- Base-base recognition of nonionic dinucleotide analogues in an apolar environment studied by low-temperature NMR spectroscopy
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Two self-complementary dinucleotide analogues TSiA and A si with a nonionic diisopropylsilyl-modified backbone were synthesized, and their association in a nonaqueous aprotic environment was studied by NMR spectroscopy. Using a CDClF2/CDF3 solvent mixture, measurements at temperatures as low as 113 K allowed the observation and structural characterization of individual complexes in the slow exchange regime. The AsiT analogue associates to exclusively form a dinucleotide antiparallel duplex with regular Watson-Crick base pairing, but both A and T nucleosides exhibit a predominant C3'-endo sugar pucker reminiscent of an A-type conformation. In contrast to AsiT the TSiA dinucleotide is found to exhibit significant variability and flexibility. Thus, different secondary structures with weaker hydrogen bonds for all T SiA structures are observed at low temperatures. Although a B-like Watson-Crick antiparallel dinucleotide duplex with a preferred C2'-endo sugar pucker largely predominates at temperatures above 153 K, two additional species, namely a dinucleotide Hoogsteen duplex with a syn glycosidic torsion angle of the adenosine nucleoside and a presumably intramoleculariy folded structure, are increasingly populated upon further cooling. By adding typical DNA intercalators like anthracene or benz[c]acridine derivatives to the A siT dinucleotide duplex in the aprotic solvent environment, no binding of the polycyclic aromatic molecules can be detected even at lower temperatures. Obviously, van der Waals and stacking interactions are insufficient to compensate for the other unfavorable contributions to the overall free energy of binding, and only in the presence of additional hydrophobic effects in an aqueous environment does binding occur.
- Xiao, Zhou,Weisz, Klaus
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scheme or table
p. 3862 - 3869
(2010/05/15)
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- Intramolecular sensitization of photocleavage of the photolabile 2-(2-nitrophenyl)propoxycarbonyl (NPPOC) protecting group: Photoproducts and photokinetics of the release of nucleosides
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Novel photolabile protecting groups based on the 2-(2-nitrophenyl)- propoxycarbonyl (NPPOC) group with a covalently linked thioxanthone as an intramolecular triplet sensitizer exhibit significantly enhanced light sensitivity under continuous illumination. Herein we present a detailed study of the photokinetics and photoproducts of nucleosides caged with these new protecting groups. Relative to the parent NPPOC group, the light sensitivity of the new photolabile protecting groups is enhanced by up to a factor of 21 at 366 nm and is still quite high at 405 nm, the wavelength at which the sensitivity of the parent compound is practically zero. A new pathway for de-protection of the NPPOC group pro_ceeding through a nitroso benzylalcohol intermediate has been discovered to complement the main mechanism, which involves β elimination. Under standard conditions of lithographic DNA-chip synthesis, some of the new compounds, while maintaining the same chip quality, react ten times faster than the unmodified NPPOC-protected nucleosides.
- Woell, Dominik,Smirnova, Julia,Galetskaya, Marina,Prykota, Tamara,Buehler, Jochen,Stengele, Klaus-Peter,Pfleiderer, Wolfgang,Steiner, Ulrich E.
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experimental part
p. 6490 - 6497
(2009/09/06)
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- An enzymatic transglycosylation of purine bases
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An enzymatic transglycosylation of purine heterocyclic bases employing readily available natural nucleosides or sugar-modified nucleosides as donors of the pentofuranose fragment and recombinant nucleoside phosphorylases as biocatalysts has been investigated. An efficient enzymatic method is suggested for the synthesis of purine nucleosides containing diverse substituents at the C6 and C2 carbon atoms. The glycosylation of N6-benzoyladenine and N2-acetylguanine and its O6-derivatives is not accompanied by deacylation of bases. Copyright Taylor & Francis Group, LLC.
- Roivainen, Jarkko,Elizarova, Tatiana,Lapinjoki, Seppo,Mikhailopulo, Igor A.,Esipov, Roman S.,Miroshnikov, Anatoly I.
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p. 905 - 909
(2008/09/17)
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- Polymer supported carbodiimide strategy for the synthesis of N-acylated derivatives of deoxy- and ribo purinenucleosides using active esters
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A cost-effective synthetic strategy has been used for the selective protection of the exocyclic amino function of purine nucleosides. Instead of using the common protecting groups in their chloride or anhydride forms, the less expensive and nontoxic acidic form was chosen. The acids were first activated to an active ester form using DCC and further successfully used for N-acylation of purine nucleosides. The contamination of the N-acylated product with DCU was inconvenient and was avoided by use of polymer supported- carbodiimide that has the additional advantage of reusability.
- Tripathi, Snehlata,Misra, Krishna,Sanghvi, Yogesh S.
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p. 5045 - 5048
(2007/10/03)
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- An improved transient method for the synthesis of N-benzoylated nucleosides
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The Jones' transient method for the synthesis of N-benzoylated nucleosides is improved by reducing the amounts of chlorotrimethylsilane (TMSCl) and benzoyl chloride to nearly equivalent quantities. The easy work-up and high yields of products are the major advantages of this approach. Jones' method is further simplified by omitting the addition of ammonium hydroxide. The utility of this modification for the preparation of some useful protected nucleosides is also presented.
- Zhu, Xue-Feng,Williams Jr., Howard J.,Scott, A. Ian
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p. 1233 - 1243
(2007/10/03)
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- Microwave assisted high yielding preparation of N-protected 2′-deoxyribonucleosides useful for oligonucleotide synthesis
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A rapid and high yielding method for the synthesis of precursors of synthons for DNA synthesis, N-protected 2′-deoxyribonucleosides is described, which occur under mild conditions using microwave irradiation. The desired material, N-protected nucleosides, was obtained in 93-96% yield in few minutes. The final products were then characterized by H-NMR and MALDI-TOF and compared with the standard samples. The method is amenable to small to moderate scale of synthesis.
- Rao,Kumar,Chauhan,Garg,Gupta
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p. 393 - 400
(2007/10/03)
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- Building blocks for the solution phase synthesis of oligonucleotides: Regioselective hydrolysis of 3′,5′-di-O-levulinylnucleosides using an enzymatic approach
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A short and convenient synthesis of 3′- and 5′-O-levulinyl-2′-deoxynucleosides has been developed from the corresponding 3′,5′-di-O-levulinyl derivatives by regioselective enzymatic hydrolysis, avoiding several tedious chemical protection/deprotection steps. Thus, Candida antartica lipase B (CAL-B) was found to selectively hydrolyze the 5′-levulinate esters, furnishing 3′-O-levulinyl-2′-deoxynucleosides 3 in >80% isolated yields. On the other hand, immobilized Pseudomonas cepacia lipase (PSL-C) and Candida antarctica lipase A (CAL-A) exhibit the opposite selectivity toward the hydrolysis at the 3′-position, affording 5′-O-levulinyl derivatives 4 in >70% yields. A similar hydrolysis procedure was successfully extended to the synthesis of 3′- and 5′-O-levulinyl-protected 2′-O-alkylribonucleosides 7 and 8. This work demonstrates for the first time application of commercial CAL-B and PSL-C toward regioselective hydrolysis of levulinyl esters with excellent selectivity and yields. It is noteworthy that protected cytidine and adenosine base derivatives were not adequate substrates for the enzymatic hydrolysis with CAL-B, whereas PSL-C was able to accommodate protected bases during selective hydrolysis. In addition, we report an improved synthesis of dilevulinyl esters using a polymer-bound carbodiimide as a replacement for dicyclohexylcarbodiimide (DCC), thus considerably simplifying the workup for esterification reactions.
- Garcia, Javier,Fernandez, Susana,Ferrero, Miguel,Sanghvi, Yogesh S.,Gotor, Vicente
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p. 4513 - 4519
(2007/10/03)
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- A facile method for deprotection of trityl ethers using column chromatography
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A mild, efficient and inexpensive detritylation method is reported that uses trifluoroacetic acid on a silica gel column to obtain pure, detritylated compounds in one-step. This method is applicable to acid stable as well as acid sensitive compounds with only slight alterations in the procedure. Nineteen examples are given.
- Pathak, Ashish K.,Pathak, Vibha,Seitz, Lainne E.,Tiwari, Kamal N.,Akhtar, Mohammad S.,Reynolds, Robert C
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p. 7755 - 7757
(2007/10/03)
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- The S-pixyl group: An efficient photocleavable protecting group for the 5' hydroxy function of deoxyribonucleosides
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The 9-phenylthioxanthyl (S-pixyl or S-Px) group has been investigated as a photocleavable protecting group for primary alcohols, and specifically as a 5' hydroxy protecting group for deoxyribonucleosides. Several alcohols, including the four nucleosides with protected exocyclic amino functions, were protected in very good to excellent yield by treatment of 9-chloro-9-phenylthioxanthene 3 in dry pyridine to reveal the derivatized compounds. Irradiation of the protected substrates in neutral, aqueous solution regenerated the starting alcohols in excellent yield.
- Coleman, Michael P.,Boyd, Mary K.
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p. 7911 - 7915
(2007/10/03)
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- The H-phosphonate approach to the synthesis of oligonucleotides and their phosphorothioate analogues in solution
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A new approach to the synthesis of oligonucleotides and oligonucleotide phosphorothioates in solution is described; it is based on H-phosphonate coupling [with bis(2-chlorophenyl) phosphorochloridate 22 as the coupling agent] at -40 deg C, followed by in situ sulfur transfer involving either 2-(4-chlorophenylsulfanyl)isoindole-1,3(2H)-dione 23a or 4-[(2-cyanoethyl)sulfanyl]morpholine-3,5-dione 26. The yields of the coupling and sulfur transfer reactions are virtually quantitative and, following unblocking by previously reported procedures, very pure products (d[ApC], d[TpGpApC], d[TpGp(s)ApC], d[Gp(s)A] and d[Cp(s)Tp(s)Gp(s)A]) are obtained.
- Reese, Colin B.,Quanlai, Song
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p. 1477 - 1486
(2007/10/03)
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- Deuterated nucleosides
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Deuterated nucleotide and nucleoside units are used to synthesize strands of RNA and DNA wherein one unit is non-deuterated, with adjacent units deuterated. The deuteration is sufficiently high in order that resonance from the deuterated units do not overlap with resonances from non-deuterated units in NMR-experiments. Thereby a "NMR"-window is created in the DNA or RNA strands, which can be beneficially used for advanced studies of structure versus biological activity in DNA and RNA.
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- Nucleoside 5'-methylene phosphonates
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Novel oligonucleotides analogs and nucleoside analogs as well as methods for their synthesis are described. The oligonucleotides are useful in diagnostic and therapeutic applications. The oligonucleotides are stable to nuclease degradation.
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- Solid-phase synthesis of branched RNA and branched DNA/RNA chimeras
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An effective method for synthesising branched oligonucleotides on solid phase in the 5' to 3' direction has been developed. Special branch-point monomers enable the synthesis of branched oligonucleotides which can have sequences of different length and base composition attached to the 2'- and 3'-hydroxyl groups of the branch point ribonucleoside. The branched oligonucleotides are assembled on commercial DNA synthesisers, the crude products are readily purified by reversed phase HPLC and the fully deprotected products are conveniently analysed by mass spectrometry.
- Grotli, Morten,Eritja, Ramon,Sproat, Brian
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p. 11317 - 11346
(2007/10/03)
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- 1,1,1,3,3,3-Hexafluoro-2-propanol for the Removal of the 4,4'-Dimethoxytrityl Protecting Group from the 5'-Hydroxyl of Acid-Sensitive Nucleosides and Nucleotides
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1,1,1,3,3,3-Hexafluoro-2-propanol is introduced as a suitable reagent and solvent for the detritylation of 5'-O-(4,4'-dimethoxytrityl)-nucleosides and -deoxy- nucleosides, especially those that are susceptible to N-glycosyl cleavage under more strongly acidic conditions.
- Leonard, Nelson J.,Neelima
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p. 7833 - 7836
(2007/10/02)
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- Synthesis of oligonucleotide phosphorodithioates
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The synthesis of DNA containing sulfur at the two nonbonding internucleotide valencies is reported. Several different routes using either tervalent or pentavalent mononucleotide synthons are described.
- Beaton,Brill,Grandas,Ma,Nielsen,Yau,Caruthers
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p. 2377 - 2388
(2007/10/02)
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- Method for producing an active protein
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An active protein can be easily, safely produced by a method comprising providing a first peptide fragment having a first amino acid sequence corresponding to part of an active protein and a second peptide fragment having a second amino acid sequence corresponding to the remaining part of the active protein, at least one of said first peptide fragment and said second peptide fragment being one which has been obtained by recombinant DNA technique or has been obtained by a method comprising producing a predetermined peptide fragment by recombinant DNA technique and deleting from or adding to said predetermined peptide fragment at its N-terminus at least one amino acid residue; and linking said first peptide fragment at its C-terminus to said second peptide fragment at its N-terminus. The method of the present invention may be practiced, with further advantages, by predeterming said first peptide fragment and said second peptide fragment so that a first occurring methionine residue subsequent to the N-terminal amino acid residue of the active protein constitutes the N-terminal amino acid of the amino acid sequence of said second peptide fragment, or so that an amino acid residue positioned near the first occurring methionine residue subsequent to the N-terminal amino acid residue of the desired protein on the side of the N-terminus of the desired protein constitutes the N-terminal amino acid residue of said second peptide fragment.
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- Simplified Liquid-Phase Preparation of Four Decadeoxyribonucleotides and their Preliminary Spectroscopic Characterization
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Four self-complementary decadeoxyribonucleotides, dApTpApTpApTpApTpApT,dApTpApTpCpGpApTpApT, dApTpApTpGpCpApTpApT and dApApApApApTpTpTpTpT, were chemically synthesized by the phosphotriester procedure.Efforts were concentrated on keeping the procedure as simple as possible, concomitant with obtaining high-purity products at each step of the process.The decamers were elaborated from the 3'-end, starting with a 3'-O-benzoylated monomer according to the scheme: monomer + monomer -> dimer + dimer -> tetramer + dimer -> hexamer + tetramer -> decamer.Putity of intermediates and of the fully blocked decamers were monitored by chromatography and by 300-MHz 1H-NMR. spectroscopy.The deblocked decadeoxyribonucleotides were characterized by their UV., CD., and 1H-NMR. spectra.
- Denny, William A.,Leupin, Werner,Kearns, David R.
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p. 2372 - 2393
(2007/10/02)
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- Transient Protection: Efficient One-Flask Syntheses of Protected Deoxynucleosides
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Application of the concept of transient protection to the synthesis of protected deoxynucleosides is described.The deoxynucleosides are first treated with trimethylchlorosilane in pyridine for protection of the hydroxyl groups, and then immediately reacted with an acylating agent - benzoyl chloride for 1a and 1b and isobutyric anhydride for 1c - to effect N-acylation.Hydrolysis of the trimethylsilyl groups takes a few hours in aqueous pyridine or a few minutes with dilute ammonia.The ammonia also effects selective hydrolysis of the initially formed N,N-dibenzoyldeoxyadenosine derivative (3a) to the desired N-benzoyldeoxyadenosine (4a).This one-flask procedure gives crystalline N-acyl deoxynucleosides 4a and 4b in 95percent yield and 4c in 75percent yield, in only a few hours.The 5'-O-dimethoxytrityl deoxynucleosides 8a and 8b are also obtained in a one-flask procedure by initial reaction of the deoxynucleosides with 4,4'-dimethoxytrityl chloride, followed by treatment with trimethylchlorosilane and then benzoyl chloride.Although with deoxycytidine some of the 4-N,5'-O-bis(dimethoxytrityl) derivative (5c) is formed, benzoyl chloride effects conversion to the 4-N-benzoyl derivative (7b).After simple purification by flash chromatography 8a and 8b are each obtained in 80-90percent overall yield from 1a or 1b.
- Ti, G. S.,Gaffney, B. L.,Jones, R. A.
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p. 1316 - 1319
(2007/10/02)
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- DIALKYL ALUMINIUM CHLORIDE: A REAGENT FOR REMOVAL OF TRITYL GROUP FROM TRITYL ETHERS OF DEOXYNUCLEOSIDES, DEOXYNUCLEOTIDES, AND OLIGODEOXYNUCLEOTIDES
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Detritylation of N-acyl-5'-O-tritylated deoxynucleosides, deoxynucleotides, and oligodeoxynucleotides have been quantitatively achieved in minutes at room temperature by using diethylaluminium chloride or diisobutylaluminium chloride.Reactions take place in unpolar solvents in homogeneous phase under completely aprotic conditions.
- Koester, H.,Sinha, N. D.
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p. 2641 - 2644
(2007/10/02)
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- SELECTIVE N-DEACYLATION OF N,O-PROTECTED NUCLEOSIDES BY ZINC BROMIDE
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N-Acyl protecting group in nucleoside derivatives can be selectively removed by treatment with zinc bromide in the presence of alcohols to give O-protected nucleosides.
- Kierzek, R.,Ito, H.,Bhatt, R.,Itakura, K.
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p. 3761 - 3764
(2007/10/02)
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- THE TRIPHENYLMETHYL (TRITYL) GROUP AND ITS USES IN NUCLEOTIDE CHEMISTRY
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The triphenylmethyl (trityl) group can be removed from 5'-trityl 2'deoxynucleosides (and their N-acyl derivatives) under aprotic neutral conditions without causing any side reactions.An efficient method for tritylation of N-acyl 2'-deoxynucleosides is described.Potential use of such derivatives for stepwise synthesis of deoxyoligonucleotides is discussed.
- Kohli, V.,Bloecker, H.,Koester, H.
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p. 2683 - 2686
(2007/10/02)
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