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On the sequence selective bis-intercalation of a homodimeric thiazole orange dye in DNA

BIOCONJUGATE CHEMISTRY 1999年第5期10卷 824-831页

作者： Bunkenborg, J Stidsen, MM Jacobsen, JP Odense Univ Dept Chem DK-5230 Odense M Denmark

The thiazole orange dye 1,1'-(4,4,8,8-tetramethyl-4,8-diazaundecamethylene)-bis-4-[(3-methyl-2,3-dihydro(benzo-1,3-thiazolyl)-2-methylidene]quinolinium tetraiodide (TOTO) binds sequence selectively to double-stranded DNA (dsDNA) by bis-intercalation. Each chromophore is sandwiched between two base pairs in a d(5'-py-p-py-3'):d(5'-pu-p-pu-3') site, and the linker spans over two base pairs in the minor groove. We have examined the binding of TOTO to various dsDNA oligonucleotides containing variations of the 5'-CTAG-3' binding motif by introducing inosine (I = inosine, 2-desaminoguanosine) and 5-methylcytosine (C-me). A one- and two-dimensional NMR spectroscopy characterization yielded detailed structural information on the binding mode and for the well-defined TOTO-complexes competition experiments allowed determination of the relative binding strengths resulting from the various structural alterations. The experimentally observed base pair preference of TOTO in the palindromic sequences investigated is (me)CG > CG > CI > TA for the flanking base pair and (CI)-C-me > CI > TA > CG > UA for the central base pair. The best binding site observed so far is the d(5-C(me)CIG-3')(2) site. This site is much more favorable than the d(5'-CTAG-3')(2) site formerly believed to be the best binding site. The present paper discusses these results in terms of different contributions to the binding affinity and offers some explanations far the site selectivity of TOTO.

关键词： 5-甲基胞嘧啶碱基配对碱基序列结合部位结合竞争性交联试剂/化学胞嘧啶/类似物和衍生物胞嘧啶/化学胞嘧啶/代谢 DNA/化学 DNA/代谢二聚作用静电学鸟苷/化学鸟苷/代谢肌苷/化学肌苷/代谢嵌入剂/化学嵌入剂/代谢动力学核磁共振生物分子核酸构象喹啉鎓化合物/化学喹啉鎓化合物/代谢构效关系底物特异性噻唑类/化学噻唑类/代谢

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Invasion of strongly binding oligonucleotides into tRNA structure

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NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2000年第7期19卷 1145-1158页

作者： Petyuk, V Serikov, R Tolstikov, V Potapov, V Giegé, R Zenkova, M Vlassov, V Novosibirsk Bioorgan Chem Inst Lab Nucl Acids Biochem Novosibirsk 630090 Russia Novosibirsk State Univ Novosibirsk 630090 Russia Shemyakin Ovchinnikov Inst Bioorgan Chem Lab Struct & Funct Human Genes Moscow 117871 Russia CNRS Inst Biol Mol & Cellulaire UPR 9002 SMBMR Dept Mecanismes & Macromol Synth Prot & Cristallo F-67084 Strasbourg France

Interaction of yeast tRNA(Phe) with oligodeoxyribonucleotides containing 5-methylcytosine, 2-aminoadenine, and 5-propynyl-2'-deoxyuridine was investigated. The modified oligonucleotides show increased binding capacity although the association rates are similar for the modified and natural oligonucleotides. The most pronounced increase in association constant (70 times) due to the incorporation of the strongly binding units was achieved in the case of oligonucleotide complementary to the sequence 65-76 of the tRNA(Phe).

关键词： 2-氨基嘌呤/类似物和衍生物 2-氨基嘌呤/化学 5-甲基胞嘧啶胞嘧啶/类似物和衍生物胞嘧啶/化学脱氧尿苷/类似物和衍生物脱氧尿苷/化学电泳聚丙烯酰氨凝胶动力学核酸构象寡脱氧核糖核苷酸类/化学寡核苷酸类/代谢 RNA 转移苯丙氨酸/化学 RNA 转移苯丙氨酸/代谢时间因素酵母菌/化学

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Synthesis and NMR characterization of diastereomeric C_PSMeG derivatives

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NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2000年第5-6期19卷 903-915页

作者： Machytka, D Sági, G Kajtár-Peredy, M Gács-Baitz, E Hungarian Acad Sci Chem Res Ctr H-1525 Budapest Hungary

Synthesis and stereochemical characterization of enantiomerically pure C(PSMe)G derivatives by NMR methods are reported. The effect of 5'-dimethoxytrityl on the conformational properties is described. It was found that in P-diastereomers the conformational differences about the C3'-O3' bond, as discernible from the Delta J values, are enhanced by the presence of this protecting group.

关键词：色谱法凝胶色谱法薄层胞嘧啶/类似物和衍生物胞嘧啶/化学合成二核苷磷酸类/化学合成鸟嘌呤/类似物和衍生物鸟嘌呤/化学合成磁共振波谱学膦酸类/化学立体异构现象

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Functionalization of the sugar moiety of oligoribonucleotides on solid support

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BIOCONJUGATE CHEMISTRY 1999年第6期10卷 921-924页

作者： Wu, XL Pitsch, S ETH Zurich Organ Chem Lab CH-8092 Zurich Switzerland

A solid-phase method for the introduction of a variety of different side chains into oligoribonucleotides is presented. It is based on a beta-D-allofuranosyl phosphoramidite with a bromopentyl-substituent tethered to the 6'-O position. After its incorporation into fully protected, immobilized RNA sequences, the bromine was substituted with a variety of soft nucleophiles which, in some cases, allowed further transformations. After deprotection and detachment, the corresponding functionalized oligoribonucleotides were purified and characterized. Incorporation of such side chains led to a slight lowering of transition temperatures, but some of them led to a significant enthalpic stabilization of an A-type RNA duplex.

关键词：酰胺类/化学碱基序列溴/化学色谱法高压液相胞嘧啶/类似物和衍生物胞嘧啶/化学药物稳定性糖轭合物/化学质谱分析法分子结构寡核糖核苷酸类/化学磷酸类/化学 RNA/化学热力学

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Sequence-specific and methylation-dependent and -independent binding of rice nuclear proteins to a rice tungro bacilliform virus vascular bundle expression element

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JOURNAL OF BIOLOGICAL CHEMISTRY 2001年第4期276卷 2644-2651页

作者： He, XY Fütterer, J Hohn, T Friedrich Miescher Inst CH-4002 Basel Switzerland Swiss Fed Inst Technol Inst Plant Sci CH-8092 Zurich Switzerland

Nuclear proteins from rice (Oryza sativa) were identified that bind specifically to a rice tungro bacilliform virus promoter region containing a vascular bundle expression element (VBE). One set of proteins of 29, 33, and 37 kDa, present in shoot and cell suspension extracts but hardly detectable in root extracts, bound to a site containing the sequence AGAAGGACCAGA within the VEE, which also contains two CpG and one CpNpG potential methylation motifs, Binding by these proteins was determined to be cytosine methylation-independent. However, a novel protein present in all analyzed extracts bound specifically to the methylated VEE. A region of at least 49 nucleotides overlapping the VEE and complete cytosine methylation of the three Cp(Np)G motifs was required for efficient binding of this methylated VBE-binding protein (MVBP).

关键词： 5-甲基胞嘧啶/类似物和衍生物杆状DNA病毒属/遗传学碱基序列 CpG岛胞嘧啶/类似物和衍生物 DNA结合蛋白质类/代谢分子序列数据核蛋白质类/代谢水稻/病毒学植物蛋白质类/代谢植物芽/代谢启动区(遗传学) 蛋白质结合组织分布

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The ganciclovir implant plus oral ganciclovir versus parenteral cidofovir for the treatment of cytomegalovirus retinitis in patients with acquired immunodeficiency syndrome: The ganciclovir cidofovir cytomegalovirus retinitis trial

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AMERICAN JOURNAL OF OPHTHALMOLOGY 2001年第4期131卷 457-467页

作者： Jabs, DA Johns Hopkins Univ Sch Med Baltimore MD 21205 USA

PURPOSE: To compare the regimen of the ganciclovir implant plus oral ganciclovir to one of intravenous cidofovir for the treatment of cytomegalovirus retinitis. METHODS: Sixty-one patients with acquired immunodeficiency syndrome and cytomegalovirus retinitis were randomized either to the regimen of the ganciclovir implant plus oral ganciclovir, 1 gm three times daily, or intravenous cidofovir, 5 mg/kg once weekly for two doses, followed by 5 mg/kg every other week. RESULTS: Mortality was similar between the two treatment groups. Mortality rates were 0.41 per person-year in patients assigned to the ganciclovir regimen and 0.49 per person-year in patients assigned to cidofovir (P = .59). Ocular outcomes were similar between the two groups. Retinitis progression occurred at a rate of 0.67 per person-year in the ganciclovir group and 0.71 per person-year in the cidofovir group (P = .72), A loss of visual acuity of 15 letters or more occurred at a rate of 0.78 per person-year in the ganciclovir group and 0.47 per person-year in the cidofovir group (P = .28). The rate of loss of visual field was 7 degrees per month in the ganciclovir group and 2 degrees per month in the cidofovir group (P = .048). Vitreous hemorrhage was more common in the ganciclovir implant group (0.13 per person year) than in the cidofovir group (no cases, P = .014), whereas uveitis appeared to be more common in the cidofovir group (0.35 per person-year) than in the ganciclovir group (0.09 per person-year, P = .066). Nephrotoxicity (serum creatinine 1.6 mg/dL or greater) occurred at a rate of 0.18 per person-year in the ganciclovir group and 0.48 per person-year in the cidofovir group (P = .10). CONCLUSIONS: Although the small number of patients in this study limits definitive interpretation, these data suggest that in the era of highly active antiretroviral therapy, the regimens of the ganciclovir implant plus oral ganciclovir and of intravenous cidofovir are similar for controlling cytomegalovirus re

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Differential destabilization of the DNA oligonucleotide double helix by a T•G mismatch, 3,N⁴-ethenocytosine, 3,N⁴-ethanocytosine, or an 8-(Hydroxymethyl)-3,N⁴-ethenocytosine adduct incorporated into the same sequence contexts

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CHEMICAL RESEARCH IN TOXICOLOGY 2000年第9期13卷 839-845页

作者： Sági, J Perry, A Hang, B Singer, B Univ Calif Berkeley Lawrence Berkeley Lab Donner Lab Div Life Sci Berkeley CA 94720 USA Hungarian Acad Sci Chem Res Ctr Inst Chem H-1525 Budapest Hungary

The T.G mismatch and the exocyclic adduct 3,N-4-ethenocytosine (epsilon C) are repaired by the same enzyme, the human G/T(U) mismatch-DNA glycosylase (TDG). This enzyme removes the T, U, or epsilon C base from duplex DNA. The rate of cleavage was found to differ with the lesion and was also affected by neighbor sequences [Hang, B., Medina, M., Fraenkel-Conrat, H., and Singer, B. (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 13561-13566]. Since sequence influences duplex stability, we determined the thermodynamic stability of T.G and epsilon C-containing 15-mer duplexes in which the bases flanking the lesion were systematically varied. The duplexes contained central 5'-TTXTT, 5'-AAXAA, 5'-CCXCC, or 5'-GGXGG sequences, where X is T, epsilon C, or two closely related structural derivatives of EC: 3,N-4-ethanocytosine (EC) and 8-(hydroxymethyl)-epsilon C (8-HM-epsilon C). Each of the four lesions, incorporated opposite G, decreased both the thermal (T,) and thermodynamic stability (Delta G degrees(37)) of the 15-mer control duplexes. On the basis of the T-m and Delta G degrees(37) values, the order of destabilization of the TTXTT sequence in 15-mer duplexes was as follows: 8-HM-epsilon C > EC > epsilon C > T.G. The Delta T-m values range from -15.8 to -9.5 degrees C when C-t = 8 mu M. Duplexes with flanking AA or TT neighbors were more destabilized, by an average of 2 degrees C, than those with flanking GG or CC neighbors. The base opposite the modified base also influenced duplex stability. Within the TT context, of the four changed bases opposite the adducts, C had the greatest destabilizing effect, up to -18.4 degrees C. In contrast, a G opposite an adduct was generally the least destabilizing, and the smallest value was -3.0 degrees C. Destabilizations were enthalpic in origin. Thus, this work shows that independently changing the modified base, the sequence, or the base opposite the lesion each affects the stability of the duplex, to significantly varying extents. The p

关键词：碱基错配碱基序列胞嘧啶/类似物和衍生物胞嘧啶/化学 DNA加合物/化学 DNA结合蛋白质类/化学鸟嘌呤/化学分子序列数据寡核苷酸类/化学热力学胸腺嘧啶/化学

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BIOLOGICAL CONSEQUENCES OF INCORPORATION OF 5-FLUOROCYTIDINE IN RNA OF 5-FLUOROURACIL-TREATED EUKARYOTIC CELLS

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 1976年第5期73卷 1528-1531页

作者： GLEASON, MK FRAENKELCONRAT, H UNIV CALIF BERKELEY DEPT MOLEC BIOL BERKELEY CA 94720 USA UNIV CALIF BERKELEY VIRUS LAB BERKELEY CA 94720 USA

Treatment of HeLa cells with 5-fluoro-[3H]uracil leads to the incorporation into cellular RNA of 5-fluorocytidine to the extent of about 0.2% of the 5-fluorouridine incorporated. In tobacco mosaic virus RNA produced in tobacco leaves, this ratio is one order of magnitude lower. Copolymers of cytidylic with 5-fluorocytidylic acids show unchanged template activity with Escherichia coli RNA polymerase, but slightly altered meassenger activity in the wheat germ system, compared to poly(C), and it is suggested that some of the biological consequences [e.g., mutagenesis] of 5-fluorouracil treatment of living cells and organisms may be attributed to this mechanism.

关键词：胞嘧啶/类似物和衍生物氟胞嘧啶/类似物和衍生物氟胞嘧啶/分析氟胞嘧啶/代谢氟尿嘧啶/代谢 HeLa细胞突变 RNA 信使/代谢 RNA 病毒/代谢构效关系模板遗传烟草花叶病毒

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CHEMICAL-TRANSFORMATIONS OF NATURALLY OCCURRING NUCLEOSIDES TO OTHERWISE DIFFICULTLY ACCESSIBLE STRUCTURES

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ANNALS OF THE NEW YORK ACADEMY OF SCIENCES 1975年第AUG8期255卷 104-120页

作者： ROBINS, MJ UNIV ALBERTA DEPT CHEM EDMONTON T6G 2G2 ALBERTA CANADA

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Protection against radiation-induced degradation of DNA bases by polyamines

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RADIATION RESEARCH 2000年第1期153卷 29-35页

作者： Douki, T Bretonniere, Y Cadet, J CEA Grenoble Dept Rech Fondamentale Mat Condensee Serv Chim Inorgan & Biol Lab Les Acides Nucl F-38054 Grenoble 9 France

Polyamines have been reported to protect DNA against the formation of radiation-induced strand breaks and crosslinks to proteins. The present study was aimed at investigating the protective effect of spermine, spermidine and putrescine against the degradation of DNA bases upon exposure to gamma rays in aerated aqueous solution. The yield of 8-oxo-7,8-dihydroguanine and 5-hydroxycytosine was found to decrease for concentrations of spermine and spermidine greater than 0.1 mM, A protection factor of 10 was observed for a concentration of 1 mM of the latter two polyamines. Putrescine afforded a lower protection, In addition, the formation yield of a series of radiation-induced degradation products of the purine and pyrimidine bases was determined within DNA in the presence or absence of spermine. The protection factor was within the same range for all the lesions measured. The latter observation ruled out the possibility of degradation of DNA by radiation-induced polyamine peroxyl radicals. This was confirmed by studies involving radiolysis of DMSO and decomposition of 2,2'-azobis(2-methyl-propionamidine) as sources of alkylperoxyl radicals. Therefore, it is likely that the polyamine-mediated protection against the radiation-induced degradation of DNA bases is due to the compaction of the DNA structure and the reduction in the accessibility of DNA to (OH)-O-. rather than by scavenging (OH)-O-. in the bulk solution or in the vicinity of the DNA, (C) 2000 by Radiation Research Society.

关键词：脒类/药理学胞嘧啶/类似物和衍生物胞嘧啶/分析胞嘧啶/化学合成 DNA/化学 DNA/代谢 DNA/辐射效应 DNA损伤/药物作用脱氧腺苷类/代谢脱氧腺苷类/辐射效应脱氧胞苷/类似物和衍生物脱氧胞苷/分析脱氧胞苷/化学合成脱氧鸟苷/类似物和衍生物脱氧鸟苷/分析脱氧鸟苷/化学合成二甲亚砜/代谢二甲亚砜/辐射效应剂量效应关系药物 γ射线气相色谱-质谱法鸟嘌呤/类似物和衍生物鸟嘌呤/分析鸟嘌呤/化学合成羟自由基/药理学氧化还原/药物作用聚胺类/药理学嘌呤类/化学嘌呤类/辐射效应腐胺/药理学嘧啶类/化学嘧啶类/辐射效应辐射防护剂/药理学溶液精脒/药理学精胺/药理学

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