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Dual color detection of wild type and mutant sequences in a single tube was tested on single cells.
The proposed approach has been successfully implemented for the identification of the single-base mutant sequences in the human KRAS gene with a detection limit of 1.8 pM.
We then constructed various mutant sequences in silico in an isolated EF-hand from troponin C and analyzed their binding behavior using molecular mechanics for binding to Tb3+ as compared to Al3+.
This HRM assay was further validated using 8 samples bearing different mutant sequences in 4 different laboratories, on 3 different instruments.
In order to test for the reproducibility of the method we have analysed 2 positive samples characterized by different mutant sequences in 3 independent experiments, each performed at 1 week interval.
In combination, LNA probes specifically detect mutant sequences in the presence of wild-type sequences.
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The 173-bp ssODN donor template is presented under the genomic DNA with a R229Q mutant sequence in green.
The LDR/hybridization flow-through biochip performed the entire assay at a relatively fast processing speed: 6.5 min for on-chip LDR, 10 min for washing, and 2.6 min for fluorescence scanning (total processing time = 19.1 min) and could screen multiple mutations simultaneously for high throughput applications at a level of one mutant sequence in 100 wild-type sequences.
Two dual luciferase reporter constructs, one with wildtype and another with mutant sequence in the miR-335 binding site seed regions were constructed.
Subsequently, a 276 bp FRB fragment was PCR-amplified from plasmid pC4-RhE (ARIAD) with primers containing BamHI/BglII sites and cloned into the BamH1 site upstream of the myc-tagged CK-B or CK-BC283S (catalytic death mutant) sequence in vector pLZRS-IRES-Zeo.
Thus, SNaPshot generally confirmed our findings with P-cycle sequencing when the proportion of mutant sequence in DNA samples was above 20%.
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