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. 2024 Nov 18;52(22):14205–14228. doi: 10.1093/nar/gkae1107

Figure 8.

Figure 8.

Schematic model of possible interaction modes of PUN motifs with nucleic acids. Sequence-unspecific interactions with phosphodiester groups of nucleic acids are mediated by positively charged side chains. (A) Two positively charged amino acids separated by a single nonpositively charged amino acid have a distance that is very similar to the spacing of two neighboring phosphodiester groups in nucleic acids. Therefore, these two amino acids can potentially interact with two adjacent phosphodiesters. (B) Due to the lengths and flexibilities of the side chains of arginine and lysine, two neighboring amino acids can also interact with adjacent phosphodiesters of the same molecule (cis). (C) When pointing in opposite directions, two neighboring side chains can contact phosphodiester groups of two nucleic acid molecules (trans). (D) In a stretch of three consecutive arginines or lysines, these amino acids will also adopt a trans conformation. This feature should allow for the simultaneous contact of two nucleic acid molecules by one PUN motif. This arrangement likely constitutes an important feature for higher organization principles, including RNA annealing and RNA-dependent phase transition.