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TAIL-PCR employs multiple low stringency annealing cycles and, thus, nonspecific products are readily amplified.
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An improved method, named hiTAIL-PCR, similarly involves two rounds of laborious DNA dilutions and multiple low and high stringency PCR cycles, thereby still providing opportunities for nonspecific product amplification [ 3].
Two related genes have been identified by low stringency Southern blot analysis.
Low stringency washes in 2× SSC/0.1 % SDS for 15 min at 37 °C were performed twice, followed by high stringency washes using 0.2× SSC/0.1 % SDS at 68 °C, following the DIG Application Manual from Roche (South San Francisco, CA, USA).
In the chosen low stringency conditions complex patterns were obtained, with a sharp band of ∼700 bp in cases where the vanA gene was present.
Post hybridization washes followed this protocol: low stringency 4×15 minutes at 37°C, then high stringency 2×30 minutes at 55°C.
Blots were washed twice with low stringency buffer at room temperature and twice with high stringency buffer at 45°C.
Low stringency amplifications were performed with an annealing temperature of 52°C.
High stringency datasets for the Nrl mutant were reported previously [25], and low stringency datasets for the Nrl mutant were obtained as described above.
Membranes were washed at low stringency in 1×SSC, 0.5% SDS at 50°C or at high stringency in 0.1×SSC, 0.5% SDS at 65°C for 1 h.
Single isolated colonies from each plate were picked, rigorously vortexed in 500 µl low stringency medium, from which 5 µl drops were placed onto low (SD/−2), medium (SD/−3) or high (SD/−4) stringency selection plates and incubated 3 days at 30°C.
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