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A oligo dT) primer [CDS III/3' PCR Primer 5'-AAG CAG TGG TAT CAA CGC AGA GTA C(T 30-3'] was used to prime the first-strand synthesis reaction, and the SMART IV Oligo (5'-AAG CAG TGG TAT CAA CGC AGA GTA CGC rGrGrG-3') served as a short, extended template at the 5' end of the mRNA.
This results in a block to transcription and trapping of RNAP on the template at the end of the repeat.
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The conditions were chosen so that all of the cDNAs amplified were still within the dynamic range to avoid saturation of one of the templates at the end of the PCR protocol.
hNAP1 was added at the start of each step, however, the supernatant containing hNAP1 was removed following magnetic isolation the transcription templates at the end of each step, and replaced with one prepared in parallel in the absence of hNAP1.
The spiral center of the template found at the end of the optimization process is the estimated location of the true TC's center.
The presence of non-template nucleotides at the 3' end in our datasets (Additional file 5) may indicate post-maturation modifications of miRNAs, as shown in mammals and insects [ 16, 18, 26, 61, 62].
The applied stress adapts each element towards a desired predefined template geometry and at the end a globally smooth mesh is achieved.
The RNA template was removed at the end by incubating the samples for 20 minutes at 37°C in the presence of 5 units RNase H (New England Biolabs, Ipswich, USA).
The as-prepared samples were clamped into the dip-coater with the wrinkle-templates at the bottom end.
To test this, we designed an unzipping template with a 601NPE at the end of the template and a Gal4 binding at a greater spacing (75 bp) from the 601NPE.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com