Effect of a Hydrogen Bonding Carboxamide Group on Universal Bases

Abstract

A number of aromatic universal base analogues have been described in the literature, but most are non-hydrogen bonding. We have examined the effect of introducing hydrogen bonding carboxamide groups onto the pyrrole ring of 5-nitroindole. The modified analogues retain universal base features, but there are no overall effects on duplex stability. This leads to the suggestion that the nitro group is within the hydrogen bonding face of the duplex, and the hydrogen bonding carboxamide group is in the duplex major groove.

Solution structure and dynamics of DNA duplexes containing the universal base analogues 5-nitroindole and 5-nitroindole 3-carboxamide

“…Recently, the effect of introducing a hydrogen bonding carboxamide group on the hybridization ability of the universal base analogue 5-nitroindole (Figure 1A) was examined (10). Combined with an alternative strategy currently being explored and based on the development of engineered polymerases, the presence of this group may enhance the ability of these bases to act as enzyme substrates, providing a way to overcome the above problems.…”

Universal Base Analogues and their Applications to Biotechnology

“…Studies of indole analogues have shown that conversion of the 5-nitro group of 2 to either the 5-amino-or 5-formamido-indole derivatives abolishes its universal base behavior [17]. Alternatively, the addition of hydrogen-bonding groups to 2, to produce 5-nitroindole-3-carboxamide (9), gave no additional advantage in terms of its hybridization properties [18]; moreover, solution studies revealed that the hydrogen-bonding carboxamide group resides in the major groove [19]. Many studies have been conducted to determine the stabilization properties of these universal base analogues.…”

“…Kool and coworkers have carried out extensive studies on the factors contributing to the aromatic stacking of several hydrophobic isosteres such as benzene and its derivatives (12, R ¼ H), naphthalene (13), phenanthrene (14), pyrene (15), indoles (16), and benzimidazoles (17,18) [25][26][27][28][29][30]. These authors found that when the non-natural hydrophobic bases were incorporated as overhanging bases, the increase in stability correlated with an increase in size of the overhanging aromatic base [25].…”

“…It was not a primer-dimer, but corresponded to the polymerase copying across the base of the proposed hairpin structure, probably using its extendase activity to jump the gap, which is good evidence for a helical self-paired hairpin system [38]. More recently, self-pairing of 5-nitroindole and its 3-carboxamide derivative has been examined in the center of a modified Dickerson dodecamer, and shown that the self-pair is more stable than the universal base with a native nucleobase [18].…”

“…The polymerases also maintained catalytic turnover, processivity and fidelity. In more recent studies, the present authors group are evolving polymerases specifically aimed at recognizing and replicating the universal base analogues5-nitroindole(2)and 5-nitroindole-3-carboxamide (9) [18].Themainselection pressure applied is that the flanking primers contain the universal base at each 3 0 -end; hence, base recognition must occur in order to amplify the encoding gene. The resultant polymerases are able to copy universal base analogues as well as to incorporate the 5 0 -triphosphate without stalling.…”