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In brief, the single-copy gene of DHPS was amplified by the primers DHPS-3 (5´-GCG CCT ACA CAT ATT ATG GCC ATT TTA AAT C-3´) and DHPS-4 (5´-GGA ACTTCTC AAC TTG GCA ACC AC-3´) by using a touchdown-PCR protocol, yielding a 370-bp fragment.
Of 26 breast tumors, 5 (19%) tested HPV positive by the standard assay and 15/26 (58%) using a touchdown protocol.
For primers using a touchdown programme the annealing temperature was decreased by 1 °C each cycle for the first 10 cycles, starting from 65 °C.
To get sufficient PCR-products nested PCR was performed, first with two outer and rather unspecific primers, followed by a nested reaction with the two newly-developed specific internal primers using a touchdown PCR-protocol (see Table 3).
Thermal cycling was carried out with a TC-512 thermal cycler (Techne, Burlington, NJ) using a touchdown PCR program from 65°C to 55°C.
The amplification reactions were performed in the Rotor-Gene Q real-time PCR system (Qiagene, Germany) using a touchdown temperature profile (Table 2).
Multiple infections were also detectable using a touchdown approach.
The amplifications were conducted using a touchdown cycle [ 23].
Sixteen SSR loci (Table 3) were amplified as previously described [ 38, 42] using a touchdown PCR profile optimised for each set of primers: touchdown 60°C to 55°C or touchdown 55°C to 50°C.
All primer pairs were initially tested using a "touchdown 58" PCR protocol.
RT-PCR was performed using a touchdown PCR program with five cycles lowered 1°C per cycle down from 61°C to 57°C followed by a further 35 cycles with a final annealing temperature of 56°C.
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