chemically synthesized rna oligomer  (Gene Design Inc)

Journal: Nucleic Acids Research

Article Title: Coordination among tertiary base pairs results in an efficient frameshift-stimulating RNA pseudoknot

doi: 10.1093/nar/gkx134

Figure Lengend Snippet: DU177 and the design of the bimolecular pseudoknots. ( A ) A schematic of the DU177 pseudoknot. Nucleotides involved in base triples or Hoogsteen base pairs are connected by dotted lines. The sequence change in the UUC mutant is indicated. ( B ) Schematics of the bimolecular pseudoknots derived from DU177. The sequence change in the mutant hairpin hp1-U3C is indicated. The series of RNA oligomers used for annealing are shown on the right. The gray shaded area highlights the corresponding stem S1 region for better comparison among various constructs. Both ss18* and ss18U* were made by in vitro transcription, and thus contained two G's (from the promoter sequence) at the 5΄ end. The others (ss11–ss18) were chemically synthesized.

Article Snippet: To make bimolecular pseudoknots, 2.5 nM of the handle-annealed hp1 construct were mixed with a 20-fold molar excess of chemically synthesized RNA oligomers (Thermo Scientific) and incubated at 37°C for 15 min.

Techniques: Sequencing, Mutagenesis, Derivative Assay, Comparison, Construct, In Vitro, Synthesized

Journal: Nucleic Acids Research

Article Title: Coordination among tertiary base pairs results in an efficient frameshift-stimulating RNA pseudoknot

doi: 10.1093/nar/gkx134

Figure Lengend Snippet: Distribution of unfolding forces for the bimolecular pseudoknots. ( A ) hp1 and ( B ) hp1-U3C, alone or annealed with the specified RNA oligomers to form bimolecular pseudoknots (see Figure for illustrations), were pulled by optical tweezers for the measurements. The average force for each construct is shown on the top-right corner of each panel. See for more details.

Article Snippet: To make bimolecular pseudoknots, 2.5 nM of the handle-annealed hp1 construct were mixed with a 20-fold molar excess of chemically synthesized RNA oligomers (Thermo Scientific) and incubated at 37°C for 15 min.

Techniques: Construct

Journal: Nucleic Acids Research

Article Title: Coordination among tertiary base pairs results in an efficient frameshift-stimulating RNA pseudoknot

doi: 10.1093/nar/gkx134

Figure Lengend Snippet: Design of and results from smFRET experiments. ( A ) Bimolecular pseudoknots constructed by annealing a hairpin (hp1 or hp1-U3C) to a single-stranded RNA (ssRNA; ss18 or ss18U). The 5΄ and 3΄ ends of the ssRNA were labeled with Dy647 and Dy547, respectively. A biotin-labeled DNA strand complementary to the 5΄ overhang of the hairpin was used for immobilization. ( B ) DNA/RNA hybrids for control experiments. The dye-labeled ssRNA was annealed to a specified single-stranded DNA (ssDNA; dna9–dna16) containing a linker and a biotin tag on the 5΄ end for immobilization. The measured FRET efficiency (see Figure ) for each construct is summarized at the top. The gray shaded area highlights the corresponding stem S1 region for comparison among various constructs.

Article Snippet: To make bimolecular pseudoknots, 2.5 nM of the handle-annealed hp1 construct were mixed with a 20-fold molar excess of chemically synthesized RNA oligomers (Thermo Scientific) and incubated at 37°C for 15 min.

Techniques: Construct, Labeling, Control, Comparison

Journal: Nucleic Acids Research

Article Title: Coordination among tertiary base pairs results in an efficient frameshift-stimulating RNA pseudoknot

doi: 10.1093/nar/gkx134

Figure Lengend Snippet: Distribution of FRET efficiency for ( A ) the bimolecular pseudoknots and ( B ) DNA/RNA hybrids (as described in Figure ). The distributions can be fit to a single Gaussian function (solid curves) for all the constructs except for hp1-U3C/ss18, which is better fit to two functions (dotted curves) with the centers at 0.88 and 0.93. The fitted FRET values are shown on the top-right corner of each panel as well as in Figure . The FRET peak at 0 is attributed to the donor-only species.

Article Snippet: To make bimolecular pseudoknots, 2.5 nM of the handle-annealed hp1 construct were mixed with a 20-fold molar excess of chemically synthesized RNA oligomers (Thermo Scientific) and incubated at 37°C for 15 min.

Techniques: Construct