You’ve heard of 4D cinema, 4D digital printing, etc.… Now, gradients too come in dimensions?!
Indeed, 1D and 2D in gradient refers to 1-dimensional and 2-dimensional, respectively. Optimization of a new PCR protocol can be highly tedious, time-consuming and costly work. To address this, many conventional cyclers in the market now comes with gradient function. The gradient PCR you are familiar with is most probably the 1D generation technology. This one-dimensional gradient technology was pioneered by Eppendorf decades ago and was one of the most revolutionary function that drove the PCR field.
Now, we see another revolution in the gradient technology – the 2-dimensional or 2D-gradient. This technology enables the user to use two gradient steps in the same PCR. The original 1D-gradient gives 12 different temperatures horizontally across the block (some brand uses 8 temperatures across the rows from top to bottom strategy). With the new 2D-gradient, the thermal block can now additionally give 8 different temperatures vertically across the block. Both 2 gradients can be combined in one PCR program, thus allowing concurrent optimization of the denaturation step and the annealing step.
So, this is how the 2D-gradient works: 1 dimension is the original gradient that you are used to, which is horizontally from left to right across the block, giving 12 different temperatures. Another dimension is vertically from bottom to top, giving 8 temperatures across the thermal block. When used together in a program, for example first in the denaturation step then followed by in the annealing step, this matrix-style optimization will show the optimal yield and specificity amplification result.