5-Nitroindole as an universal base analogue

Abstract

4-, 5- and 6-Nitroindole have been investigated and compared with 3-nitropyrrole as universal bases in oligodeoxynucleotides. Of these the 5-nitroindole derivative was found to be superior giving higher duplex stability, and behaving indiscriminately towards each of the four natural bases in duplex melting experiments. 3-Nitropyrrole, whilst not discriminating between the natural bases, was found to lead to considerable destabilisation of the duplexes, particularly when multiple substitutions were made, in contrast to the 5-nitroindole nucleoside.

Whole Genome Analysis of Genetic Alterations in Small DNA Samples Using Hyperbranched Strand Displacement Amplification and Array–CGH

“…Thus, although it is possible to obtain very high amplification yields with standard random primers, reactions initiated with very small inputs of genomic DNA tend to be contaminated with spurious DNA sequences. We explored the use of modified primers with one or two 5Ј-terminal nitroindole (universal base) residues, which in theory will stabilize primer binding without increasing the sequence complexity of the primer (Loakes and Brown 1994;Loakes et al 1997). Primers containing nitroindole residues have been used to obtain improved signal intensity in cycle sequencing reactions (Ball et al 1998).…”

Synthesis and fluorescence study of 7-azaindole in DNA oligonucleotides replacing a purine base

“…Compound 2 crystallized readily during the reaction and was easily isolated and purified. Tritylation of 2 with 1.5-equivalent of 4,4′-dimethoxytrityl chloride partially protected both the 5′-and 3′-hydroxyl groups of the sugar as revealed by 1 H-NMR spectrum of the isolated main product (not shown), although such procedure performed on other modified bases protected only the 5′-hydroxyl group [10,15,16,20,22]. Therefore, only 1.1-equivalent of 4,4′-dimethoxytrityl chloride was used for the reaction and a 75% yield for 3 was achieved after chromatography purification.…”

“…The glycosylation of 7a In with l-(α)-chloro-3,5-di-O-(p-toluoyl)-2-deoxy-D-ribose was accomplished at − 10 °C with an admirable yield (66%). Prior to this procedure, several attempts at room temperature (20 °C) yielded multiple by-products, although most chemists were successful with the glycosylation of other bases at room temperature [11,20,40], The by-products were not characterized. Lowering the reaction temperature by 30 °C effectively eliminated the unwanted reactions to yield 1.…”

“…There are mainly two groups of 'bases' synthesized and incorporated into DNA oligomers: those made by minor modification of the natural bases or the derivatives of cyclic aromatic compounds. While the former includes 2-aminopurine [1][2][3][4][5][6][7][8], inosine [9] and isoinosine [9][10][11], 3-and 7-deazaadenine [12][13][14][15], and 3-and 7-deazaguanine [14,16], the latter includes analogs of pteridine [17][18][19] and indole [20][21][22][23][24], benzene [23][24][25][26], naphthalene and pyrene derivatives [24], The first group of compounds, when replacing a natural base in duplex DNA, can still form hydrogen bonds with the base in the opposite strand, while the second group of compounds cannot form any hydrogen bonds.…”

“…The fluorescence properties of the above base analogs have been utilized for studying DNA structure and duplex stability [1,2,10,14,15,22,26], protein-DNA interactions [4][5][6][7][8]13,18,25], or simply as universal base analogs [20,27]. Some of the unusual 'bases' are used as anti-HIV or anti-cancer drugs [28][29][30].…”