Fig. 5: Heterotypic base-pairing modulates molecular dynamics and viscosity of patchyDNA condensates.
From: Sequence-encoded intermolecular base pairing modulates fluidity in DNA and RNA condensates
a Schematic showing design of a primary patchyDNA with inducible inter-molecular cross-linking. The primary strand forms complex coacervates with spermine but this sequence does not contain self-associative hybridization sites (left). Addition of an appropriate secondary patchyDNA strand may cross-link the two DNAs (right). b Estimated hybridization energy for heterotypic cross-links (εheterotypic) with the indicated secondary patch sequence. Patch sequence for primary strand is CTCCTC. c, d Fluorescence recovery after photobleaching for the primary patchyDNA and f, g MSD of embedded beads with lag time, where εheterotypic was modulated either by varying the secondary patchyDNA (c, f) or by varying the temperature for the indicated secondary patchyDNA (d, g). Data depict mean ± SD, n = 5 and mean, n = 5 for (c, d) and (f, g), respectively. Plots showing that the logarithm of self-diffusivity (Dself) (e) and viscosity (η) (h) of the primary patchyDNA scales linearly with εheterotypic. Dotted line denotes the least square fit (slope (mean ± SE) = −0.34 ± 0.01, R2 = 0.92 and 0.33 ± 0.02, R2 = 0.83, for e and h respectively). The solid and open symbols indicate that εheterotypic was varied by changing the secondary patchyDNA or by changing the temperature, respectively. Each data point denotes mean ± SD. The number of technical replicates (n) for e, at 22 °C for CTCCTC + GG (n = 8), CTCCTC + AGGA (n = 8), CTCCTC + GAGG (n = 10), CTCCTC + GAGGAG (n = 9) and for CTCCTC + GAGGAG at various temperatures 25 °C (n = 5), 30 °C (n = 5), 35 °C (n = 6), 40 °C (n = 5), and 45 °C (n = 5). For h: at 22 °C for CTCCTC + GG (n = 5), CTCCTC + AGGA (n = 5), CTCCTC + GAGG (n = 6), CTCCTC + GAGGAG (n = 8) and for CTCCTC + GAGGAG at various temperatures 25 °C (n = 8), 30 °C (n = 8), 35 °C (n = 7), 40 °C (n = 9), and 45 °C (n = 9). The color bars in (c, d, f, g) indicate the range of εheterotypic. Error bars for some data points in (e) are smaller than the symbols, and thus not visible in the plots (see Supplementary Fig. 16e, f).
