The use of BrCN for assembling modified DNA duplexes and DNA-RNA hybrids; comparison with water-soluble carbodiimide

Abstract

Both cyanogen bromide (BrCN) and 1-ethyl-3-(3'-dimethylaminopropyl) carbodiimide may be used as coupling reagents for the template-directed assembly of DNA duplexes containing the sugar-phosphate backbone modification. Both reagents show similar ligation site structure-specific trend. Practical recommendations are given for selection of the condensing reagent depending on the properties of the duplex. Based on 31P NMR spectroscopy data, a scheme is suggested for BrCN activation of the nucleotide phosphomonoester group. Using both condensing reagents, we studied the condensation of oligonucleotides containing ribo-segments (from mononucleotide residue to full sequence) on the DNA template. Efficiency of the chemical ligation of RNA oligomers was shown to be much lower than that of DNA analogues. The coupling yield depends on the position of the RNA segment in the hybrid duplexes and on the position of the phosphate group in the nick.

Circular RNA oligonucleotides. Synthesis, nucleic acid binding properties, and a comparison with circular DNAs

“…Comparison of circular DNAs with linear 12mers Since one explanation for the behavior of the DRD-type complexes is Watson-Crick binding without significant Hoogsteen- (30,34,35). In the present work, the synthesis of the circular RNAs by the nonenzymatic ligation method presented no particular difficulties, and proceeded with high conversion.…”

“…In the present work, the synthesis of the circular RNAs by the nonenzymatic ligation method presented no particular difficulties, and proceeded with high conversion. The strategy may be general for the construction of circular RNAs for triplex-type binding; it is possible, however, that sequence-dependent variations in cyclization efficiency (35) involving circle 2 indicates a stabilization of the complexes by protonation. These two results strongly suggest that the cyclic RNAs bind their complements, whether DNA or RNA, by triple helix formation.…”

Chemical Primer Extension: Individual Steps of Spontaneous Replication

“…This demonstrates how much more efficient primer extension is when the more reactive amino-terminal primer (and a DNA template) are being used. (We note that the nature of the template can also be important for the rate of the reaction, as demonstrated by the elegant work of Gçbel and co-workers [31], as well as by others [45], but this effect appears more modest than that of the nature of the nucleophilic group on the primer.) 4.2.…”

Taming Prebiotic Chemistry: The Role of Heterogeneous and Interfacial Catalysis in the Emergence of a Prebiotic Catalytic/Information Polymer System

“…In these investigations, 1-methylimidazole (1-MeIm) was found to be the best additive (better than 2-MeIm) [23]. Others studied in situ activation agents, such as cyanamide [28] and cyanogen [29,30], which seem even more prebiotically plausible [31], which were also shown to be efficient for chemical ligation reactions between nucleic acid oligomers.…”