Showing papers in "Nucleosides, Nucleotides & Nucleic Acids in 1997"
TL;DR: Differences exist in their effects on biological activity in cell culture in spite of virtually identical effects on RNA-binding affinity, and activity enhancement was most pronounced for a 2′-O-methoxyethyl substituent.
Abstract: 6′-substituted carbocyclic deoxyribonucleosides and 2′-O-ethylene glycol substituted ribonucleosides have been evaluated as building blocks for antisense oligonucleotides. Within the former class 6′-hydroxy substituted building blocks in combination with internucleoside phosphorothioate linkages have the potential to enhance antisense activity. 2′-O-ethylene glycol substituted ribonucleosides generally allow for the construction of potent antisense oligonucleotides with reduced phosphorothioate content, but differences exist in their effects on biological activity in cell culture in spite of virtually identical effects on RNA-binding affinity. Activity enhancement was most pronounced for a 2′-O-methoxyethyl substituent.
92 citations
TL;DR: A flow cytometric, single molecule approach to DNA sequencing is described, where a single, fluorescently labeled DNA fragment is suspended in a flow stream and detected and identified by laser-induced fluorescence.
Abstract: A flow cytometric, single molecule approach to DNA sequencing is described. A single, fluorescently labeled DNA fragment is suspended in a flow stream. An exonuclease is added to sequentially cleave the end base into the flow stream where it is detected and identified by laser-induced fluorescence.
78 citations
TL;DR: A short multigram synthesis of 2′-O-methylpseudouridine and its phosphoramidite derivative is described which avoids the use of protecting groups on the nitrogens, and a binding study of oligonucleotides containing this modification suggest an increased binding affinity to RNA when compared to oligon nucleotides incorporating this modification.
Abstract: A short multigram synthesis of 2′-O-methylpseudouridine and its phosphoramidite derivative is described which avoids the use of protecting groups on the nitrogens. A binding study of oligonucleotides containing this modification suggest an increased binding affinity to RNA when compared to oligonucleotides incorporating 2′-O-methyluridine.
45 citations
TL;DR: Splicing of the DMD gene pre-mRNA is being examined as a model system to study the skipping of mutant exons, especially where disrupted translational reading frames are restored.
Abstract: Splicing of the DMD gene pre-mRNA is being examined as a model system to study the skipping of mutant exons, especially where disrupted translational reading frames are restored. Naturally-occurring examples and induced exon skipping by specific synthetic RNA oligonucleotides are under investigation.
41 citations
TL;DR: In this paper, a two-step method to make 2′-O-methyluridine using only inexpensive reagents and no chromatography was described, which is applicable for some other alkyls as well as some other pyrimidine derivatives.
Abstract: A highly efficient, two-step method to make 2′-O-methyluridine is described using only inexpensive reagents and no chromatography. The method is applicable for some other alkyls as well as some other pyrimidine derivatives.
38 citations
TL;DR: In this article, a modified synthesis for (+)-5′-noraristeromycin was presented for hepatitis B virus (HBV) replication in 2.2.15 cells in culture, while the (-) enantiomer was found to be inactive.
Abstract: (+)-5′-Noraristeromycin has selective activity against hepatitis B virus (HBV) replication in 2.2.15 cells in culture, while the (-) enantiomer was found to be inactive. A modified synthesis is presented for (+)-5′-noraristeromycin.
37 citations
TL;DR: A series of pyrene-containing reagents have been synthesized and used for the fluorescent labeling of oligonucleotides and shown the versatility of these reagents in terms of their application in nanofiltration and photolysis.
Abstract: A series of pyrene-containing reagents have been synthesized and used for the fluorescent labeling of oligonucleotides.
35 citations
TL;DR: In this paper, the reactive intermediates for the preparation of derivatives of uridine, thymidine and 2′-deoxyuridine which are modified at C-4.
Abstract: 4-(4-Nitrophenoxy)-1-(βD-ribofuranosyl) pyrimidin-2(1H)-one 15, 5-methyl-4-(1, 2, 4-triazol-1-yl)-1-(βD-2-deoxyribofu-nosyl) pyrimidin-2(1H)-one 7a and 4-(4-nitro-phenoxy)-1-(β-D-2-deoxyribofurnosyl) pyrimidin-2(1H)-one 17a, respectively, have been prepared and are recommended as reactive intermediates for the preparation of derivatives of uridine, thymidine and 2′-deoxyuridine which are modified at C-4.
33 citations
TL;DR: This presentation synopsis covers the rationale, detailed SAR on the optimization process of this linkage vs. others, various synthetic strategies to construct MMI linkage and a brief discussion on the biological properties of the modified oligonucleotides.
Abstract: Methylene(methylimino) or MMI linkage is a novel backbone modification that has enormous potential in the oligonucleotide-based antisense therapeutics as a replacement for the natural phosphodiester linkage. This presentation synopsis covers the rationale, detailed SAR on the optimization process of this linkage vs. others, various synthetic strategies to construct MMI linkage and a brief discussion on the biological properties of the modified oligonucleotides.
32 citations
TL;DR: In this paper, the sugar moieties of a series base-modified purine-2′-deoxynucleosides on the basis of vicinal [1H,1H] coupling constants are presented.
Abstract: Conformational analyses of the sugar moieties of a series base-modified purine-2′-deoxynucleosides on the basis of vicinal [1H,1H] coupling constants is presented (PSEUROT 6.2) Fluorescence data of several 7-deaza- and 8-azapurine 2′-deoxynucleosides are given.
32 citations
TL;DR: The biochemical properties of the purified enzymes and the sequences of their cDNA;s have been determined and TK2 and dGK show high homology to dCK and the herpes virus kinases but not to TK1.
Abstract: Deoxynucleoside kinases are key enzyme in deoxyribonucleoside salvage, phosphorylating many important anti cancer and anti viral drugs. There are four kinases in animal cells; cytosolic thymidine kinase (TK1) and deoxycytidine kinase (dCK) and the mitochondrial thymidine kinase (TK2) and deoxyguanosine kinase (dGK). The biochemical properties of the purified enzymes and the sequences of their cDNA;s have been determined. In case of TK2 and dGK this was done very recently and they show high homology to dCK and the herpes virus kinases but not to TK1. The evolutionary and functional consequences of this fact will be discussed.
TL;DR: Derivatisation of the free hydroxyl group with LCAA-CPG gave a novel universal solid support for use in oligonucleotide synthesis and phosphoramidite-based combinatorial chemistry.
Abstract: Protection of 1,4-anhydro-D-ribitol with the bidentate reagent 1,3-dichloro-1,1,3,3-tetraisopropyldisiloxane, followed by 4,4′-dimethoxytritylation, selective cleavage of the silyl group at the secondary oxygen, chloroacetylation, and desilylation at the 5-position, afforded 1,4-anhydro-3-O-chloroacetyl-2-O-(4, 4′-dimethoxytrityl)-D-ribitol. Derivatisation of the free hydroxyl group with LCAA-CPG gave a novel universal solid support for use in oligonucleotide synthesis and phosphoramidite-based combinatorial chemistry. This solid support was used for synthesis of a number of oligonucleotides, for which the purity and identity with oligonucleotides synthesised on commercial supports was demonstrated.
TL;DR: The transamination side product formed with the commonly used dCbz has been eliminated by the use of dCAc phosphoramidite and this system has successfully been used in the synthesis of oligonucleotides and oligon nucleoside phosphorothioates.
Abstract: We have investigated the use of alkylamines as fast cleavage and deprotection reagents for the solid phase synthesis of oligonucleotides and found methylamine/ammonium hydroxide (or methylamine) as an efficient reagent. The transamination side product formed with the commonly used dCbz has been eliminated by the use of dCAc phosphoramidite. This system has successfully been used in the synthesis of oligonucleotides and oligonucleoside phosphorothioates. DMT dCAc hydrogen phosphonate and DMT ribo CAc-2′-O Me phosphoramidite also have been prepared and used in the synthesis of oligonucleotides.
TL;DR: In this article, the synthesis of 7-substituted 7-deaza- and 8-aza-7-deazapurine 2′-deoxyribonucleosides, their incorporation into oligonucleotides, and the stability of corresponding duplexes is described.
Abstract: The synthesis of 7-substituted 7-deaza- and 8-aza-7-deazapurine 2′-deoxyribonucleosides, their incorporation into oligonucleotides, and the stability of corresponding duplexes is described.
TL;DR: Two new approaches to synthesize the boranophosphate oligonucleotides are presented, one of which can be carried out by effective chemical synthesis using the H-phosphonate approach, instead of previously used phosphoramidite methodology.
Abstract: Recently our laboratory reported a new backbone-modified class of oligonucleotides, with a borane (B33−) group replacing one of the non-bridging oxygen atoms. Here we present two new approaches to synthesize the boranophosphate oligonucleotides. All-stereoregular boranophosphate oligonucleotides can be prepared by enzymatic template extension reactions using nucleoside a-boranotriphosphates, which are good substrates for a number of polymerases. Larger scale synthesis of boranophosphate oligonucleotides can be carried out by effective chemical synthesis using the H-phosphonate approach, instead of previously used phosphoramidite methodology. The main advantage of H-phosphonate methodology is the ability to carry out one boronation reaction, after oligonucleotide chain elongation has been completed, using mild conditions without base damage and producing the desired boranophosphate oligonucleotides in high yield.
TL;DR: A short, flexible route toward the corresponding nucleosides and NMR evidence concerning their preferred solution conformations is discussed in this paper. But this route is not suitable for certain 2′-C-alkylalkylribonucleotides.
Abstract: Certain 2′-C-alkylribonucleotides have been designed as potential mechanism-based inactivators of ribonucleotide reductases. A short, flexible route toward the corresponding nucleosides and NMR evidence concerning their preferred solution conformations are discussed.
TL;DR: An improved protocol for delivering oligodeoxynucleotides into the cytoplasm and nucleus of human cells in culture using streptolysin O is described, allowing reduced target protein expression to result from antisense suppression of target mRNA levels.
Abstract: An improved protocol for delivering oligodeoxynucleotides into the cytoplasm and nucleus of human cells in culture using streptolysin O is described. The new procedure permitted reduced target protein expression to result from antisense suppression of target mRNA levels.
TL;DR: In this article, the antiviral features of the acyclic nucleoside phosphonate (ANP) analogues are reviewed, with a special focus on the most recent findings concerning the biochemistry and clinical efficacy of HPMPC and PMEA.
Abstract: This article reviews the antiviral features of the acyclic nucleoside phosphonate (ANP) analogues, with a special focus on the most recent findings concerning the biochemistry and clinical efficacy of HPMPC [(S)-1-(3-hydroxy-2-phosphonylmethoxypropyl)cytosine; cidofovir; Vistide(R)] and PMEA [9-(2-phosphonylmethoxyethyl)adenine; adefovir].
TL;DR: To enhance the cellular uptake for antisense oligonucleotides or analogues a lipophilic steroid moiety was linked to the 5′-O- or 2′- O-position of appropriate protected thymidine or uridine simply by acid catalysed reaction with cholesterylvinylether.
Abstract: To enhance the cellular uptake for antisense oligonucleotides or analogues a lipophilic steroid moiety was linked to the 5′-O- or 2′-O-position of appropriate protected thymidine or uridine simply by acid catalysed reaction with cholesterylvinylether. The corresponding cholesteryl-acetals were derivatized to the 3′-O- or 5′-O-phosphoramidites and then introduced as 5′-end terminating agents or incorporated within the sequence of oligodeoxyribonucleotides up to a chain length of 18 bases. 3′ -end linkage was achieved by using the corresponding 2′-O-cholesteryluridine building unit, tethered via a 3′-O-/5′-O-succinate-bridge to polystyrene as solid support.
TL;DR: The data suggest that phosphorothioate pharmacokinetics are primarily determined by chemical class and are consistent across species, show dose-dependency, and are independent of sequence.
Abstract: The pharmacokinetic parameters determined for different phosphorothioate oligonucleotides were compared. The data suggest that phosphorothioate pharmacokinetics are primarily determined by chemical class. The pharmacokinetics are consistent across species, show dose-dependency, and are independent of sequence.
TL;DR: In this article, the synthesis of N-1 and NH-4 disulfonylpyrimidine derivatives is described. But the synthesis process is not described in detail, except for the N 1 and NH 4 derivatives.
Abstract: The synthesis of several novel N-1 and N-1,NH-4-disulfonylpyrimidine derivatives are described.
TL;DR: Gemcitabine is a nucleoside analog that acts by multiple mechanisms and incorporation of the triphosphate and subsequent inhibition of DNA replication and repair appears to be the major mode of action.
Abstract: Gemcitabine is a nucleoside analog that acts by multiple mechanisms. Incorporation of the triphosphate and subsequent inhibition of DNA replication and repair appears to be the major mode of action. Ribonucleotide reductase is inhibited by gemcitabine diphosphate, an activity that leads to metabolic self-potentiating effects.
TL;DR: In this paper, the chemistry and biological activity of nucleoside analogues comprising a chiral axis was reviewed with emphasis on anti-HIV agent adenallene (1a) and anti-HBV analogue cytallene(1b).
Abstract: Chemistry and biological activity of nucleoside analogues comprising a chiral axis will be reviewed with emphasis on anti-HIV agent adenallene (1a) and anti-HIV/HBV analogue cytallene (1b). Possible mechanism of action, activity toward the enzymes of nucleic acid metabolism and structure-activity relationships will be discussed.
TL;DR: An improved synthesis of 5′-cycloSal-FdUMP 3a-g and 3′,5′-bis-cycles-phosphotriesters 3 and 9 as potential prodrugs of FdU 1 is described.
Abstract: An improved synthesis of 5′-cycloSal-FdUMP 3a-g and 3′,5′-bis-cycloSal-FdUMP 9a-g as potential prodrugs of FdU 1 is described. In hydrolysis studies, phosphotriesters 3 released FdUMP 2 selectively by a tandem reaction. The biological activity of cycloSal-phosphotriesters 3 and 9 was evaluated in different cell lines.
TL;DR: It is shown that an oligonucleotide containing a -OP(O)(O−)S- link can be used as an effective template in PCR amplification and that oligon nucleotide probes containing stilbenedicarboxamide groups can serve in monitoring the presence of mismatched bases in an olig onucleotide target.
Abstract: Several efficient means for joining oligonucleotides in dilute solution by non-natural internucleotide bridges are discussed. It is also shown that an oligonucleotide containing a -OP(O)(O−)S- link can hnction as an effective template in PCR amplification and that oligonucleotide probes containing stilbenedicarboxamide groups can serve in monitoring the presence of mismatched bases in an oligonucleotide target.
TL;DR: In this paper, reaction of 6-aryl-5-cyano-2-thiouracils 2a-d with glycosyl halides 4a,b under alkaline conditions gave the respective bisglycosylated derivatives 5a-h.
Abstract: Reaction of 6-aryl-5-cyano-2-thiouracils 2a-d with glycosyl halides 4a,b under alkaline conditions gave the respective bisglycosylated derivatives 5a-h. However, their deacetylation with ammonia in methanol caused a cleavage of the S-glycosyl residue and gave the N-3 glycosylated analogues 6a-h.
TL;DR: Several purine and pyrimidine β-L-dideoxynucleosides were stereospecifically synthesized and their antiviral properties examined in this paper, where they were found to have significant anti-human immunodeficiency virus (HIV) and anti-hepatitis B virus (HBV) activities.
Abstract: Several purine and pyrimidine β-L-dideoxynucleosides were stereospecifically synthesized and their antiviral properties examined. Two of them, namely β-L-2′,3′-dideoxyadenosine (β-L-ddA) and its 2′,3′-didehydro derivative (β-L-d4A) were found to have significant anti-human immunodeficiency virus (HIV) and anti-hepatitis B virus (HBV) activities in cell culture.
TL;DR: A review of both chemical and enzymatic methods for ligation of self-complementary oligonucleotide sequences which form 14-or 16-base pair dumbbells is presented; an improved enzyme method is described as well.
Abstract: The chemical (cyanogen bromide) and enzymatic (T4 DNA ligase) ligation of five different self-complementary oligonucleotide sequences which form 14-or 16-base pair dumbbells are described and compared here. A review of both chemical and enzymatic methods is presented; an improved enzymatic method is described as well. While both methods of ligation are effective, chemical ligation may be preferred since it is faster and less costly.
TL;DR: The structure-activity relationship of sixteen 3-deaza, C-4 substituted pyrimidines and imidazo[1,2-c]pyrimidine bases of 1,3-oxathiolanes and 1,4-dioxolanes revealed good anti-HBV activity in 2.15 cells transfected with human hepatitis B virus of the imidazole nucleosides.
Abstract: The structure-activity relationship of sixteen 3-deaza, C-4 substituted pyrimidines and imidazo[1,2-c]pyrimidine bases of 1,3-oxathiolanes and 1,3-dioxolanes revealed good anti-HBV activity in 2.2.15 cells transfected with human hepatitis B virus of the imidazo[1,2-c]pyrimidine nucleosides 21, 25 and 29. Two procedures for the preparation of C-4 substituted analogues are reported based on nucleophilic displacement of a sulfonamide or imidazole by a variety of nitrogen nucleophiles.
TL;DR: The pyrrolopyrimidine nucleoside GP3269 was shown to be a potent and selective inhibitor of human adenosine kinase and to exhibit anticonvulsant activity in rats after oral administration.
Abstract: The pyrrolopyrimidine nucleoside GP3269 (12) was shown to be a potent and selective inhibitor of human adenosine kinase (IC50 = 11 nM) and to exhibit anticonvulsant activity in rats after oral administration. Synthesis of GP3269 was accomplished in 4 steps from 4-chloro-5-iodopyrrolopyrimidine (9) and the protected 5-deoxy-1-α-chlororibose (8) using a base-catalyzed nucleoside coupling reaction and the Suzuki reaction to replace the 5-iodo substituent with phenyl.