A DNA-based display console for molecular readouts

We know DNA as the genetic blueprint of life. DNA can be chemically synthesized and used to build nanoscale structures and devices. DNA-based nanodevices can respond to cues such as other molecules, pH, temperature and ionic conditions; such DNA devices are used as biosensors. Some DNA nanodevices are designed to provide visual outputs that tell us about the molecular events that occurred. Scientists have previously used atomic force microscopy (AFM) to display single nucleotide polymorphisms (a DNA sequence variation that causes abnormalities) as alphabetic characters, and to compute simple math such as multiplication the result of which is shown on a nanoscale digital display. In my recent research, shape-changing DNA nanostructures are used to recognize and react to specific input DNA strands, with the resulting output graphically displayed on an agarose gel.

 The nanoswitch is a long linear duplex with single-straned extensions acting as  address  strands. On binding a complementary  input  strand, the nanoswitch changes conformation to a looped state. The  on  and  off  states are easily identifiable on an agarose gel providing a binary readout.

The nanoswitch is a long linear duplex with single-straned extensions acting as address strands. On binding a complementary input strand, the nanoswitch changes conformation to a looped state. The on and off states are easily identifiable on an agarose gel providing a binary readout.

The DNA nanoswitch has two states. The off state is a linear duplex formed by a long single strand (~7 kilobases) hybridized to short complementary backbone oligonucleotides. Two of the backbone oligonucleotides can be modified to contain single-stranded extensions (address strands) that are partly complementary to the input DNA strand. Binding of the input strand to the nanoswitch creates a looped on state that can be easily identified on a gel (see figure on the left).

The DNA nanoswitch is programmable. Address strands can be inserted anywhere along the scaffold thus resulting in different loop sizes. Nanoswitches with multiple address strands are used to create "DNA pixels" that can store and display alphanumeric characters. The read-out of the stored information is inspired by digital display circuits where a series of bits display a particular pattern (for example, a number or a letter). This multi-input nanoswitch can recognize different input strands. These input DNA strands are complementary (i.e. can bind) to a pair of address sites and trigger loops of specific sizes, which result in different bands on a gel (see figure below).

 The nanoswitch (top) can bind five different input strands resulting in five unique loops for each (middle). Selective combinations of input strands can be chosen to display graphical outputs such as alphanumeric characters (bottom).

The nanoswitch (top) can bind five different input strands resulting in five unique loops for each (middle). Selective combinations of input strands can be chosen to display graphical outputs such as alphanumeric characters (bottom).

Now imagine the gel as a segmented display board with a 5x5 readout matrix, where each looped band provides a "pixel" on the matrix. Specific input strands were used to trigger and display three alphabet characters "r", "N", and "A" (see figure on right). While this is not a pixelated image display such as the recent Mona Lisa made out of DNA origami plates, the main use of this system lies in a simple digital output for molecular reactions. We had earlier encoded the words Hello World using this system, erased it using toehold-mediated strand displacement (where the input strand is removed using a fully complementary eraser strand), and rewrote Good Bye on the same system. A library of such nanoswitches with distinct address strand pairs can be the future of point-of-care biosensors and DNA barcodes.

Read the original article published in ChemBioChem here: Reconfigurable DNA nanoswitches for graphical readout of molecular signals.

A version of this post appeared in Science Trends.