RESUMEN
We have employed a tandem Sonogashira/annulation reaction between 5-iodocytosine derivatives and terminal alkynes to yield the fluorescent bicyclic nucleobase pyrrolcytosine. Pyrrolocytosine bearing substituents only on the pyrrole ring are conveniently synthesized from 5-iodocytosine. Water soluble pyrrolocytosines are being investigated as reporter groups in SNP analysis.
Asunto(s)
Citosina/análogos & derivados , Química Farmacéutica/métodos , Citosina/síntesis química , Citosina/química , Modelos Químicos , Conformación Molecular , Sondas de Ácido Nucleico/química , Sondas de Ácido Nucleico/farmacología , Polimorfismo de Nucleótido Simple , Análisis de Secuencia de ADN/métodos , Agua/químicaRESUMEN
We have investigated the incorporation of C6-derivatives of uracil into polypyrimidine peptide nucleic acid oligomers (PNA). Starting with orotic acid (uracil-6-carboxylic acid) we have prepared a PNA monomer containing the methyl orotate nucleobase which is compatible with Fmoc-based synthesis. Treatment of the resin-bound oligomers with hydroxide or amines cleanly converted the ester to an orotic acid or orotamide-containing PNA. Alternatively, the methyl orotate-containing PNA was liberated from the resin by standard acidolysis. PNA bearing a modified nucleobase was found to hybridize to both poly(rA) and poly(dA). Complexes with poly(rA) were more stable than those with poly(dA) but both were destabilized relative to an unmodified PNA. Modification of a terminal residue was tolerated better than modification of an internal position. The type of charge provided by the modification affected the complex stability. In the worst case, an internal modification was nearly as detrimental as a base mismatch.
Asunto(s)
Ácido Orótico/análogos & derivados , Ácidos Nucleicos de Péptidos/síntesis química , Composición de Base , Disparidad de Par Base , Modelos Químicos , Conformación Molecular , Conformación de Ácido Nucleico , Desnaturalización de Ácido Nucleico , Oligodesoxirribonucleótidos/química , Oligonucleótidos/química , Ácido Orótico/química , Ácidos Nucleicos de Péptidos/química , Poli A/química , Estructura Terciaria de Proteína , Electricidad EstáticaRESUMEN
We report recent developments in the optimization of a submonomer synthesis of peptide nucleic acid based on the Fukuyama-Mitsunobu reaction. The key steps in the submonomer synthesis are the installation of an appropriately protected 2-aminoethyl group on the alpha-nitrogen of an amino acid and its subsequent acylation with a protected nucleobase derivative. The aggressive alkylation conditions require a scheme of maximal protection for the nucleobases and that is proposed herein for the pyrimidines.
Asunto(s)
Ácidos Nucleicos de Péptidos/síntesis química , Aminoácidos , Citosina/química , Indicadores y Reactivos , Nitrógeno , FosfinasRESUMEN
En route to a circular bis-PNA molecule, we have synthesized and characterized the DNA binding of several "clamp"-type bis-PNAs. In order to incorporate charge into a circular PNA, a new linker based on the achiral 2-aminoethylglycine has been used.
Asunto(s)
Oligodesoxirribonucleótidos/química , Ácidos Nucleicos de Péptidos/síntesis química , Péptidos Cíclicos/síntesis química , Secuencia de Bases , Sitios de Unión , ADN/química , Indicadores y Reactivos , Conformación de Ácido Nucleico , Ácidos Nucleicos de Péptidos/química , Péptidos Cíclicos/químicaRESUMEN
The Pd0/Cu1 catalyzed cross-coupling of terminal alkynes onto peptide nucleic acid monomers or submonomers bearing iodinated nucleobases has been utilized as a route to base-modified oligomers. Both 5-iodouracil and 5-iodocytosine derivatives undergo the cross-coupling to give the expected products in moderate to good yields. However, depending on the particular substrates and reaction conditions, the cross-coupling may be followed by a ring closing reaction to give the fluorescent furano- and pyrrolo-fused uracil and cytosine derivatives, respectively.