101
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Mikhailov SN, Rozenski J, Efimtseva EV, Busson R, Van Aerschot A, Herdewijn P. Chemical incorporation of 1-methyladenosine into oligonucleotides. Nucleic Acids Res 2002; 30:1124-31. [PMID: 11861902 PMCID: PMC101250 DOI: 10.1093/nar/30.5.1124] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2001] [Revised: 01/14/2002] [Accepted: 01/14/2002] [Indexed: 11/13/2022] Open
Abstract
The base moiety of 1-N-methyladenosine can be protected with a chloroacetyl group for incorporation of this modified nucleoside into DNA and RNA. Carefully controlled anhydrous conditions are needed for deprotection of the oligonucleotides.
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102
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Declercq R, Van Aerschot A, Read RJ, Herdewijn P, Van Meervelt L. Crystal structure of double helical hexitol nucleic acids. J Am Chem Soc 2002; 124:928-33. [PMID: 11829600 DOI: 10.1021/ja016570w] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A huge variety of chemically modified oligonucleotide derivatives has been synthesized for possible antisense applications. One such derivative, hexitol nucleic acid (HNA), is a DNA analogue containing the standard nucleoside bases, but with a phosphorylated 1',5'-anhydrohexitol backbone. Hexitol nucleic acids are some of the strongest hybridizing antisense compounds presently known, but HNA duplexes are even more stable. We present here the first high-resolution structure of a double helical nucleic acid with all sugars being hexitols. Although designed to have a restricted conformational flexibility, the hexitol oligomer h(GTGTACAC) is able to crystallize in two different double helical conformations. Both structures display a high x-displacement, normal Watson-Crick base pairing, similar base stacking patterns, and a very deep major groove together with a minor groove with increased hydrophobicity. One of the conformations displays a major groove which is wide enough to accommodate a second HNA double helix resulting in the formation of a double helix of HNA double helices. Both structures show most similarities with the A-type helical structure, the anhydrohexitol chair conformation thereby acting as a good mimic for the furanose C3'-endo conformation observed in RNA. As compared to the quasi-linear structure of homo-DNA, the axial position of the base in HNA allows efficient base stacking and hence double helix formation.
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103
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Rozenski J, Chaltin P, Aerschot AV, Herdewijn P. Characterization and sequence confirmation of unnatural amino acid containing peptide libraries using electrospray ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2002; 16:982-987. [PMID: 11968131 DOI: 10.1002/rcm.672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The content of 24 12-membered heptapeptide libraries was investigated using capillary liquid chromatography coupled with an electrospray ionization quadrupole orthogonal acceleration time-of-flight mass spectrometer. Adjustment of the chromatographic parameters led to the separation of most of the components. Extraction of the [M + 2H]2+ ions allowed us to demonstrate the presence of all expected species in the library and to evaluate their relative abundance in the mixture. Rapid sequence confirmation was achieved by subtraction of product ion spectra, a way to eliminate common ions and to simplify the spectra for interpretation. This technique can also easily be applied to other libraries consisting of components with a common core.
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104
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Zhang Z, Van Aerschot A, Chaltin P, Busson R, Herdewijn P. Epimerization During Coupling to the Unnatural Amino Acid in Solid Phase Peptide Synthesis. ACTA ACUST UNITED AC 2001. [DOI: 10.1135/cccc20010923] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Extensive epimerization was observed during the coupling of Fmoc-L-Trp(Boc) and Fmoc-L-Pro to D-Ual, a synthetic α-amino acid with a nucleobase in the side chain. This unnatural amino acid was used extensively in the construction of nucleic acids recognition libraries. Reaction protocols based on the use of DIC-HOAt-DIEA mixture without preactivation of the coupling mixture has been proven to suppress the epimerization reaction significantly.
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105
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Wang J, Verbeure B, Luyten I, Lescrinier E, Froeyen M, Hendrix C, Rosemeyer H, Seela F, Van Aerschot A, Herdewijn P. Cyclohexene Nucleic Acids (CeNA): Serum Stable Oligonucleotides that Activate RNase H and Increase Duplex Stability with Complementary RNA. J Am Chem Soc 2000. [DOI: 10.1021/ja000018+] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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106
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Boudou V, Langridge J, Van Aerschot A, Hendrix C, Millar A, Weiss P, Herdewijn P. Synthesis of the Anticodon HairpintRNAfMet ContainingN-{[9-(β-D-Ribofuranosyl)-9H-purin-6-yl]carbamoyl}-L-threonine (=N6-{{[(1S,2R)-1-Carboxy-2-hydroxypropyl]amino}carbonyl}adenosine, t6A). Helv Chim Acta 2000. [DOI: 10.1002/(sici)1522-2675(20000119)83:1<152::aid-hlca152>3.0.co;2-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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107
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Allart B, Khan K, Rosemeyer H, Schepers G, Hendrix C, Rothenbacher K, Seela F, Van Aerschot A, Herdewijn P. D-Altritol Nucleic Acids (ANA): Hybridisation Properties, Stability, and Initial Structural Analysis. Chemistry 1999. [DOI: 10.1002/(sici)1521-3765(19990802)5:8<2424::aid-chem2424>3.0.co;2-w] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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108
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Maurinsh Y, Rosemeyer H, Esnouf R, Medvedovici A, Wang J, Ceulemans G, Lescrinier E, Hendrix C, Busson R, Sandra P, Seela F, Van Aerschot A, Herdewijn P. Synthesis and Pairing Properties of Oligonucleotides Containing 3-Hydroxy-4-hydroxymethyl-1-cyclohexanyl Nucleosides. Chemistry 1999. [DOI: 10.1002/(sici)1521-3765(19990702)5:7<2139::aid-chem2139>3.0.co;2-k] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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109
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Lescrinier T, Hendrix C, Kerremans L, Rozenski J, Link A, Samyn B, Van Aerschot A, Lescrinier E, Eritja R, Van Beeumen J, Herdewijn P. DNA-Binding Ligands from Peptide Libraries Containing Unnatural Amino Acids. Chemistry 1998. [DOI: 10.1002/(sici)1521-3765(19980310)4:3<425::aid-chem425>3.0.co;2-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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110
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Hossain N, Wroblowski B, Van Aerschot A, Rozenski J, De Bruyn A, Herdewijn P. Oligonucleotides Composed of 2‘-Deoxy-1‘,5‘-anhydro-d-mannitol Nucleosides with a Purine Base Moiety. J Org Chem 1998. [DOI: 10.1021/jo9718511] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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111
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Ceulemans G, Van Aerschot A, Wroblowski B, Rozenski J, Hendrix C, Herdewijn P. Oligonucleotide Analogues with 4-Hydroxy-N-Acetylprolinol as Sugar Substitute. Chemistry 1997. [DOI: 10.1002/chem.19970031215] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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112
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Ceulemans G, Aerschot AV, Rozenski J, Herdewijn P. Oligonucleotides with 3-hydroxy-N-acetylprolinol as sugar substitute. Tetrahedron 1997. [DOI: 10.1016/s0040-4020(97)01047-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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113
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Hendrix C, Rosemeyer H, De Bouvere B, Van Aerschot A, Seela F, Herdewijn P. 1′,5′-Anhydrohexitol Oligonucleotides: Hybridisation and Strand Displacement with Oligoribonucleotides, Interaction with RNase H and HIV Reverse Transcriptase. Chemistry 1997. [DOI: 10.1002/chem.19970030920] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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114
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Maurinsh Y, Schraml J, De Winter H, Blaton N, Peeters O, Lescrinier E, Rozenski J, Van Aerschot A, De Clercq E, Busson R, Herdewijn P. Synthesis and Conformational Study of 3-Hydroxy-4-(Hydroxymethyl)-1-Cyclohexanyl Purines and Pyrimidines. J Org Chem 1997; 62:2861-2871. [PMID: 11671649 DOI: 10.1021/jo962204x] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cyclohexane nucleosides with a 1,4-relationship between nucleoside base and hydroxymethyl moiety were synthesized using a conjugated addition reaction of the nucleobases to ethyl 1,3-cyclohexadiene-1-carboxylate and hydroboration of the cyclohexenyl precursor. The lack of antiviral activity of the compounds was correlated with the conformation of these nucleosides as deduced from NMR and X-ray analysis.
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115
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Hendrix C, Rosemeyer H, Verheggen I, Van Aerschot A, Seela F, Herdewijn P. 1′, 5′ -Anhydrohexitol Oligonucleotides: Synthesis, Base Pairing and Recognition by Regular Oligodeoxyribonucleotides and Oligoribonucleotides. Chemistry 1997. [DOI: 10.1002/chem.19970030118] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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116
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Lescrinier T, Busson R, Rozenski J, Janssen G, Van Aerschot A, Herdewijn P. Incorporation of 5-hydroxytryptophan in oligopeptides. Tetrahedron 1996. [DOI: 10.1016/0040-4020(96)00301-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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117
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Efimtseva EV, Ermolinsky BS, Fomitcheva MV, Meshkov SV, Padyukova NS, Mikhailov SN, Van Aerschot A, Rozenski J, Herdewijn P. Synthesis of disaccharide nucleosides and their incorporation into oligonucleotides. ACTA ACUST UNITED AC 1996. [DOI: 10.1135/cccc1996s206] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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118
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Doboszewski B, De Winter H, Van Aerschot A, Herdewijn P. Synthesis of 3′-Deoxy-3′-C-Hydroxymethyl-aldopentopyranosyl Nucleosides and their Incorporation in Oligonucleotides. Part II 1. Tetrahedron 1995. [DOI: 10.1016/0040-4020(95)00777-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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119
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Van Aerschot A, Verheggen I, Hendrix C, Herdewijn P. 1,5-Anhydrohexit-Nucleinsäuren, neue potentielle Antisense-Wirkstoffe. Angew Chem Int Ed Engl 1995. [DOI: 10.1002/ange.19951071227] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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120
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Rozenski J, Samson I, Janssen G, Busson R, Van Aerschot A, Herdewijn P. Characterization of modification sites during peptide synthesis using liquid secondary ion/collision-induced dissociation mass spectrometry and a computer program. ACTA ACUST UNITED AC 1994. [DOI: 10.1002/oms.1210291113] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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121
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Herdewijn P, De Winter H, Doboszewski B, Verheggen I, Augustyns K, Hendrix C, Saison-Behmoaras T, De Ranter C, Van Aerschot A. Hexopyranosyl-Like Oligonucleotides. ACTA ACUST UNITED AC 1994. [DOI: 10.1021/bk-1994-0580.ch006] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
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122
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Van Calenbergh S, Van Den Eeckhout E, Herdewijn P, De Bruyn A, Verlinde C, Hol W, Callens M, Van Aerschot A, Rozenski J. Synthesis and Conformational Analysis of 2?-Deoxy-2?-(3-methoxybenzamido)adenosine, a rational-designed inhibitor of trypanosomal glyceraldehyde phosphate dehydrogenase (GAPDH). Helv Chim Acta 1994. [DOI: 10.1002/hlca.19940770306] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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123
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Vandendriessche F, Augustyns K, Van Aerschot A, Busson R, Hoogmartens J, Herdewijn P. Acyclic oligonucleotides: possibilities and limitations. Tetrahedron 1993. [DOI: 10.1016/s0040-4020(01)87200-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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124
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Vandendriessche F, Van Aerschot A, Voortmans M, Janssen G, Busson R, Van Overbeke A, Van den Bossche W, Hoogmartens J, Herdewijn P. Synthesis, enzymatic stability and base-pairing properties of oligothymidylates containing thymidine dimers with different N-substituted guanidine linkages. ACTA ACUST UNITED AC 1993. [DOI: 10.1039/p19930001567] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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125
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Herdewijn PAM, Van Aerschot A, Jie L, Esmans E, Feneau-Dupont J, Declercq JP. Radical-induced cyclization of the S-methyl dithiocarbonate of 1,2-O-isopropylidene-α-xylose. ACTA ACUST UNITED AC 1991. [DOI: 10.1039/p19910001729] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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