Synthesis of oligodeoxyribonucleotides using N-(benzyloxycarbonyl)-blocked nucleosides

Watkins, Bruce E.; Kiely, John S.; Rapoport, Henry

doi:10.1021/ja00385a026

Cited by 85 publications

(45 citation statements)

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“…Attempts to protect the exocyclic 6-amino functionality with Cbz-Cl resulted in a complex mixture of products. However, the use of N-(benzyloxycarbonyl)-N'-ethylimidazolium tetrafluoroborate (Rapoports reagent) [29] proceeds smoothly to give the desired product. The other synthetic routes ( Figure 5 b) involve the initial protection of the 6-amino group of adenine.…”

Section: Pna Monomeric Building Blocks With An Aminoethylglycine Backmentioning

confidence: 99%

PNA: Synthetic Polyamide Nucleic Acids with Unusual Binding Properties

Uhlmann¹,

Peyman²,

Breipohl³

et al. 1998

Angewandte Chemie International Edition

397

217

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The astonishing discovery that peptide nucleic acids (PNAs, B=nucleobase), in spite of their drastic structural difference to natural DNA, are better nucleic acid mimetics than many other oligonucleotides has resulted in an explosion of research into this class of compounds. The synthesis, physical properties, and biological interactions of PNAs as well as their chimeras with DNA and RNA are summarized here.

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Section: Pna Monomeric Building Blocks With An Aminoethylglycine Backmentioning

confidence: 99%

PNA: Synthetic Polyamide Nucleic Acids with Unusual Binding Properties

Uhlmann¹,

Peyman²,

Breipohl³

et al. 1998

Angewandte Chemie International Edition

397

217

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“…Blocked-BrdUMP, 5'-O-(dimethoxytrityl)-5-bromo-2'-deoxyuridine 3'-0x2-chlorophenyl phosphate) triethylammonium salt, was synthesized from BrdUrd according to published methods (30). Other blocked monomer phosphates were purchased from Biosearch.…”

Section: Synthesis Of Nucleotide-protein Conjugates and Oligonucleotidesmentioning

confidence: 99%

“…For example, we report here that one disadvantge of Mabs IU-1 (30) and B-44 (14) is that both require a high local linear density of BrdUrd substitution in the DNA strand in order to bind. The magnitude of binding depends both on the total amount of incorporated BrdUrd as well as the spacing between BrdUrd residues.…”

mentioning

confidence: 91%

Improved high‐affinity monoclonal antibody to lododeoxyuridine

et al. 1986

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Three monoclonal antibodies (Mabs), IU-1, IU-4, and B-44 were evaluated in enzyme immunoassays (ELISA) and by flow cytometry for their abilities to recognize bromodeoxyuridine (BrdUrd)-and iododeoxyuridine (1dUrd)-substituted DNA's, nucleotides, and nucleosides. IU-4 is a new Mab, derived from mice immunized with 5-iodo-2'-deoxyuridine-5'-monophosphate (IdUMP) conjugated through the phosphate group to albumin. This immunogen was selected to resemble IdUMP in DNA. In competition ELISA assays, IU-4 prefers IdUrd to BrdUrd and prefers halogenated nucleotides over the corresponding nucleosides. In both ELISA and flow analysis, IU-4 recognizes IdUrd in DNA at substitution frequencies at least as low as one IdUrd one per 1,000 normal bases. The high affinity of IU-4 for IdUrd-DNA contrasts with IU-1 and B-44, which show a strong binding dependency on the frequency of base substitution and require DNA that is essentially fully substituted with BrdUrd for binding in bath flow and ELISA assays. The high affinity of IU-4 for IdUrd in DNA and its independence of IdUrd residue spacing make it a superior reagent for the quantitative labeling of halogenated thymidine analogues in whole cells.Key terms: Fj-Rromo-Z'-deoxyuridine, flow cytometry, 5-iodo-2'-deoxyuridine, ELISA, DNA immunoassay, cell kineticsImmunoassays for DNA substituted with the halogenated nucleosides bromodeoxyuridine (BrdUrd) and iododeoxyuridine (IdUrd) are widely used in applications such as the quantification of cell cycle kinetics, the detection of unscheduled DNA synthesis, and the isolation of nascent DNA (7,15). Several monoclonal antibodies (Mabs) suitable for these assays have been reported, and all share some common developmental histories and properties (13,14,25,28,29). In all cases, the immunogen was a halogenated ribouracil conjugated to a carrier protein using the periodatehorohydride method developed by Erlanger and Beiser (11). This conjugation method changes the ribose to a six-membered ring containing nitrogen. The epitope in common with DNA is limited to the halogenated uracil. The choice of bromine or iodine in the base appears not to influence antibody specificity, since, where reported, the resulting antibodies react equally with both IdUrd and BrdUrd. The antibodies are of generally low affinity (Ka's of approximately lo6 M-for BrdUrd in solution) and only recognize the altered base in single-stranded DNA (ss-DNA), not in native DNA. For many applications, these characteristics have not been limiting, and the antibodies have found wide use.For a number of experiments, however, the antibodies are unsuitable. For example, we report here that one disadvantge of Mabs IU-1(30) and B-44 (14) is that both require a high local linear density of BrdUrd substitution in the DNA strand in order to bind. The magnitude of binding depends both on the total amount of incorporated BrdUrd as well as the spacing between BrdUrd residues. High linear density is readily obtained for assays on cell lines grown in vitro but is harder to achieve when tissues...

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“…Further modifications to a basic structure of compound 28 produced a complete loss of activity (30,31). Similar substitutions in ribofuranosyl series were not significant (16,17).…”

Section: Resultsmentioning

confidence: 92%

Design, Synthesis and Anti Flaviviridae Activity of N6-, 5',3'-O- and 5',2'-O-Substituted Adenine Nucleoside Analogs

Angusti

Manfredini

Durini

et al. 2008

CHEMICAL & PHARMACEUTICAL BULLETIN

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The Flaviviridae virus family presents linear, plus sense, single-stranded RNA genome of 9.6 to 12.3-kilobases in length and is responsible for about seventy diseases, of which thirteen in humans. The viruses belonging to this family, are divided in three different genera, showing a great similarity in virion morphology, genome organization and replication strategy:1) Hepacivirus [Hepatitis C Virus (HCV)], Flavivirus [e.g. Yellow Fever Virus (YFV), Dengue Fever Virus (DFV), West Nile Virus (WNV)], and Pestivirus [Bovine Viral Diarrhea Virus (BVDV), Border Disease Virus (BDV)]. [2][3][4][5] Bovine viral diarrhea virus (BVDV), the prototype representative of the Pestivirus genus, is ubiquitous and causes a range of clinical manifestations, including abortion, teratogenesis, respiratory problems, chronic wasting syndrome, immune system dysfunction, and predisposition to secondary viral and bacterial infections. 5)Regardless of the availability of vaccines 6) against BVDV and the increasingly elaborate eradication or control of programs, BVDV continues to be a financial burden to the farming industry. An alternative approach against BVDV infections could be the use of antiviral agents that specifically inhibit the replication of the virus. Although not suited to treat large herds, it could be important to have selective anti-Pestivirus compounds on hand.Recently, a number of selective anti-BVDV compounds have been reported. These include the following: polymerase inhibitors i.e. N-propyl-N-[2-(2H-1,2,4-triazino[5,6-b]indol-3-ylthio)ethyl]-1-propanamine (VP32947), 7) a thiazole urea derivative, 8) a cyclic urea derivative 9) and inhibitors of the NS3/NS4A protease, for example, a boron-modified peptidyl mimetic.10) Aromatic cationic molecules have also been reported to inhibit BVDV replication, although the mechanism of action remains to be elucidated.11) Other BVDV inhibitors target cellular enzymes such as the a-glucosidase 12-14) and inosine monophosphate dehydrogenase (IMPDH).15) Recently, a new highly selective BVDV polymerase inhibitor of pestivirus replication, 5-[(4-bromophenyl)methyl]-2-phenyl-5H-imidazo[4,5-c]pyridine (BPIP), was reported. 16)Like BVDV, HCV also belongs to the Flaviviridae family. It is an important cause of chronic hepatitis throughout the world and is the most common factor involved in the development of liver cirrhosis and hepatocellular carcinoma. 17,18) The licensed therapy based on the combination of pegylated interferon-a with the broad spectrum antiviral agent ribavirin, has a limited efficacy (about 60%) and there are important side effects associated with the therapy. Therefore, highly effective and selective inhibitors of HCV replication are urgently required. 19) BVDV is considered to be a valuable surrogate virus model for identifying and characterizing antiviral agents for use against HCV. 20) In some aspects of viral replication, BVDV is more advantageous than the currently used HCV replicon systems 21,22) because this latter does not present a complete replication cycle thus...

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Synthesis of oligodeoxyribonucleotides using N-(benzyloxycarbonyl)-blocked nucleosides

Cited by 85 publications

References 0 publications

PNA: Synthetic Polyamide Nucleic Acids with Unusual Binding Properties

PNA: Synthetic Polyamide Nucleic Acids with Unusual Binding Properties

Improved high‐affinity monoclonal antibody to lododeoxyuridine

Design, Synthesis and Anti Flaviviridae Activity of N6-, 5',3'-O- and 5',2'-O-Substituted Adenine Nucleoside Analogs

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