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. 2020 Jun 19;11:3137. doi: 10.1038/s41467-020-16891-5

Fig. 2. Cationic proto-peptide mixtures generated in dry-down reactions stabilize duplex RNA.

Fig. 2

Dry-down reaction products were dissolved in deionized water to give a 100 mM stock solution based on the amount of monomers used at the start of the dry-down. The mixtures contain diverse oligomers at varying abundances, so the concentration of a given oligomer in the mixture would be substantially lower. Control dry-down reactions contained the amino acid alone, with no hydroxy acid (AA control)39. a Schematic depicting the process used here to generate proto-peptide mixtures. RNA stability studies used either crude dry-down product mixtures, or dialyzed mixtures from which unreacted monomers and short oligomers had been removed with a 500–1000 Da cut-off membrane. For panels b–d, the experiments employed a 10-mer RNA duplex (5′-6-FAM-rCrGrCrUrArArArUrCrG-3′ & 5′-rCrGrArUrUrUrArGrCrG-3IABkFQ-3′, 2.5 μM strand) in buffer (100 mM MES-TEA, 2.5 mM NaCl, pH 7.5). The final pH of the samples was between 5.6 and 6.8, unless otherwise noted. b Thermal denaturation curves for the RNA duplex in the presence of various Arg-containing dry-down reaction mixtures or control mixtures. c Changes in RNA duplex Tm relative to the corresponding amino acid control (dry-down reaction of the amino acid without a hydroxy acid) for crude dry-down mixtures. d Changes in RNA duplex Tm upon addition of dialyzed depsipeptide oligomers. Data are shown as a scatter plot of duplicate experiments. The non-cationic glc + Ala oligomers were included as a control. For the RNA alone condition, three technical replicates from each of the duplicate experiments are shown, for a total of six data points. e Changes in RNA duplex Tm values upon addition of crude polyester and depsipeptide mixtures obtained by drying hab or hah, either alone or with Gly or Ala (at a 1:1 molar ratio), or non-dried controls. Data are shown as a scatter plot of two independent experiments. f Structures of polyesters derived from drying hab or hah, showing potential routes of oligomer degradation via intramolecular O,N acyl transfer.