Synthesis, NMR and structure of oligonucleotide phosphorodithioates

Piotto, Martial; Granger, Jill Nelson; Cho, Yesun; Farschtschi, Nasser; Gorenstein, David G.

doi:10.1016/s0040-4020(01)81780-4

Cited by 28 publications

(12 citation statements)

References 43 publications

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“…There are few literature reports describing the purification of PS2 analogues and most describe purification by reversed-phase chromatography (11,12,23,24,33). IEC chromatographic purification of PS2 analogues containing a small number of PS2 linkages is briefly mentioned in the literature (23,33).…”

Section: Discussionmentioning

confidence: 99%

“…The formation of achiral internucleotide dithioate linkage by phosphorothioamidite coupling in the solidphase synthesis of PS2 analogues (11,12,23,25) has been demonstrated recently. The thymidine 3-O-phosphorodithioate oligonucleotide of the base sequence 5Ј-CCAGGAGATTCCAC-3Ј and its complementary sequence of 5Ј-GTGGAATCTCCTGG-3Ј were purified on a Mono-Q column by which separation of PS2 analogues from PS and PO impurities was achieved (22).…”

Section: Comparative Analysis Of Po Ps and Ps2 Analoguesmentioning

confidence: 99%

“…Rapid degradation of natural oligonucleotides by nucleases (6, 7) necessitated chemical modification of the oligonucleotides. Among a large variety of modifications, synthetic phosphate-modified analogues of oligonucleotides, such as methylphosphonate (8), monothiophosphate (9, 10) (PS), 3 dithiophosphate (11,12) (PS2), and amidophosphate (13) oligonucleotides, are more nuclease resistant and have received a growing amount of attention from chemists and biologists who have recognized their advantages for targeting specific sequences of single-and doublestranded nucleic acids (14 -20).…”

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confidence: 99%

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Separation of Synthetic Oligonucleotide Dithioates from Monothiophosphate Impurities by Anion-Exchange Chromatography on a Mono-Q Column

Yang

Hodge²,

Luxon

et al. 2002

Analytical Biochemistry

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Section: Discussionmentioning

confidence: 99%

Section: Comparative Analysis Of Po Ps and Ps2 Analoguesmentioning

confidence: 99%

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confidence: 99%

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Separation of Synthetic Oligonucleotide Dithioates from Monothiophosphate Impurities by Anion-Exchange Chromatography on a Mono-Q Column

Yang

Hodge²,

Luxon

et al. 2002

Analytical Biochemistry

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“…The dithiophosphate oligonucleotide analogues of d(CGCTTAAGCG) possessing a dithiophosphate linkage in a single site has been synthesized by a manual solid phase methodology (13,18,41,42). The dithiophosphoryl analogue d(CGCTpS2fAAGCG) [10-mer-S] was prepared in ca.…”

Section: Solid Phase Synthesis Of Dithiophosphate Modified Oligonuclementioning

confidence: 99%

“…With the demonstration that oligonucleotides and various analogues of oligonucleotides exhibit antiviral and anti-oncogene activity, considerable interest has developed around the synthesis, structural characterization and biological activity of various "antisense" oligonucleotide agents (2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20). Oligodeoxyribonucleotides, oligodeoxynucleoside methylphosphonate, phosphorothioate, phosphoroamidate and phosphorodithioate analogues among others have been studied.…”

Section: Introductionmentioning

confidence: 99%

2D¹H and³¹P NMR Spectra and Distorted A-DNA-Like Duplex Structure of a Phosphorodithioate Oligonucleotide

Cho

Zhu

Luxon

et al. 1993

Journal of Biomolecular Structure and Dynamics

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Assignment of the 1H and 31P NMR spectra of a phosphorodithioate modified oligonucleotide decamer duplex, d(CGCTTpS2-AAGCG)2 (10-mer-S; a site of dithioate substitution is designated with the symbols pS2-), was achieved by two-dimensional homonuclear TOCSY, NOESY and 1H-31P Pure Absorption phase Constant time (PAC) heteronuclear correlation spectroscopy. In contrast to the parent palindromic decamer sequence (1) which has been shown to exist entirely in the duplex B-DNA conformation under comparable conditions (100 mM KCl), the dithiophosphate analogue forms a hairpin loop. However, the duplex form of the dithioate oligonucleotide can be stabilized at lower temperatures, higher salt and strand concentration. The solution structure of the decamer duplex was calculated by an iterative hybrid relaxation matrix method (MORASS) combined with 2D NOESY-distance restrained molecular dynamics. These backbone modified compounds, potentially attractive antisense oligonucleotide agents, are often assumed to possess similar structure as the parent nucleic acid complex. Importantly, the refined structure of the phosphorodithioate duplex shows a significant deviation from the parent unmodified, phosphoryl duplex. An overall bend and unwinding in the phosphorodithioate duplex is observed. The structural distortion of the phosphorodithioate duplex was confirmed by comparison of helicoidal parameters and groove dimensions. Especially, the helical twists of the phosphorodithioate decamer deviate significantly from the parent phosphoryl decamer. The minor groove width of phosphorodithioate duplex 10-mer-S varies between 8.4 and 13.3 A which is much wider than those of the parent phosphoryl decamer d(CGCTTAAGCG)2 (4.2 approximately 9.4 A). The larger minor groove width of 10-mer-S duplex contributes to the unwinding of the backbone and indicates that the duplex has an overall A-DNA-like conformation in the region surrounding the dithiophosphate modification.

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Stereokontrollierte Synthese von Oligonucleosidphosphorothioaten

Stec

Wilk

1994

Angewandte Chemie

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Bei der Modulation der Genexpression durch Antisense‐Oligonucleotide oder deren Analoga wurden Ergebnisse erzielt, die auf eine neue Generation von Therapeutica gegen virale Infektionen, Krebs und andere Krankheiten hoffen lassen. Oligonucleosidphosphorothioate (Oligo‐S) sind die wirksamsten Analoga bei der Unterdrückung der Biosynthese „ungewollter”︁ Proteine. Erste klinische Untersuchungen von Oligo‐S als Antisense‐Präparate gegen Warzen im Genitalbereich und akute myeloische Leukämie werden zur Zeit durchgeführt; auch gegen Aids sollen Oligo‐S getestet werden. Details des Wirkungsmechanismus, der Aufnahme in die Zelle, des Zelltransports, der subzellulären Lokalisierung und der Wechselwirkung mit zellulären Proteinen sind noch nicht bekannt. A priori wird bei der Applikation angenommen, daß eine rasche und effiziente molekulare Erkennung der Ziel‐RNA durch Oligo‐S erfolgt. Der Einfluß der Chiralität als Eigenschaft des Oligo‐S‐Gesamtmoleküls konnte bislang nicht geklärt werden, da diese Verbindungen nicht stereokontrolliert herstellbar sind. Aufgrund fehlender analytischer Methoden wurde die Diastereomerenzusammensetzung nie bestimmt. Da jedes Diastereomer eine eindeutig definierte stereochemische Einheit ist, stellt sich die Frage, welche Diastereomere die beobachtete biologische Antwort, die positive (heilende) Wirkung und die mögliche negative (toxische) Nebenwirkung, bewirken. Das Ziel dieser Übersicht ist, eine (zum Teil auch spekulative) Abschätzung der Probleme, die mit einer stereokontrollierten Synthese von Oligo‐S verbunden sind, zu liefern sowie den Forschungsstand zu referieren, wobei auch auf Strategien eingegangen werden soll, die zu Oligo‐S mit vorbestimmter Chiralität führen könnten. Dieser Ansatz soll keinesfalls Wissenschaftler von Untersuchungen mit Oligo‐S‐Diastereomerengemischen als Pharmaca abhalten, denn in der medizinischen Chemie wurden viele nützliche Medikamente ohne die genaue Kenntnis der Struktur entwickelt und angewandt. So ist z.B. heute noch die Struktur von Impfstoffen, die Pasteur entdeckte, nicht geklärt.

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Synthesis, NMR and structure of oligonucleotide phosphorodithioates

Cited by 28 publications

References 43 publications

Separation of Synthetic Oligonucleotide Dithioates from Monothiophosphate Impurities by Anion-Exchange Chromatography on a Mono-Q Column

Separation of Synthetic Oligonucleotide Dithioates from Monothiophosphate Impurities by Anion-Exchange Chromatography on a Mono-Q Column

2D¹H and³¹P NMR Spectra and Distorted A-DNA-Like Duplex Structure of a Phosphorodithioate Oligonucleotide

Stereokontrollierte Synthese von Oligonucleosidphosphorothioaten

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Synthesis, NMR and structure of oligonucleotide phosphorodithioates

Cited by 28 publications

References 43 publications

Separation of Synthetic Oligonucleotide Dithioates from Monothiophosphate Impurities by Anion-Exchange Chromatography on a Mono-Q Column

Separation of Synthetic Oligonucleotide Dithioates from Monothiophosphate Impurities by Anion-Exchange Chromatography on a Mono-Q Column

2D1H and31P NMR Spectra and Distorted A-DNA-Like Duplex Structure of a Phosphorodithioate Oligonucleotide

Stereokontrollierte Synthese von Oligonucleosidphosphorothioaten

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2D¹H and³¹P NMR Spectra and Distorted A-DNA-Like Duplex Structure of a Phosphorodithioate Oligonucleotide