Silicon-based PCR chip (Credit: Tim Stakenborg, Senior Scientist, imec)
The PCR technique has given medical doctors and researchers a powerful tool to detect specific DNA sequences in a sample. With PCR, they can determine, for example, if a blood sample contains a virus (and in which quantities). Or they can examine the genetic makeup of a patient’s tumor, to choose the best-matching treatment. In 2013, engineers from imec and Panasonic succeeded in integrating the technique on a chip using silicon microfluidics, albeit still with external heaters and pumps. Imec’s scientists are now working on fully-integrated PCR for use in lab-on-chip solutions. And they are looking to bring other PCR techniques to chip, such as digital droplet PCR.
PCR Finds the Needle in the DNA Haystack
PCR – shorthand for polymerase chain reaction – is used to amplify a few copies, or even a single copy, of a specific piece of DNA across several orders of magnitude, generating thousands to millions of copies.
The method relies on cycles of repeated heating and cooling.
Heating causes a DNA string to melt, i.e. to split into its two constituting single strands. After subsequent cooling to the appropriate temperature, primer sequences attach to the single strands. These primers are short strings of DNA material that are designed so that they will only stick to the beginning or end of the DNA sequence that is looked for. They form the starting point for a polymerase enzyme that will complement the single strand – beginning from our target sequence – into a double-helix DNA.
Then the thermal cycle starts again, every time doubling the sequence flagged by the primers. In a typical PCR reaction, the sample may go through 30 such thermal cycles, taking some 30 minutes to finish. If the target DNA sequence was present in the sample, it will now be available in millions of copies, so that it can be detected using optical or electrochemical techniques.