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1.
Leonid Beigelman Alexander Karpeisky Nassim Usman 《Nucleosides, nucleotides & nucleic acids》2013,32(3-5):901-905
Abstract 5′-C-Methyl-D-allo & L-talo-ribonucleoside 3′-O-phosphoramidites were prepared from L-rhamnose in 13 and 15 steps respectively. Incorporation of L-talo residues in the hammerhead ribozyme and the resulting activity and stability of the modified ribozymes is described. 相似文献
2.
《Nucleosides, nucleotides & nucleic acids》2013,32(5-8):1347-1350
Abstract Four fluoro modified universal nucleobases have been synthesized. The universal nucleobases 1 and 2 , containing a 2,4-difluorobenzene as nucleobase and a 4,6-difluorobenzimidazole, respectively, were chemically incorporated into a selected hammerhead ribozyme sequence which has already been retrovirally expressed as an anti-HIV ribozyme to investigate their effect on the catalytic activity of the ribozymes. The substitution of the natural nucleosides with either 1 or 2 results only in a small decrease of the catalytic activity. The Km value for the monosubstituted ribozyme with a 2,4-difluorobenzene is 309 nM?1, the corresponding kcat is 2.91 · 10?3 min?1. A disubstituted hammerhead ribozyme carrying one of each modification has also been synthesized. For a further stabilization of the ribozyme/substrate complex 2′-(β-aminoethoxy) modified fluorinated nucleosides 15 and 16 have been developed. 相似文献
3.
Makoto Koizumi Yuji Ozawa Ryuichi Yagi Takashi Nishigaki Masakatsu Kaneko Shin-ichi Oka 《Nucleosides, nucleotides & nucleic acids》2013,32(1-3):207-218
Abstract Three ribozymes, a hairpin ribozyme (HR112) and two hammerhead ribozymes (RZ115 and RZ119) containing a 5′C(UUCG)G3′ loop were designed to cleave the U5 region in the long terminal repeat (LTR) of HIV-1 RNA. The t½ values of chemically synthesized substrates mediated by three ribozymes were measured. The transformed CEM cells possessing these three ribozyme-encoding genes were challenged with a HIV-1IIIB strain, and two of these three ribozymes, HR112 and RZ119, were shown to possess strong anti-HIV-1 activity. 相似文献
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6.
《Nucleosides, nucleotides & nucleic acids》2013,32(10-11):1851-1858
The HDV ribozyme is proposed to catalyze its self cleavage reaction by a proton transfer mechanism wherein the N3 of its C75 acts as a general acid. The C75 to U mutation, which raises the N3 pKa from about 4 to almost 10, abolishes all enzymatic activity. To test if a U analogue with a neutral pKa can restore ribozyme function we incorporated 6-azauridine (n6U), a uridine analogue with histidine-like N3 pKa, into the genomic HDV ribozyme active site by 2′-O-ACE oligoribonucleotide protection chemistry. The resulting ribozymes were analyzed for their ability to undergo the HDV ribozyme cis-cleavage reaction. Incorporation of n6U at nucleotide position 75 did not restore ribozyme function compared to the U75 mutant. This suggests that the HDV ribozyme reaction mechanism involves more than positioning of a neutral nucleobase at the active site and implies that the exocyclic amino group of C75 participates in establishing the proper active site fold. 相似文献
7.
Yuichiro Habu Takashi Nagawa Norihiko Matsumoto Hiroaki Takeuchi Naoko Miyano-Kurosaki Hiroshi Takaku 《Nucleosides, nucleotides & nucleic acids》2013,32(10-12):1907-1917
We previously demonstrated the function of an HIV-1-dependent ribozyme expression vector, with which the site-specific excision of loxP sequences can be achieved by using the Cre-loxP system (ON/OFF) as a molecular switch in an acute HIV-1 infection. However, this expression system also revealed the lower, non-specific expression of the anti-HIV-1 ribozyme in the absence of tat. To circumvent this problem, we used the more efficient HIV-1-dependent Cre recombinase gene expression vector, encoding the LTR-gag-p17 (extending from the 5′-LTR to the middle of the gag gene (pLTR-gag-p17-Cre)). Comparatively, the pLTR-gag-p17-Cre induces a higher Cre-protein expression level in an HIV-1 infection-dependent manner than the minimal pLTR-Cre. Furthermore, we constructed the ploxP-Rz-U5 and pLTR-gag-p17-Cre plasmids and also combined them into a single vector, pLTR-gag-p17-Cre/loxP-Rz-U5, for a comparison of their anti-HIV-1 activities. The resultant simultaneous expression of the Cre protein and the homologous recombination of the two loxP sequences induced a high level of HIV-1 replication inhibition (95%). Significantly, a high steady-state of ribozyme expression was observed in the RT-PCR analysis. These data imply that targeting the HIV-1 genes with the pLTR-gag-p17-Cre/loxP-Rz-U5 vector, which mediates HIV-1-dependent ribozyme expression, would be a useful tool for HIV-1 gene therapy applications. 相似文献
8.
Leonid Beigelman Alexander Karpeisky Jasenka Matulic-Adamic Carolyn Gonzalez Nassim Usman 《Nucleosides, nucleotides & nucleic acids》2013,32(3-5):907-910
Abstract The synthesis of 1-deoxy-D-ribofuranose-3-(2-cyanoethyl N,N-diisopropylphosphoramidite) (6) from D-ribose and its incorporation into a hammerhead ribozyme is described. 相似文献
9.
Panagiotis Ioannidis Björn Classon Bertil Samuelsson Ingemar Kvarnström 《Nucleosides, nucleotides & nucleic acids》2013,32(6):1205-1218
Abstract Nucleoside analogues analogues1-(2′,3′-dideoxy-2′-C-hydroxymethyl-β-D-erythro-pentofuranos-yl)thymine (1), 2′,3′-dideoxy-2′-C-hydroxymethylcytidine (2), 2′,3′-dideoxy-2′-C-hydroxymethyladenosine (3), 1-(2′-C-azidomethyl-2′,3′-dideoxy-β-D-erythro-pento-furanosyl)thymine (4), 2′-C-azidomethyl-2′,3′-dideoxycytidine (5), and 2′3′-dideoxy-2′-C-methylcytidine (6) have been synthesized from (S)-4-hydroxymethyl-y-butyro-lactone (7) 相似文献
10.
Akira Matsuda Hitomi Okajima Akira Masuda Akio Kakefuda Yuichi Yoshimura Tohru Ueda 《Nucleosides, nucleotides & nucleic acids》2013,32(2-4):197-226
Abstract New methods for the synthesis of 2′,3′-didehydro-2′,3′-dideoxy-2′ (and 3′)-methyl-5-methyluridines and 2′,3′-dideoxy-2′ (and 3′)-methylidene pyrimidine nucleosides have been developed from the corresponding 2′ (and 3′)-deoxy-2′ (and 3′)-methylidene pyrimidine nucleosides. Treatment of a 3′-deoxy-3′-methylidene-5-methyluridine derivative 8 with 1,1′-thiocarbonyldiimidazole gave the allylic rearranged 2′,3′-didehydro-2′,3′-dideoxy-3′-[(imidazol-1-yl)carbonylthiomethyl] derivative 24. On the other hand, reaction of 8 with methyloxalyl chloride afforded 2′-O-methyloxalyl ester 25. Radical deoxygenation of both 24 and 25 gave 26 exclusively. Palladium-catalyzed reduction of 2′,5′-di-O-acetyl-3′-deoxy-3′-methylidene-5-methyluridine (32) with triethylammonium formate as a hydride donor regioselectively afforded the 2′,3′-dideoxy-3′-methylidene derivative 35 and 2′,3′-didehydro-2′,3′-dideoxy-3′-methyl derivative 34 in a ratio of 95:5 in 78% yield. These reactions were used on the corresponding 2′-deoxy-2′-methylidene derivatives. An alternative synthesis of 2′,3′-dideoxy-2′-methylidene pyrimidine nucleosides (43, 52, and 54) was achieved from the corresponding 1-(3-deoxy-β-D-thero-pentofuranosyl)pyrimidines (44 and 45). The cytotoxicity against L1210 and KB cells and inhibitory activity of the pathogenicity of HIV-1 are also described 相似文献
11.
Shinya KIKUCHI Tomohiro MAEKAWA Katsumaro MINAMOTO Keizo TANIGAWA 《Nucleosides, nucleotides & nucleic acids》2013,32(8):1365-1372
Abstract 2′,3′-Dibromo-2′,3′-dideoxy-5′-O-trityl-2′,3′-secouridine (8) with sdKF gave the 3′,4′-didehydro-2,2′-anhydro nucleoside 9, which was deprotected to 10. Hydrolysis of 9 gave 3′,4′-didehydro-3′-deoxy-5′-O-trityl-2′,3′-secouridine (11a). Similarly, compound 9 with pyridinium halides gave the corresponding 2′-deoxy-2′-halo nucleosides (11b-d). Compound 11d with azide ion gave 2′-azido analogue 11e. Compound 9 with an excess amount of azide ion gave the 2′-azido triazole (13). 相似文献
12.
Andreas Hanne Muktevi V. Ramanujam Thomas RüUcker Guido Krupp 《Nucleosides, nucleotides & nucleic acids》2013,32(9-11):1835-1850
Abstract Fluorescence resonance transfer (FRET) was applied for real time monitoring of ribozyme reactions. Group I ribozyme ligation was followed with two separate, fluorescent-labeled RNA substrates. For hammerhead ribozyme cleavage, a double-fluorescent-labeled substrate was used. For the first time we analyzed multiple turnover conditions. Real time monitoring permits convenient analysis of ribozyme kinetics and the sequence-specific, quantitative detection of RNAs in femtomole amounts. 相似文献
13.
Peihua Shang Hua Wang Changmei Cheng Hongchao Zheng Yufen Zhao 《Nucleosides, nucleotides & nucleic acids》2013,32(12):1272-1281
A general method is described for synthesizing 3′,5′-dithio-2′-deoxypyrimidine nucleosides 6 and 13 from normal 2′-deoxynucleosides. 2,3′-Anhydronucleosides 2 and 9 are applied as intermediates in the process to reverse the conformation of 3′-position on sugar rings. The intramolecular rings of 2,3′-anhydrothymidine and uridine are opened by thioacetic acid directly to produce 3′-S-acetyl-3′-thio-2′-deoxynucleosides 3 or 5. To cytidine, OH? ion exchange resin was used to open the ring and 2′-deoxycytidine 10 was abtained in which 3′-OH group is in threo-conformation. The 3′-OH is activated by MsCl, and then substituted by potassium thioacetate to form the S,S′-diacetyl-3′,5′-dithio-2′-deoxycytidine 12. The acetyl groups in 3′,5′ position are removed rapidly by EtSNa in EtSH solution to afford the target molecules 6 and 13. The differences of synthetic routes between uridine and cytidine are also discusssed. 相似文献
14.
Abdalla Elsayed A. Hassan Satoshi Shuto Akira Matsuda 《Nucleosides, nucleotides & nucleic acids》2013,32(1-3):197-211
Abstract Reaction of 2′-deoxy-2′-methylidene-5′-O-trityluridine (1) with diethylamino-sulfur trifluoride (DAST) in CH2Cl2 resulted in the formation of a mixture of (3′R)-2′,3′-dideoxy-3′-fluoro-2′-methylidene derivative 3 and 2′,3′-didehydro-2′,3′-dideoxy-2′-fluoromethyl derivative 4 (3:4 = 1:1.5) in 65% yield. A similar treatment of 1-(2-deoxy-2-methylidene-5-O-trityl-β-D-threo-pentofuranosyl)uracil (19) with DAST in CH2Cl2 afforded (3′S)-2′,3′-dideoxy-3′-fluoro-2′-methylidene derivatives 20 and 4 in 38% and 17% yields respectively. Transformation of the uracil nucleosides 4, 12, and 20 into cytosines followed by deprotection furnished the corresponding cytidine derivatives 29, 18, and 25, respectively. The corresponding thymidine congener 27 was also synthesized in a similar manner. All of the newly synthesized nucleosides were evaluated for their inhibitory activities against HIV and for their antiproliferative activities against L1210 and KB cells. 相似文献
15.
Hirofumi Furusho Takahiro Ogata Akihisa Kato Yoshie Sato Tohru Endo Akira Kaji 《Nucleosides, nucleotides & nucleic acids》2013,32(4):739-753
Abstract Several acyclic analogues of guanosine, 2′-deoxy-2′, 3′-secoguanosine(3), 3′-deoxy-2′, 3′-secoguanosine (4), and 2′-, 3′-dideoxy-2′-, 3′-secoguanosine were synthesized from guanosine. In addition, the 3′-, 5′-cyclic phosphate (21) and 3′-, 5′-cyclic methylphosphonates (22a, b) of 3 were also prepared. At concentrations up to 300 μM none of these compounds had significant antiherpetic activity in antiviral assays in vitro. 相似文献
16.
Abstract The syntheses of 2′,3′-didehydro-2′,3′-dideoxyisoinosine (d4isoI, 4) as well as 7-deaza-2′,3′-didehydro-2′,3′-dideoxyisoinosine (d4c7isoI, 5) are described. Compounds 4 and 5 show both strong fluorescence. Compound 4 is oxidized by xanthine oxidase to give the corresponding xanthine 2′,3′-dideoxy-2′,3′-didehydronucleosides. A preparative chemo-enzymatic synthesis of 2′-deoxyxanthosine (3) is described. 相似文献
17.
Galina V. Zaitseva Evgenii I. Kvasyuk Elena V. Vaaks Vladimir N. Barai Sergei B. Bokut Anatolii I. Zinchenko 《Nucleosides, nucleotides & nucleic acids》2013,32(1-3):819-834
Abstract Treatment of O2, 3′-anhydro-5′-O-trityl derivatives of thymidine (1) and 2′-deoxyuridine (2) with lithium azide in dimethylformamide at 150 °C resulted in the formation of the corresponding isomeric 3′-azido-2′, 3′-dideoxy-5′-O-trityl-β-D-ribofuranosyl N1- (the major products) and N3-nucleosides (3/4 and 5/6). 3′-Amino-2′, 3′-dideoxy-β-D-ribofuranosides of thymidine [Thd(3′NH2)], uridine [dUrd(3′NH2)], and cytidine [dCyd(3′NH2)] were synthesized from the corresponding 3′-azido derivatives. The Thd(3′NH2) and dUrd(3′NH2) were used as donors of carbohydrate moiety in the reaction of enzymatic transglycosylation of adenine and guanine to afford dAdo(3′NH2) and dGuo(3′NH2). The substrate activity of dN(3′NH2) vs. nucleoside phosphotransferase of the whole cells of Erwinia herbicola was studied. 相似文献
18.
Abstract Crystal structure analysis of 2′,3′-dideoxy-3′-fluorocytidine (1) and its prodrug derivative, N4-dimethylaminomethylene-2′,3′-dideoxy-3′-fluorocytidine (2), active anti-HIV nucleoside analogues, reveals that both structures adopt an anti conformation about the glycosyl bond. The furanose ring is C2′-endo for (2) and C2′-endo/C1′-exo and C2′-endo/C3′-exo for the two independent molecules of (1), respectively. 相似文献
19.
《Nucleosides, nucleotides & nucleic acids》2013,32(4-7):879-882
The thioamide derivatives 3′-deoxy-5′-O-(4,4′-dimethoxytrityl)-3′-[(2-methyl-1-thioxo-propyl)amino]thymidine 1 and 3′-deoxy-5′-O-(4,4′-dimethoxytrityl)-3′-{{6-{[(9H-(fluo-ren-9-ylmethoxy)carbonyl]-amino}-1-thioxohexyl}amino} thymidine 2 were synthesized by regioselective thionation of their corresponding amides 7 and 8 with 2,4-bis(4-methoxyphenyl)-1,3,2,4-dithiadiphosphet-ane-2,4-disulfide (Lawesson's reagent). The thioamides were converted into the corresponding 5′-triphosphates 3 and 4. Compound 3 was chosen for DNA sequencing experiments and 4 was further labelled with fluorescein. 相似文献
20.
Masato Katahira Takashi Sugiyama Mayumi Kanagawa Mi Hee Kim Seiichi Uesugi Toshiyuki Kohno 《Nucleosides, nucleotides & nucleic acids》2013,32(1-3):489-503
Abstract The structure of a lead ribozyme, which consists of two RNA strands, at neutral pH has been studied by NMR. Nearly all resonances of imino protons, base protons (H2, H5, H6 and H8) and sugar protons (H1′ and H2′) were assigned sequentially. Interesting structural features which deviate from the standard structure were found for the residues at an active site which consists of an internal loop. No indication of stable G:A base pairs was found in the loop. The effect of addition of Pb2+ was studied by the use of a non-cleavable analogue in which the cytidine at a cleavage site is replaced by 2′-O-methylcytidine. It was suggested that Pb2+ binds close to the cleavage site and that the structural change induced by Pb2+ is moderate and localized. 相似文献