Barbora Knappeova

Abstract The uracil:uracil (U:U) base pair is one of the most common mismatches observed in RNA. It is notable for its ability to adopt multiple conformational states depending on its structural environment, particularly on the identity of the flanking canonical base pairs.

Abstract Mixed double helices formed by RNA and DNA strands, commonly referred to as hybrid duplexes or hybrids, are essential in biological processes like transcription and reverse transcription. They are also important for their applications in CRISPR gene editing and nanotechnology. Yet, despite their significance, the hybrids have been seldom modeled by atomistic molecular dynamics methodology, and there is no benchmark study systematically assessing the force-field performance.

The gene expression process inevitably involves formation of mixed RNA and DNA duplexes (hybrids) during the transcription, with the newly synthesized RNA strand temporarily base paired to its DNA template. (1) The opposite process occurs during the reverse transcription, when the DNA is synthesized based on the RNA template. (2) The combination of ubiquity and relatively short lifetimes makes hybrids an important but less studied component of cellular biology.