Metal-Free Catalysts for the Hydrolysis of RNA Derived from Guanidines, 2-Aminopyridines, and 2-Aminobenzimidazoles

Abstract

2-aminopyridine and 2-aminobenzimidazole were chosen as structural analogues to substitute guanidinium groups in receptor molecules designed as phosphoryl transfer catalysts. Shifting the pKa of the guanidinium analogues toward 7 was expected to raise catalytic activities in aqueous buffer. Although the pKa's of both heterocycles are similar (6.2 and 7.0), only 2-aminobenzimidazole led to active RNA cleavers. All cleavage assays were run with fluorescently labeled substrates and a DNA sequencer. RNase contaminations would degrade RNA enantioselectively. In contrast, achiral catalysts such as 9b and 10b necessarily induce identical cleavage patterns in RNA and its mirror image. This principle allowed us to safely rule out contamination effects in this study. The most active catalysts, tris(2-aminobenzimidazoles) 9b and 10b, were shown by fluorescence correlation spectroscopy (FCS) to aggregate with oligonucleotides. However, at very low concentrations the compounds are still active in the nonaggregated state. Conjugates of 10b with antisense oligonucleotides or RNA binding peptides, therefore, will be promising candidates as site specific artificial ribonucleases.

Chiral benzimidazoles as hydrogen bonding organocatalysts

“…In 2005, Göbel's group discovered that 2-aminobenzimidazoles were good candidates for acid/base catalysis and can substitute guanidinium groups in receptor molecules designed as phosphoryl transfer catalysts. 7 Thus, amine 2 ( Figure 1) was able to cleave RNA by phosphate activation by means of hydrogen bonding under neutral conditions. In supramolecular chemistry, the combination of two benzimidazole units bonded to 4,5-diamino-9,9-dimethylxanthene 3 ( Figure 1) provided an excellent receptor for neutral guests with oxygen atom such as sulfoxides, ketones and alcohols.…”

In Vitro DNA-Binding, Cleavage Activity with pBR322, Molecular Docking and Antiproliferative Studies of Newly Synthesized Steroidal Imidazolidine Hybrids

“…Metal complexes have been widely investigated as cleaving agents of nucleic acids and are found to be reasonably efficient [15], but their use in pharmacy is restricted because of serious issues over the liability and toxicity produced due to free radical generation of some transition metals during the redox processes [16]. To overcome these limitations of liability and toxicity, Scheffer and co-workers [17] put forward the concept of 'metal-free cleaving agents' which are being applied to active phosphodiesters like 'nucleic acid mimic' and RNA. In continuation of our previous work [18] herein, we report the synthesis of new steroidal imidazolidines as metal free DNA binding agents.…”

On Facts and Artefacts: The Difficulty to Evaluate an Artificial Nuclease

“…In aqueous solution and with RNA substrates, however, the catalytic efficiency decreased to low values. In an attempt to optimize compounds 1b and 2b for RNA cleavage, a series of guanidine mimics have been synthesized recently [7]. The most striking effects in this series were observed with 2-[(3-{[(1H-benzimidazol-2-yl)amino]methyl}phenyl)methyl]amino-1H-benzimidazole (3b), a close structural analogue of 1b and 2b.…”

“…The fluorescent cyanine dye allows detection of the RNA and of all degradation products with high sensitivity on a DNA sequencer [7] [13 ± 15]. A short stretch of DNA (T 10 ) was placed between the dye and the RNA sequence to prevent the formation of very short fragments that would complicate the electrophoretic separation (the RNA part of oligonucleotides 7 and 8 is adopted from [16]).…”

“…At 1 mm 5b, typically 35% of the substrate was hydrolyzed and, at 0.1 mm, 3.4%. By coincidence of peaks with a ladder of all possible hydrolytic fragments, cleavage sites could be localized [7] [13] [14]. All fragmentations occurred after pyrimidine nucleotides.…”