- Fluorescence enhancement of oligodeoxynucleotides modified with green fluorescent protein chromophore mimics upon triplex formation
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Green fluorescent protein (GFP)-based molecular-rotor chromophores were attached to the 5-positions of deoxyuridines, and subsequently, incorporated into the middle positions of oligodeoxynucleotides. These oligonucleotides were designed to form triplex D
- Kanamori, Takashi,Takamura, Akihiro,Tago, Nobuhiro,Masaki, Yoshiaki,Ohkubo, Akihiro,Sekine, Mitsuo,Seio, Kohji
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- 5-amino-2'-deoxyuridine, a novel thymidine analogue for high-resolution footprinting of protein-DNA complexes.
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[formula: see text] 5-Amino-2'-deoxyuridine 5'-triphosphate, an analogue of deoxythymidine triphosphate, was synthesized and found to be a substrate of Taq DNA polymerase. The DNA-borne analogue underwent selective chemical reaction with permanganate. The use of 5-amino-dU as an interference probe was validated using the Ada protein/ada promoter complex. The performance of 5-amino-dU in interference footprints is similar to that of the previously described analogue 5-hydroxy-dU, but the former is incorporated more readily into DNA during enzymatic polymerization.
- Storek, Michael J,Suciu, Alexandru,Verdine, Gregory L
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- EFFECT OF C5-AMINO SUBSTITUENT ON 2'-DEOXYURIDINE BASE PAIRING WITH 2'-DEOXYADENOSINE: INVESTIGATION BY 1H AND 13C NMR SPECTROSCOPY
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Substituents at 5-position of a pyrimidine base are known to affect its base pairing properties with complementary purines, either by altering the imino N3-H acidity or by modifying the acceptor strength of C2 and C4 carbonyls.This paper reports comparative base pair property of 5-methyl-2'-deoxyuridine (dT) and 5-amino-2'-deoxyuridine (dUNH2) with 2'-deoxyadenosine (dA) as their 3',5'-di-t-butyldimethylsilyl derivatives in chloroform-d.Using 1H and 13C NMR, it is demonstrated that the 5-NH2 substituent in 2'-deoxyuridine results in (i) decreased association (lower Ka) with 2'-deoxyadenosine compared to dA:dT complexation and (ii) increased receptor strength of C2 carbonyl compared to C4 carbonyl and (iii) lower temperature for separation of 6-amino protons of dA due to its complexation with dUNH2 compared to that with dT.
- Barawkar, Dinesh A.,Kumar, R. Krishna,Ganesh, K. N.
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- Highly efficient and facile synthesis of 5-azido-2'-deoxyuridine
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Previously reported syntheses of the photoaffinity label 5-azido-2'-deoxyuridine are rather inefficient and involve the tedious preparation of a 5-nitro intermediate. To overcome these inconveniences, we have developed a new approach from the commercially available 5-bromo-2'- deoxyuridine nucleoside. Our synthetic route makes use of a benzylamination reduction sequence. Using this strategy, the 5-azido-2'-deoxyuridine photolabel is prepared in three steps and quantitative yields. Copyright Taylor and Francis Group, LLC.
- Gourdain, Stephanie,Petermann, Christian,Harakat, Dominique,Clivio, Pascale
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experimental part
p. 542 - 546
(2011/09/13)
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- Importance of 3′-hydroxyl group of the nucleosides for the reactivity of thymidine phosphorylase from Escherichia coli
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Thymidine phosphorylase in phosphate buffer catalyzed the conversion of thymidine to unnatural nucleosides. The 3′-OH, but not the 5′-OH of ribosyl moiety is necessary to be recognized as a substrate. Thus 3′-deoxythymidine could not convert to 5-fluorouracil-2′,3′- dideoxyribose. However, 5′-deoxythymidine was converted to 5-fluorouracil-2′,5′-dideoxyribose. Copyright
- Hatano, Akihiko,Harano, Aiko,Kirihara, Masayuki
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p. 232 - 233
(2007/10/03)
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- Uridine analogs and techniques for making and using
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Uridine analogs and techniques for making and using uridine analogs are disclosed in this invention. These uridine analogs include nucleoside phosphates having a 5-aminouracil group. These nucleotides can be incorporated into a nucleic acid as an unnatural base, as a substitute for uridine or thymine. The nucleic acid can then be treated with an oxidizing agent and an alkaline solution, which causes cleavage of the nucleic acid at the position of the unnatural base. The nucleoside phosphate analogs can be used in many ways, including measuring chemical interactions between nucleic acids and other compounds, or sequencing nucleic acids. Additional compounds can also be derivitized onto the amino group, allowing other functionalities to be added to the nucleoside phosphate, or to the nucleic acid incorporating the nucleoside phosphate.
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- Preparation of oligonucleotides containing 5-bromouracil and 5-methylcytidine
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A previously described side reaction on 5-bromouracil during standard oligonucleotide deprotection conditions has been studied in detail. The side product, 5-amino-2′-deoxyuridine, is isolated and characterized. The use of several 5-methylcytidine protected derivatives for the preparation of oligonucleotides containing 5-bromouracil and 5-methylcytidine free of 5-amino-2′-deoxyuridine is discussed.
- Ferrer, Elisenda,Fabrega, Carme,Garcia, Ramon Gueimil,Azorin, Ferran,Eritja, Ramon
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p. 907 - 921
(2007/10/03)
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