(A) Schematic illustration of rolling circle synthesis (RCS). Red product RNA strand is extended by a triplet at the 3′-end while three base pairs dissociate at the 5′-end keeping the total …
Gel images and numerical values.
Identification and dissection of circularized RNA were performed by denaturing PAGE. Representative SyBr Gold stained 10% Urea PAGE gel is shown here for illustrating the circularization process of …
Gel images.
(A) Product strand of primer extension experiments with primer P10 (red) and eight triplet scRNA template strands. Potential beyond full-length circle synthesis triplets are shaded opaque. (B) …
Gel images and numeric values.
(A) Comparison between linear and circular primer extension using the CHES reaction buffer system (similar to main text Figure 1D that is in the Tris buffer system). Extensions performed at −7°C for …
Gel images and numeric values.
(A) Main conformations (and zoom-in to relevant regions [squares]) observed from simulations in 100 mM MgCl2 on scRNA exploring consecutive states of primer extension, from 9 to 30 bp dsRNA with …
We observe a series of melting and reannealing events in the 3′-end (purple and light green) during the first half of the simulation and in the 5′-end (dark blue and dark green) during the second …
We observe a series of melting and reannealing events in the 5′-end (dark blue and dark green). The rest of the color code is the same as Figure 3—figure supplement 1.
(A) Linear RNAs solvated with the three buffers (100 mM KCl, 200 mM MgCl2, and 500 mM MgCl2). (B) Rolling circle RNA synthesis (RCS) simulations solvated with 100 mM KCl. (C) RCS simulations …
(A–E) Averages and standard deviations (as error bars) of bp-step parameters (roll, slide, and twist) together with major and minor groove widths (MajW and MinW, respectively) calculated over the …
These areas are the molecular regions where cations localize preferentially. In the case of 200 mM KCl, these align along the grooves, whereas, in the case of MgCl2, they tend to be closer to the …
(Top) Averages and standard deviations (as error bars) of radial distribution functions (RDFs) of cations around RNA backbone phosphates. The RDFs indicate the probability of finding an ion within a …
(A) Product strands of primer extension experiments with linear and scRNA templates A–D with primer P91. Opaque sequence illustrate potential beyond full-length synthesis on scRNA. Barcode triplets …
Full analysis of sequencing data used in Figure 4B.
(A) Representative SyBr Gold stained 10% Urea PAGE gel showing linear and circularized templates A–D. Circularized RNA was retained in the gel as expected. A small degree of hydrolyzed RNA is seen …
Gel images.
(A) Plot shows the fidelity ratio at the noted triplet positions between extension reactions where the templates were incubated either in one-pot (Mix) or in individual tubes (Ind). This is shown …
(A) Product strand of primer extension experiments with scRNA template containing two priming sites (I and II) for primer P91. Depending on the priming site two different products will be made (I or …
Gel images and full data analysis of sequencing data used in Figure 5D.
Excised gel piece is marked with green.
(A) Illustration of the µHHz (−) and (+) strand. (B) Schematic illustration of the RNA-catalyzed viroid-like replication with steps comprising RNA-catalyzed combined RCS (steps 1–3), resection …
Gel images.
We observe fraying and annealing of 5′- and 3′-ends demonstrating the quick timescales of these transitions.
We observe again fraying and annealing of 5′- and 3′-ends demonstrating the quick timescales of these transitions.
Oligonucleotide sequences.