Synchronous coefficient of drag alteration
Synchronous coefficient of drag alteration (SCODA) is a biotechnology method for purifying, separating and/or concentrating bio-molecules.
SCODA has the ability to separate molecules whose mobility (or drag) can be altered in sync with a driving field.
For explanatory purposes consider an electrophoretic particle moving (driven) in an electric field.
) can be expressed in Cartesian coordinates as: Combining (5), (6) and (7) we get: Further consider the field E is applied in a plane and it rotates counter-clockwise at angular frequency
, such that the field components are: Substituting (10) and (11) in (8) and (9) and simplifying using trigonometric identities results in a sum of constant terms, sine and cosine, at angular frequency
will yield non-zero net drift velocity - therefore we need only evaluate these terms, which will be abbreviated
such that: Substituting (14) and (15) into (12) and (13) and taking the time average we obtain: which can be summarized in vector notation to: Equation (18) shows that for all positions
the time averaged velocity is in the direction toward the origin (concentrating the particles towards the origin), with speed proportional to the mobility coefficient k, the strength of the rotating field E and the strength of the perturbing quadrupole field
DNA molecules are unique in that they are long, charged polymers which when in a separation medium, such as agarose gel, can exhibit highly non-linear velocity profiles in response to an electric field.
As such, DNA is easily separated from other molecules that are not both charged and strongly non-linear, using SCODA[2] To perform SCODA concentration of DNA molecules, the sample must be embedded in the separation media (gel) in locations where the electrophoretic field is of optimal intensity.
This initial translocation of the sample into the optimal concentration position is referred to as "injection".
The optimal position is determined by the gel geometry and location of the SCODA driving electrodes.
Injection is achieved by the application of a controlled DC electrophoretic field across the sample chamber which results in all charged particles being transferred into the concentration gel.
To obtain a good stacking of the sample (i.e. tight DNA band) multiple methods can be employed.
If the sample chamber buffer has a low conductivity and the concentration gel buffer has a high conductivity this results in a sharp drop off in electric field at the gel-buffer interface which promotes stacking.
Once the DNA is positioned optimally in the concentration gel the SCODA rotating fields are applied.
The frequency of the fields can be tuned such that only specific DNA lengths are concentrated.
To prevent boiling during the concentration stage due to Joule heating the separation medium may be actively cooled.
As only particles that exhibit non-linear velocity experience the SCODA concentrating force, small charged particles that respond linearly to electrophoretic fields are not concentrated.
These particles instead of spiraling towards the center of the SCODA gel orbit at a constant radius.
If a weak DC field is superimposed on the SCODA rotating fields these particles will be "washed" off from the SCODA gel resulting in highly pure DNA remaining in the gel center.
As the DNA does not experience non-linear mobility in buffer it accumulates in the extraction well.
DNA concentration and purification has been achieved directly from tar sands samples resuspended in buffer using the SCODA technique.
DNA sequencing was subsequently performed and tentatively over 200 distinct bacterial genomes have been identified.
An application of this technique is the detection of rare tumour-derived DNA (ctDNA) from blood samples.
