Question

What are touchdown PCR and colony PCR?

Answer 1

Polymerase chain reaction (PCR) is a widely used method for rapidly producing millions to billions of copies (complete or partial copies) of a specific DNA sample, allowing scientists to take a small sample of DNA and amplify it (or a portion of it) to a large enough amount to study in detail. Kary Mullis, an American biochemist at Cetus Corporation, invented PCR in 1983.

Complete answer:
Touchdown PCR uses a cycling program that gradually lowers the annealing temperature (e.g. 1-2°C/every second cycle). The initial annealing temperature should be several degrees higher than the primers' estimated Tm. The annealing temperature is then gradually reduced until it reaches or falls below the calculated annealing temperature of the primers. The amplification process is then carried on using this annealing temperature.
Touchdown PCR is a PCR variant that reduces the amount of nonspecific primer annealing. The annealing temperature is lowered between cycles to accomplish this.
Colony PCR is a method for quickly screening colonies of yeast or bacteria that have grown up on selective media following a transformation step to check for the presence of the desired genetic construct or to amplify a portion of the construct.
In contrast, bacterial clones such as E.coli could be screened for accurate ligation products using colony PCR. A sterile toothpick is used to pick up colonies from an agarose plate, which are then daybed into sterile water or master mix. Primer is then added. The PCR protocol should be started at 950°C for long periods.

Note:
Nested PCR is a PCR variation that improves the specificity and yield of the desired amplicons. Two sets of PCR primers are used in this method: one set flanks a region of DNA containing the amplicon of interest, and the other set (nested primers) corresponds to the precise region of DNA to be amplified. In the first round of PCR, the outer primers are used to amplify the target with extended flanking regions.