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From Computational RNA Structure Prediction to the Design of Biologically Active RNA-Based Nanostructures
Published in Peixuan Guo, Kirill A. Afonin, RNA Nanotechnology and Therapeutics, 2022
W.K. Kasprzak, Bruce A. Shapiro
From the structural point of view RNA is a polymer chain containing a combination of four nucleotides with a directionality corresponding to the natural order of RNA chain synthesis (transcription), from the 5′ to 3′ end. The bases that give nucleotides their names, usually referred to by the single letters A, G, C, and U, are Adenine, Guanine, Cytosine, and Uracil. A primary structure of RNA is defined by a sequence of nucleotides. Conceptually single-stranded, RNA chains are sufficiently flexible to fold onto themselves and base pair Gs with Cs and As with Us in the canonical, Watson-Crick scenario. An additional, so-called “wobble” base pair G-U is also frequent. In general, all kinds of non-canonical interactions are found in natural RNAs. The pattern of paired and unpaired nucleotides defines the secondary structure of a sequence. Pairing interactions stabilize the folded RNA. Unpaired regions, out of which emanate two or more helices (or branches), are called loops, and they tend to destabilize the secondary structure.
Novel horizons of the conformationally-tautomeric transformations of the G·T base pairs: quantum-mechanical investigation
Published in Molecular Physics, 2022
Ol’ha O. Brovarets’, Alona Muradova, Dmytro M. Hovorun
In this work it has been used the following abbreviations of the considered G·T base pairs: WC – Watson–Crick; rWC – reverse Watson–Crick; wWC – wobble base pair, which bases are bounded from the Watson–Crick edge; rwWC – reverse wobble base pair, which bases are bounded from the Watson–Crick edge; H – Hoogsteen; rH – reverse Hoogsteen; wH – wobble base pair, which bases are bounded from the Hoogsteen edge; rwH – reverse wobble base pair, which bases are bounded from the Hoogsteen edge.