products and their gel-isolated impurities allowed for this first molecular identification of 'n - 1', 'n - 2' and other oligomeric impurities in S-ODNs obtained from state-of-the-art solid-phase synthesis and reversed-phase HPLC purification methods.
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Affiliation(s)
- K L Fearon
- Lynx Therapeutics, Inc., Hayward, CA 94545, USA
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Jen-Jacobson L. Structural-perturbation approaches to thermodynamics of site-specific protein-DNA interactions. Methods Enzymol 1995; 259:305-44. [PMID: 8538460 DOI: 10.1016/0076-6879(95)59050-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- L Jen-Jacobson
- Department of Biological Sciences, University of Pittsburgh, Pennsylvania 15260, USA
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25
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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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26
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Stereoselective interaction with chiral phosphorothioates at the central DNA kink of the EcoRI endonuclease-GAATTC complex. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)35836-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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27
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Dahl O. Preparation of Nucleoside Phosphorothioates, Phosphorodithioates and Related Compounds. ACTA ACUST UNITED AC 1991. [DOI: 10.1080/01961779108048765] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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28
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Kuijpers WH, Huskens J, Koole LH, van Boeckel CA. Synthesis of well-defined phosphate-methylated DNA fragments: the application of potassium carbonate in methanol as deprotecting reagent. Nucleic Acids Res 1990; 18:5197-205. [PMID: 2402444 PMCID: PMC332142 DOI: 10.1093/nar/18.17.5197] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A new deprotection procedure in the synthesis of (partially) phosphate-methylated oligodeoxynucleotides has been developed, involving treatment of fully protected DNA fragments with methanolic potassium carbonate. It is shown that base deprotection can be accomplished in potassium carbonate/methanol without affecting the methyl phosphotriesters. This methodology enables us to synthesize, both in solution and on a solid support, DNA fragments which are phosphate-methylated at defined positions. The solid phase synthesis, however, turns out to be accompanied by considerable demethylation of the phosphotriesters. It is demonstrated that this demethylation does not occur during the deprotection or work-up procedure. Furthermore, it was found that the latter side-reaction is suppressed when the standard capping procedure with acetic anhydride is included.
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Affiliation(s)
- W H Kuijpers
- Department of Organic Chemistry, Eindhoven University of Technology, The Netherlands
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30
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Olsen D, Kotzorek G, Sayers J, Eckstein F. Inhibition of the restriction endonuclease BanII using modified DNA substrates. Determination of phosphate residues critical for the formation of an active enzyme-DNA complex. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(18)77314-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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31
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Kuijpers W, Huskens J, van Boeckel C. The 2-(acetoxymethyl)benzoyl (AMB) group as a new base-protecting group, designed for the protection of (phosphate) modified oligonucleotides. Tetrahedron Lett 1990. [DOI: 10.1016/s0040-4039(00)97159-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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32
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Uznanski B, Grajkowski A, Wilk A. The isopropoxyacetic group for convenient base protection during solid-support synthesis of oligodeoxyribonucleotides and their triester analogs. Nucleic Acids Res 1989; 17:4863-71. [PMID: 2748339 PMCID: PMC318037 DOI: 10.1093/nar/17.12.4863] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Isopropoxyacetic anhydride was successfully used for protection of exoaminofunctions of 2'-deoxyadenosine, -guanosine and -cytidine. N-isopropoxyacetylated nucleosides are stable under the conditions of the synthesis of oligodeoxyribonucleotides on the solid support. Removal of N-isopropoxyacetyl is much faster than that of commonly used benzoyl or isobutyryl groups viz. it is completed within the operation of cleavage of the oligodeoxyribonucleotide from the solid support. This observation enabled synthesis of -OCH2CH3 and -OCH2CF3 triesters, which hydrolyse partially or completely when standard deprotection conditions are applied.
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Affiliation(s)
- B Uznanski
- Polish Academy of Sciences, Department of Bioorganic Chemistry, Lodz
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33
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Weinfeld M, Drake AF, Kuroda R, Livingston DC. Isolation and characterization of the diastereoisomers of a series of phosphate-ethylated dinucleoside monophosphates. Anal Biochem 1989; 178:93-101. [PMID: 2729585 DOI: 10.1016/0003-2697(89)90362-x] [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: 01/02/2023]
Abstract
Internucleotide phosphate esterification is a common reaction of many potent carcinogenic alkylating agents. It can give rise to two stereochemically distinct molecules about a triesterified phosphorus atom. The eight individual diastereoisomers derived from phosphate ethylation of d-ApT, d-CpT, d-GpT, and d-TpT were prepared from o-chlorophenyl phosphotriester intermediates and isolated by reverse-phase HPLC. Each pair of isomers, together with its parent analog, was examined by variable temperature circular dichroism. The results are interpreted in terms of secondary structure changes from which the absolute configurations of the ethylated phosphate groups can be inferred. These configurational assignments were confirmed by 31P NMR.
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Affiliation(s)
- M Weinfeld
- Chemistry Department, Imperial Cancer Research Fund, London, United Kingdom
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34
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Koziolkiewicz M, Uznanski B, Stec WJ. Phosphate-Modified Oligonucleotides. The Synthesis, Stereochemistry and ECO Ri Endonuclease Substrate Ability of Decanucleotides d[GGGAATTCCC] Bearing Altered Internucleotide Phosphate Function Between A and A1. ACTA ACUST UNITED AC 1989. [DOI: 10.1080/07328318908054167] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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35
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Abramova TV, Vlassov VV, Lebedev AV, Ryte AS. Complementary addressed modification of nucleic acids with the alkylating derivatives of oligothymidylate ethyl phosphotriesters. Effect of the phosphotriester fragments' configuration. FEBS Lett 1988; 236:243-5. [PMID: 2456955 DOI: 10.1016/0014-5793(88)80323-5] [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: 01/01/2023]
Abstract
The alkylating derivatives of four individual diastereomers of the oligonucleotide [dTp(Et)]3dTpU and two individual diastereomers of oligonucleotide [dTp(Et)dTp]4 have been synthesized. The reagents with the phosphorus atoms in the enantiomeric p" configuration are shown to be more efficient in reacting with poly(dA) and with nucleic acids in Krebs-2 ascites carcinoma cells compared to those with the phosphorus atoms in the p' configuration.
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Affiliation(s)
- T V Abramova
- Institute of Bioorganic Chemistry, Siberian Division, USSR Academy of Sciences, Novosibirsk
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36
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Marcus-Sekura CJ. Techniques for using antisense oligodeoxyribonucleotides to study gene expression. Anal Biochem 1988; 172:289-95. [PMID: 3056098 DOI: 10.1016/0003-2697(88)90447-2] [Citation(s) in RCA: 120] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Molecular biology is providing powerful tools for cloning and sequencing genes. The more difficult task is that of ascribing functions to the specific DNA sequences that appear to code for proteins, the "open reading frames," or of regulating the expression of known genes in biological systems in order to determine their contributions to cellular functions. The classical genetic approach of making mutants is difficult in eukaryotic systems, with the exception of yeasts and viruses, and has proved of limited utility. A promising approach to this problem has been to introduce into either the in vitro assay or tissue culture system oligodeoxyribonucleotides with nucleotide sequences complementary to the protein coding or "sense" sequence, usually referred to as "antisense" oligonucleotides. The term MATAGEN (MAsking TApe for Gene ExpressioN) has also been used for these compounds, which appear to inhibit gene expression predominantly by hybridization arrest of translation. Interest in the use of antisense molecules for the study of gene expression and regulation has increased dramatically in the past few years. The demonstrated utility of the antisense oligomer in both in vitro and tissue culture assays, the increased availability of nucleotide sequence data as well as improvements in nucleic acid sequencing techniques, and the automation of synthetic procedures for their preparation have made studies using these molecules more practical. This review focuses on short oligodeoxyribonucleotides, which offer important stability and synthetic advantages over the use of antisense RNA transcripts, and is intended as an introduction to practical approaches in the use of antisense oligodeoxyribonucleotides in biological systems. For synthetic techniques, the reader is referred to the individual references cited.
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Affiliation(s)
- C J Marcus-Sekura
- Division of Virology, Food and Drug Administration, Bethesda, Maryland 20892
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37
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Brill WKD, Caruthers MH. Synthesis and p-diastereomeric resolution of nucleoside 3′-O(s-alkyl) and nucleoside 3′-O(s-aryl) methylphosphonothioates. Tetrahedron Lett 1988. [DOI: 10.1016/s0040-4039(00)80262-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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38
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Marcus-Sekura CJ, Woerner AM, Shinozuka K, Zon G, Quinnan GV. Comparative inhibition of chloramphenicol acetyltransferase gene expression by antisense oligonucleotide analogues having alkyl phosphotriester, methylphosphonate and phosphorothioate linkages. Nucleic Acids Res 1987; 15:5749-63. [PMID: 3475677 PMCID: PMC306020 DOI: 10.1093/nar/15.14.5749] [Citation(s) in RCA: 153] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Several classes of oligonucleotide antisense compounds of sequence complementary to the start of the mRNA coding sequence for chloramphenicol acetyl transferase (CAT), including methylphosphonate, alkyltriester, and phosphorothioate analogues of DNA, have been compared to "normal" phosphodiester oligonucleotides for their ability to inhibit expression of plasmid-directed CAT gene activity in CV-1 cells. CAT gene expression was inhibited when transfection with plasmid DNA containing the gene for CAT coupled to simian virus 40 regulatory sequences (pSV2CAT) or the human immunodeficiency virus enhancer (pHIVCAT) was carried out in the presence of 30 microM concentrations of analogue. For the oligo-methylphosphonate analogue, inhibition was dependent on both oligomer concentration and chain length. Analogues with phosphodiester linkages that alternated with either methylphosphonate, ethyl phosphotriester, or isopropyl phosphotriester linkages were less effective inhibitors, in that order. The phosphorothioate analogue was about two-times more potent than the oligo-methylphosphonate, which was in turn approximately twice as potent as the normal oligonucleotide.
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Bower M, Summers MF, Powell C, Shinozuka K, Regan JB, Zon G, Wilson WD. Oligodeoxyribonucleoside methylphosphonates. NMR and UV spectroscopic studies of Rp-Rp and Sp-Sp methylphosphonate (Me) modified duplexes of (d[GGAATTCC])2. Nucleic Acids Res 1987; 15:4915-30. [PMID: 3601658 PMCID: PMC305927 DOI: 10.1093/nar/15.12.4915] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
1H NMR chemical shift assignments for the title compounds were made for most of the 1H signals using two-dimensional nuclear Overhauser effect (2D-NOE) data, which were also used to establish the absolute configuration at the modified phosphorus. The chemical shifts were similar to those reported [Broido, M.S., et al. (1985) Eur. J. Biochem. 150, 117-128] for the unmodified, parent, B-type duplex [d(GGAATTCC)]2. Differences in chemical shifts were mostly localized to the nucleotides on the 5'- and 3'-sides of the modified phosphorus. The Rp-Rp isomers exhibited UV-derived Tm values similar to that of the parent duplex. On the other hand, the Sp-Sp isomers generally exhibited lower Tm values which correlated with P-CH3--H3' (n-1 nucleotide) cross peak intensities and 31P spectral parameters. The combined data argue for increased steric interactions with the Sp-P-Me methyl group as the modification position is moved toward the center of the oligomer. All of the Tm results can be explained in terms of three factors which result from replacement of a phosphate by a methylphosphonate group: reduction of oligomer charge; electronic and other substituent effects; steric interactions.
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40
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Bower M, Summers MF, Kell B, Hoskins J, Zon G, Wilson WD. Synthesis and characterization of oligodeoxyribonucleotides containing terminal phosphates. NMR, UV spectroscopic and thermodynamic analysis of duplex formation of [d(pGGAATTCC)]2, [d(GGAATTCCp)]2 and [d(pGGAATTCCp)]2. Nucleic Acids Res 1987; 15:3531-47. [PMID: 3575099 PMCID: PMC340747 DOI: 10.1093/nar/15.8.3531] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Derivatives of the oligomer [d(GGAATTCC)]2 with 5' (5'-P), 3' (3'-P) and both 5' and 3' (5',3'-P2) terminal phosphate groups have been synthesized and studied by temperature dependent UV and NMR spectroscopic methods. Thermodynamic studies of the helix to strand transition indicate that addition of 3' phosphate groups has very little effect on the delta G degree for helix formation at 37 degrees C while addition of 5' phosphate groups adds approximately -0.5 kcal/mole to the delta G degree for duplex formation. The helix stabilization by 5' phosphate groups occurs at salt concentrations of 0.1 M and above, and is primarily enthalpic in origin. Tm studies as a function of ionic strength also indicate that the oligomers fall into two groups with the parent and 3'-P derivatives being similar but less stable than the 5'-P and 5',3'-P2 derivatives. Imino proton and 31P NMR studies also divide the oligomers into these same two groups based on spectral comparisons and temperature induced chemical shift and linewidth changes. 31P NMR analysis suggests that addition of 5' phosphate groups results in a small change in phosphodiester torsional angles in the g,t to g,g direction, indicating improved base stacking at the 5' end of the modified oligomer. No such changes are seen at the 3' end of the oligomer on adding 3' phosphate groups.
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LaPlanche LA, James TL, Powell C, Wilson WD, Uznanski B, Stec WJ, Summers MF, Zon G. Phosphorothioate-modified oligodeoxyribonucleotides. III. NMR and UV spectroscopic studies of the Rp-Rp, Sp-Sp, and Rp-Sp duplexes, [d(GGSAATTCC)]2, derived from diastereomeric O-ethyl phosphorothioates. Nucleic Acids Res 1986; 14:9081-93. [PMID: 3786144 PMCID: PMC311930 DOI: 10.1093/nar/14.22.9081] [Citation(s) in RCA: 68] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
2D-NOE and 1H NMR chemical shift data obtained for the title oligonucleotides were compared with similar data previously reported [Broido et al. (1985) Eur. J. Biochem. 150, 117-128] for the unmodified "parent" structure, [d(GGAATTCC)]2. The spectroscopically detectable structural perturbations caused by replacement of phosphate oxygen with sulfur were mostly localized within the GsA moiety, and were greater for the Rp configuration wherein sulfur is oriented into the major groove of the B-helix. UV-derived Tm measurements gave the following order of stability for the duplexes in 0.4 M NaCl: unmodified (33.9 +/- 0.1 degrees C) approximately Sp-Sp (34.1 degrees C) greater than Rp-Rp (31.7 degrees C). The title compounds were prepared by a new and convenient synthetic route which utilized HPLC to separate the diastereomeric O-ethyl phosphorothioate precursors, (Rp)- and (Sp)-d[GG(S,Et)AATTCC], for subsequent de-ethylation by ammonia in water.
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43
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Iyengar R, Bhat M, Riser M, Birnbaumer L. Receptor-specific desensitization of the S49 lymphoma cell adenylyl cyclase. Unaltered behavior of the regulatory component. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)69325-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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