Diastereomers of Nucleoside 3'-O-(2-Thio-1,3,2-oxathia(selena)phospholanes): Building Blocks for Stereocontrolled Synthesis of Oligo(nucleoside phosphorothioate)s

Stec, Wojciech J.; Grajkowski, Andrzej; Kobylańska, Anna; Karwowski, Bolesław T.; Koziołkiewicz, Maria; Misiura, Konrad; Okruszek, And̀rzej; Wilk, Andrzej; Guga, Piotr; Boczkowska, Małgorzata

doi:10.1021/ja00154a001

Cited by 143 publications

(108 citation statements)

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“…Thymidine 3Ј-phosphorothioate and thymidine 5Ј,3Ј-bisphosphorothioate were synthesized by means of the modified oxathiaphospholane method. 9 Nucleoside transport inhibitors (nitrobenzylthioinosine [NBTI], dipyridamole, and dilazep); ␣,␤-methyleneadenosine 5Ј-diphosphate (␣,␤-methylene-ADP); and ␣,␤-methylene-ATP were also purchased from Sigma. T4 polynucleotide kinase was purchased from Amersham (Buckinghamshire, United Kingdom).…”

Section: Chemicalsmentioning

confidence: 99%

“…Some earlier data [5][6][7][8] have also shown that deoxyribonucleosides influence the growth of leukemia cell lines, but there is no evidence that other types of cells are also sensitive to mononucleotides or their phosphorothioate analogs. Because we have studied the synthesis and therapeutic application of phosphorothioate oligonucleotides, [9][10][11] we have undertaken efforts to explain their potential nonantisense cytotoxicity.…”

Section: Introductionmentioning

confidence: 99%

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The mononucleotide-dependent, nonantisense mechanism of action of phosphodiester and phosphorothioate oligonucleotides depends upon the activity of an ecto-5′-nucleotidase

Koziołkiewicz

Gendaszewska

Maszewska

et al. 2001

Blood

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Section: Chemicalsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The mononucleotide-dependent, nonantisense mechanism of action of phosphodiester and phosphorothioate oligonucleotides depends upon the activity of an ecto-5′-nucleotidase

Koziołkiewicz

Gendaszewska

Maszewska

et al. 2001

Blood

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“…Moreover, the contribution of each diastereomer cannot be described by the 2-n relationship, because each step of chain elongation is slightly stereoselective (16). Our recently elaborated oxathiaphospholane method for the synthesis of PS-oligos is, thus far, the only one allowing P stereocontrolled chemical synthesis of oligo(nucleoside phosphorothioates) (17,18) longer than tetramers in either the Sp orRp configuration (19,20). Having this method of synthesis in hand we decided to check the influence of 'chirality' (21) of PS-oligos upon their proclivity towards RNA duplex formation and the response of RNase H towards double-stranded DNA-RNA structures containing PS-oligos of predetermined chiral sense (absolute configuration) at the phosphorus at each intemucleotide phosphorothioate function.…”

Section: Introductionmentioning

confidence: 99%

Stereodifferentiation—the effect of P chirality of oligo (nucleoside phosphorothioates) on the activity of bacterial RNase H

et al. 1995

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“…Our choice of the mechanism as presented in Fig. 1A is based upon arguments concerning the stereoselectivity of Serratia enzyme towards stereoregular oligo(nucleoside phosphorothioate)s [6,7]. Since 1995, it has been known that Serratia marcescens endonuclease is stereoselective toward oligo(nucleoside phosphorothioate)s and cleaves only internucleotide phosphorothioates of R P configuration ( Fig.…”

mentioning

confidence: 99%

“…Steric arguments were used for explanation of the inability of Mn 2+ ion to rescue catalysis in the case of the 3',5'-exonuclease of E. coli DNA polymerase [15,16]. Third, the stereocontrolled replacement at each internucleotide bond, which is feasible due to the development of enzymatic [17] and chemical methods of stereocontrolled synthesis [6,18], prevents the "hoping effect" of exonucleases as was noticed earlier by Benkovic et al [19] and also reported by others [20]. Therefore, particularly in the case of nonsequence-specific endonucleases, a sliding enzyme does not avoid any particular phosphate due to, for instance, steric effect, since the probability for that type of restriction resulting from steric requirements of a sulfur atom exists at any internucleotide bond.…”

mentioning

confidence: 99%

Stereochemical support for Serratia endonuclease active-site geometry

Stec¹,

Koziołkiewicz²,

Taira³

2000

Pure and Applied Chemistry

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Earlier observation that stereoregular All-R p -PS-oligonucleotides in the presence of nonsequence-specific Serratia endonuclease undergo nucleolytic degradation, confronted with recently published results on the active-site architecture of this enzyme, strongly supports an involvement of 3′-bridging and pro-Sp-nonbridging oxygen atoms of scissile internucleotide bond in the interactions with hydrated magnesium ion anchored by Asn-119 residue of this endonuclease.Recently, the similarity between the active site of I-PpoI specific endonuclease and Serratia marcescens nonsequence-specific endonuclease was pointed out by two independent groups [1,2]. The different folding of these two proteins determines the specificity requirement, but both proteins contain conserved essential asparagine and histidine residues at their active sites and exhibit a similar one metalion co-ordination pattern. Therefore, all main active-site components required for the cleavage of the internucleotide phosphorus-oxygen bond are in the similar arrangement.The general-base histidine 98 (I-PpoI) or 89 (Serratia) residue activates a water molecule for its nucleophilic attack at phosphorus and this occurs opposite from the site of the leaving 3'-oxygen. The ligand for the protein is comprised of the magnesium ion surrounded by three water molecules and Asn-119. Upon binding of the protein, the magnesium ion stabilizes the transition state by coordinating two oxygens of scissile phosphate, namely the 3'-oxygen of P-O-C 3' bond and the pro-Sp-nonbridging oxygen ( Fig. 1A; a) [3]. This magnesium ion does not coordinate a water molecule for nucleophilic attack at phosphorus opposite the leaving 3'-oxygen. Such architecture of the active site of the Serratia marcescens endonuclease comprising coordination of two oxygen atoms of the same scissile phosphate to the metal ion seems to be more plausible than the alternate mechanism for the mode of action of Serratia enzyme discussed by Miller et al. [4] and presented in Fig. 1B. The metal-bound water is deprotonated by a general base and attacks the phosphorus atom of the negatively charged phosphate, coordinated to the same metal ion through the 3'-bridging oxygen.Neither of two nonbridging oxygens of phosphate moiety contacts the metal ion. Such a model of active site was also preferred by Flick et al. [5], discussing the mode of action of homing endonuclease I-PpoI. Our choice of the mechanism as presented in Fig. 1A is based upon arguments concerning the stereoselectivity of Serratia enzyme towards stereoregular oligo(nucleoside phosphorothioate)s [6,7]. Since 1995, it has been known that Serratia marcescens endonuclease is stereoselective toward oligo(nucleoside phosphorothioate)s and cleaves only internucleotide phosphorothioates of R P configuration ( Fig. 1A; b) [6]. Although that cleavage required 10 3 higher concentration of enzyme than that effective for the cleavage of isosequental PO-oligonucleotide, a further increase in enzyme concentration does not cause the cleavage of any ...

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Diastereomers of Nucleoside 3'-O-(2-Thio-1,3,2-oxathia(selena)phospholanes): Building Blocks for Stereocontrolled Synthesis of Oligo(nucleoside phosphorothioate)s

Cited by 143 publications

References 0 publications

The mononucleotide-dependent, nonantisense mechanism of action of phosphodiester and phosphorothioate oligonucleotides depends upon the activity of an ecto-5′-nucleotidase

The mononucleotide-dependent, nonantisense mechanism of action of phosphodiester and phosphorothioate oligonucleotides depends upon the activity of an ecto-5′-nucleotidase

Stereodifferentiation—the effect of P chirality of oligo (nucleoside phosphorothioates) on the activity of bacterial RNase H

Stereochemical support for Serratia endonuclease active-site geometry

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