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Schmidt KS, Boudvillain M, Schwartz A, van der Marel GA, van Boom JH, Reedijk J, Lippert B. Monofunctionally trans-diammine platinum(II)-modified peptide nucleic acid oligomers: a new generation of potential antisense drugs. Chemistry 2002; 8:5566-70. [PMID: 12458496 DOI: 10.1002/1521-3765(20021216)8:24<5566::aid-chem5566>3.0.co;2-#] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A solid-phase approach is described that provides facile access to monofunctionally trans-PtII-modified PNA oligomers of arbitrary sequence for potential use both in antigene and antisense strategies. The approach includes the synthesis of a platinated building block 1 and its subsequent incorporation into three different PNA oligomers 5-7 by solid-phase synthesis. In a model cross-linking reaction one of the latter is found to recognize sequence-specifically a target oligonucleotide 8 and to cross-link to it. The resulting structure is the trans-PtII-cross-linked PNA/DNA duplex 9 as revealed by mass spectrometry in combination with a Maxam-Gilbert sequencing experiment.
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Jones C, Aguilera B, van Boom JH, Buchanan JG. Confirmation of the D configuration of the 2-substituted arabinitol 1-phosphate residue in the capsular polysaccharide from Streptococcus pneumoniae Type 17F. Carbohydr Res 2002; 337:2353-8. [PMID: 12433501 DOI: 10.1016/s0008-6215(02)00185-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The absolute configuration of the 2-substituted arabinitol 1-phosphate residue present in the repeating unit of the capsular polysaccharide (CPS) from Streptococcus pneumoniae Type 17F is confirmed as D, based on a comparison of proton and carbon chemical shifts in a synthetic oligosaccharide and in an oligosaccharide derived from the CPS by degradation.
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53
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de Koning MC, Filippov DV, Meeuwenoord N, Overhand M, van der Marel GA, van Boom JH. An approach to the synthesis of peptide–PNA–peptide conjugates via native ligation. Tetrahedron Lett 2002. [DOI: 10.1016/s0040-4039(02)01856-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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54
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van den Berg RJ, Korevaar CG, van der Marel GA, Overkleeft HS, van Boom JH. A simple and low cost synthesis of d-erythro-sphingosine and d-erythro-azidosphingosine from d-ribo-phytosphingosine: glycosphingolipid precursors. Tetrahedron Lett 2002. [DOI: 10.1016/s0040-4039(02)01807-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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55
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Rapozzi V, Burm BEA, Cogoi S, van der Marel GA, van Boom JH, Quadrifoglio F, Xodo LE. Antiproliferative effect in chronic myeloid leukaemia cells by antisense peptide nucleic acids. Nucleic Acids Res 2002; 30:3712-21. [PMID: 12202756 PMCID: PMC137404 DOI: 10.1093/nar/gkf451] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Peptide nucleic acid (PNA) is a synthetic DNA analogue that is resistant to nucleases and proteases and binds with exceptional affinity to RNA. Because of these properties PNA has the potential to become a powerful therapeutic agent to be used in vivo. Until now, however, the use of PNA in vivo has not been much investigated. Here, we have attempted to reduce the expression of the bcr/abl oncogene in chronic myeloid leukaemia KYO-1 cells using a 13mer PNA sequence (asPNA) designed to hybridise to the b2a2 junction of bcr/abl mRNA. To enhance cellular uptake asPNA was covalently linked to the basic peptide VKRKKKP (NLS-asPNA). Moreover, to investigate the cellular uptake by confocal microscopy, both PNAs were linked by their N-terminus to fluorescein (FL). Studies of uptake, carried out at 4 and 37 degrees C on living KYO-1 cells stained with hexidium iodide, showed that both NLS-asPNA-FL and asPNA-FL were taken up by the cells, through a receptor-independent mechanism. The intracellular amount of NLS-asPNA-FL was about two to three times higher than that of asPNA-FL. Using a semi-quantitative RT- PCR technique we found that 10 micro M asPNA and NLS-asPNA reduced the level of b2a2 mRNA in KYO-1 cells to 20 +/- 5% and 60 +/- 10% of the control, respectively. Western blot analysis showed that asPNA promoted a significant inhibition of p210(BCR/ABL) protein: residual protein measured in cells exposed for 48 h to asPNA was approximately 35% of the control. Additionally, asPNA impaired cell growth to 50 +/- 5% of the control and inhibited completion of the cell cycle. In summary, these results demonstrate that a PNA 13mer is taken up by KYO-1 cells and is capable of producing a significant and specific down-regulation of the bcr/abl oncogene involved in leukaemogenesis.
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MESH Headings
- Antineoplastic Agents/metabolism
- Antineoplastic Agents/pharmacology
- Apoptosis/drug effects
- Base Sequence
- Cell Cycle/drug effects
- Cell Division/drug effects
- DNA, Antisense/chemistry
- DNA, Antisense/genetics
- DNA, Antisense/pharmacology
- Down-Regulation
- Flow Cytometry
- Fluorescein/chemistry
- Fusion Proteins, bcr-abl/genetics
- Humans
- K562 Cells
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Microscopy, Confocal
- Molecular Sequence Data
- Nuclear Localization Signals/genetics
- Peptide Nucleic Acids/genetics
- RNA, Messenger/drug effects
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Tumor Cells, Cultured/drug effects
- Tumor Cells, Cultured/metabolism
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56
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Sabatini R, Meeuwenoord N, van Boom JH, Borst P. Site-specific interactions of JBP with base and sugar moieties in duplex J-DNA. Evidence for both major and minor groove contacts. J Biol Chem 2002; 277:28150-6. [PMID: 12029082 DOI: 10.1074/jbc.m201487200] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Beta-D-Glucosyl-hydroxymethyluracil, also called base J, is an unusually modified DNA base conserved among Kinetoplastida. Base J is found predominantly in repetitive DNA and correlates with epigenetic silencing of telomeric variant surface glycoprotein genes. We have previously identified a J-binding protein (JBP) in Trypanosoma, Leishmania, and Crithidia, and we have shown that it is a structure-specific binding protein. Here we examine the molecular interactions that contribute to recognition of the glycosylated base in synthetic DNA substrates using modification interference, modification protection, DNA footprinting, and photocross-linking techniques. We find that the two primary requirements for J-DNA recognition include contacts at base J and a base immediately 5' of J (J-1). Methylation interference analysis indicates that the requirement of the base at position J-1 is due to a major groove contact independent of the sequence. DNA footprinting of the JBP.J-DNA complex with 1,10-phenanthroline-copper demonstrates that JBP contacts the minor groove at base J. Substitution of the thymine moiety of J with cytosine reduces the affinity for JBP approximately 15-fold. These data indicate that the sole sequence dependence for JBP binding may lie in the thymine moiety of base J and that recognition requires only two specific base contacts, base J and J-1, within both the major and minor groove of the J-DNA duplex.
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Verhoeven EEA, van Kesteren M, Turner JJ, van der Marel GA, van Boom JH, Moolenaar GF, Goosen N. The C-terminal region of Escherichia coli UvrC contributes to the flexibility of the UvrABC nucleotide excision repair system. Nucleic Acids Res 2002; 30:2492-500. [PMID: 12034838 PMCID: PMC117173 DOI: 10.1093/nar/30.11.2492] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Nucleotide excision repair in Escherichia coli involves formation of the UvrB-DNA complex and subsequent DNA incisions on either site of the damage by UvrC. In this paper, we studied the incision of substrates with different damages in varying sequence contexts. We show that there is not always a correlation between the incision efficiency and the stability of the UvrB-DNA complex. Both stable and unstable UvrB-DNA complexes can be efficiently incised. However some lesions that give rise to stable UvrB-DNA complexes do result in a very low incision. We present evidence that this poor incision is due to sterical hindrance of the damage itself. In its C-terminal region UvrC contains two helix-hairpin-helix (HhH) motifs. Mutational analysis shows that these motifs constitute one functional unit, probably folded as one structural unit; the (HhH)2 domain. This (HhH)2 domain was previously shown to be important for the 5' incision on a substrate containing a (cis-Pt).GG adduct, but not for 3' incision. Here we show that, mainly depending on the sequence context of the lesion, the (HhH)2 domain can be important for 3' and/or 5' incision. We propose that the (HhH)2 domain stabilises specific DNA structures required for the two incisions, thereby contributing to the flexibility of the UvrABC repair system.
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58
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Robinson H, van Boom JH, Wang AHJ. 5'-CGA Motif Induces Other Sequences To Form Homo Base-Paired Parallel-Stranded DNA Duplex: The Structure of (G-A)n Derived from Four DNA Oligomers Containing (G-A)3 Sequence. J Am Chem Soc 2002. [DOI: 10.1021/ja00083a050] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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59
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Duff RJ, de Vroom E, Geluk A, Hecht SM, van der Marel GA, van Boom JH. Evidence for C-1' hydrogen abstraction from modified oligonucleotides by iron-bleomycin. J Am Chem Soc 2002. [DOI: 10.1021/ja00061a052] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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60
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van Oijen AH, Behrens S, Mierke DF, Kessler H, van Boom JH, Liskamp RMJ. Synthesis and structure of cyclic phosphopeptides containing a phosphodiester linkage. J Org Chem 2002. [DOI: 10.1021/jo00066a026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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61
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van Oijen AH, Huck NPM, Kruijtzer JAW, Erkelens C, van Boom JH, Liskamp RMJ. Syntheses of Amino Acid Based Phosphodiester Linkage-Containing Cryptands as well as Diphosphorylated Macrocycles. J Org Chem 2002. [DOI: 10.1021/jo00088a022] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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62
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Sabatini R, Meeuwenoord N, van Boom JH, Borst P. Recognition of base J in duplex DNA by J-binding protein. J Biol Chem 2002; 277:958-66. [PMID: 11700315 DOI: 10.1074/jbc.m109000200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
beta-d-Glucosylhydroxymethyluracil, also called base J, is an unusual modified DNA base conserved among Kinetoplastida. Base J is found predominantly in repetitive DNA and correlates with epigenetic silencing of telomeric variant surface glycoprotein genes. We have previously found a J-binding protein (JBP) in Trypanosoma, Leishmania, and Crithidia. We have now characterized the binding properties of recombinant JBP from Crithidia using synthetic J-DNA substrates that contain the glycosylated base in various DNA sequences. We find that JBP recognizes base J only when presented in double-stranded DNA but not in single-stranded DNA or in an RNA:DNA duplex. It also fails to interact with free glucose or free base J. JBP is unable to recognize nonmodified DNA or intermediates of J synthesis, suggesting that JBP is not directly involved in J biosynthesis. JBP binds J-DNA with high affinity (K(d) = 40-140 nm) but requires at least 5 bp flanking the glycosylated base for optimal binding. The nature of the flanking sequence affects binding because J in a telomeric sequence binds JBP with higher affinity than J in another sequence known to contain J in trypanosome DNA. We conclude that JBP is a structure-specific DNA-binding protein. The significance of these results in relation to the biological role and mechanism of action of J modification in kinetoplastids is discussed.
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Burg D, Filippov DV, Hermanns R, van der Marel GA, van Boom JH, Mulder GJ. Peptidomimetic glutathione analogues as novel gammaGT stable GST inhibitors. Bioorg Med Chem 2002; 10:195-205. [PMID: 11738622 DOI: 10.1016/s0968-0896(01)00269-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Elevated levels of glutathione-S-transferase (GST) isoenzymes are found in many tumor cells and are thought to play a role in the onset of multidrug resistance (MDR). To evaluate the contribution of GST to this process, inhibitors are needed. Glutathione (GSH) conjugates, although good GST inhibitors, cannot be used in vivo, because they are eliminated rapidly. In this paper, we describe the synthesis of a series of novel peptidomimetic glutathione analogues that are stabilized against peptidase mediated breakdown. The peptide bonds in GSH were replaced by isosteres, such as the 'reduced' amide (which was prepared using a novel method), N-methylamide, urethane, and methylene linkages. The in vitro evaluation of the compounds focuses on GST inhibition and stability towards gamma-glutamyl-transpeptidase (gammaGT), the main enzyme involved in GSH breakdown. The compounds were conjugated to the model electrophile ethacrynic acid (EA) to resemble GS-EA, an efficient GST inhibitor. All novel GSH-analogues were shown to inhibit rat liver cytosolic GSTs. Furthermore, peptidomimetic changes of the gamma-glutamyl-cysteine amide bond greatly improved stability towards gammaGT. These compounds may therefore be useful in the design of novel in vivo applicable GST inhibitors.
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Ovaa H, Lastdrager B, Codée JDC, van der Marel GA, Overkleeft HS, van Boom JH. A flexible synthesis of cyclopentitol derivatives based on ring-closing metathesis of carbohydrate-derived 1,6-dienes. ACTA ACUST UNITED AC 2002. [DOI: 10.1039/b207509a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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65
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van Hooft PAV, van Swieten PF, van der Marel GA, van Boeckel CAA, van Boom JH. Montmorillonite K-10 Clay Assisted Transformation of Vinylketoses into Spirochromans and Arylketoses. Synlett 2001. [DOI: 10.1055/s-2001-10761] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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66
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Turner JJ, Leeuwenburgh MA, van der Marel GA, van Boom JH. A convenient route to α-amino acids with β-alkyne substituents from a serine derived aziridine. Tetrahedron Lett 2001. [DOI: 10.1016/s0040-4039(01)01886-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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67
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Timmer MS, Ovaa H, Filippov DV, van der Marel GA, van Boom JH. Synthesis of phosphorus mono- and bicycles by catalytic ring-closing metathesis. Tetrahedron Lett 2001. [DOI: 10.1016/s0040-4039(01)01740-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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68
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Ovaa H, van der Marel GA, van Boom JH. A convenient approach towards 2′-analogs of zoapatanol from d-glucose. Tetrahedron Lett 2001. [DOI: 10.1016/s0040-4039(01)00932-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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69
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Turner JJ, Filippov DV, Overhand M, van der Marel GA, van Boom JH. Synthesis of novel amino acid carbohydrate hybrids via Mitsunobu glycosylation of nitrobenzenesulfonamides. Tetrahedron Lett 2001. [DOI: 10.1016/s0040-4039(01)01062-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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70
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Turner JJ, Sikkema FD, Filippov DV, van der Marel GA, van Boom JH. Synthesis of β-Lactams via Ring Opening of a Serine Derived Aziridine. Synlett 2001. [DOI: 10.1055/s-2001-18090] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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71
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de Koning MC, Filippov DV, Meeuwenoord N, Overhand M, van der Marel GA, van Boom JH. Synthesis of a PNA-Peptide Conjugate by Chemical Ligation. Synlett 2001. [DOI: 10.1055/s-2001-17455] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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72
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van Well RM, Overkleeft HS, Overhand M, Vang Carstenen E, van der Marel GA, van Boom JH. Parallel synthesis of cyclic sugar amino acid/amino acid hybrid molecules. Tetrahedron Lett 2000. [DOI: 10.1016/s0040-4039(00)01693-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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73
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Timmer MS, Ovaa H, Filippov DV, van der Marel GA, van Boom JH. An expeditious route to phosphorus heterocycles based on ring-closing metathesis. Tetrahedron Lett 2000. [DOI: 10.1016/s0040-4039(00)01511-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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74
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de Kort M, Regenbogen AD, Overkleeft HS, John Challiss R, Iwata Y, Miyamoto S, van der Marel GA, van Boom JH. Synthesis and Biological Evaluation of Cyclophostin: A 5′,6″-Tethered Analog of Adenophostin A. Tetrahedron 2000. [DOI: 10.1016/s0040-4020(00)00480-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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75
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Ouwerkerk N, van Boom JH, Lugtenburg J, Raap J. Chemo-Enzymatic Synthesis of Thymidine13C-Labelled in the 2′-Deoxyribose Moiety. European J Org Chem 2000. [DOI: 10.1002/(sici)1099-0690(200003)2000:5<861::aid-ejoc861>3.0.co;2-e] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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