Journal: RNA Biology

Article Title: Functional sequestration of microRNA-122 from Hepatitis C Virus by circular RNA sponges

doi: 10.1080/15476286.2018.1435248

Figure Lengend Snippet: Preparation and analysis on circular RNA in vitro . (A) Schematic of in vitro circularization constructs. Transcripts to be circularized consist of a terminal 10 nt open loop structure (black) and a reverse-complementary repeat sequence of 11 nt, which forms an intramolecular stem (red). This structure is followed by a 63 nt constant region for detection by northern blot or PCR (blue), followed by the miRNA-122 sponge (bulge; perfect) or a scrambled control sequence (shuffle) in grey. (B) Schematic of the in vitro ligation reaction. 4-fold excess of GMP over GTP results in ∼80% of the transcripts containing a 5′-monophosphate, enabling efficient in vitro ligation by T4 RNA ligase. Ligation products are circular RNAs (intramolecular ligation) or linear dimers (intermolecular ligation). (C) In vitro ligation reactions described in (B) were analyzed on 5%, 6% or 7% polyacrylamide-urea gels by ethidium bromide staining. While mobility of linear RNAs remains unchanged compared to RNA marker, the apparent mobility of circular RNA is lower in higher percentage gels (indicated by dash/double dash or circle). (D) Purified linear or circular RNAs from (C) were transfected in HuH-7.5 cells and total RNA was prepared after 4, 8, 14, 24 and 32 h. RNAs were detected by ³²P-northern blot analysis using identical probes in the constant region [labeled blue in (A)]. (E) HuH-7.5 cells transfected with circular RNA or linear RNA from (C) were subjected to sub-cellular fractionation and cytoplasmic or nuclear fractions were analyzed by ³²P-northern blot detecting transfected RNAs along with U1 snRNA and by western blot against hnRNP A1 or GAPDH proteins as a fractionation control. In the circRNA-transfected samples, a degradation product is detected at linear monomer size (“linearized”).

Article Snippet: Next, T4 RNA ligase buffer and RNaseOUT (Thermo Fisher Scientific) were added and incubated for 10 min at 37°C.

Techniques: In Vitro, Construct, Sequencing, Northern Blot, Polymerase Chain Reaction, Ligation, Staining, Marker, Purification, Transfection, Labeling, Cell Fractionation, Western Blot, Fractionation

Journal: Plant Methods

Article Title: A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters

doi: 10.1186/1746-4811-8-41

Figure Lengend Snippet: Adenylation of 3’ adapter using T4 RNA ligase 1. ( A ) Effect of PEG8000 concentration on adenylation efficiency. A synthetic oligo BL1 mimicking the first small RNA cloning linker reported by Lau et al. (2001) was adenylated overnight with 1 U/μL T4 RNA ligase at various PEG concentration. Non-adenylated oligo as the negative control (NC) is loaded on the left lane. ( B ) Effect of temperature and 5’ nucleotide composition on adenylation efficiency. Oligos were adenylated overnight in the presence of 20% PEG8000 at various temperatures. ( C ) Impact of oligo concentration on adenylation efficiency. Substrates with different concentrations were adenylated overnight with 20% PEG8000 at room temperature. All adenylation products were analyzed on the 20% denatured PAGE, stained with SYBR-Gold and photograph under UV.

Article Snippet: Reagents T4 RNA liagse 2, truncated (NEB) 50% PEG8000 (NEB) 10 mM ATP (NEB) RNase Inhibitor (Promega) T4 RNA ligase 1 (Enzymatics) SuperScriptIII Reverse Transcriptase (Invitrogen) Phusion Hotstart DNA Polymerase (NEB) MinElute Gel Extraction kit (Qiagen) Quant-iT HS DNA assay kit (Inivtrogen)

Techniques: Concentration Assay, Clone Assay, Negative Control, Polyacrylamide Gel Electrophoresis, Staining