Editorial Feature

Using DNA Microscopy to Capture Cells at Genomic Levels

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The recent introduction of a novel DNA microscopy technique developed by MIT researchers hopes to overcome current microscopy limitations for the visualization of genetic material.

Integrating Microscopy and Genomics

Since the first light microscope was developed hundreds of years ago, the microscopy of both cells and tissues has remained an essential component of almost every scientific advancement. As researchers have become increasingly interested in identifying and measuring the specific genomic sequences present in tissues, particularly tumors, they have had to turn to a number of separate genetic assays due to the inherent limitations of most microscopy techniques for this purpose.

Some of the earliest developments of hybridization methods emerged in an effort to bridge the gap that traditionally existed between the microscopic analysis of tissues and both genomic and transcriptomic sequencing. These approaches have recently progressed towards current optical readout methods that integrate experimental systems with both physical registration and molecule mapping technology. When these methods are not employed, researchers instead will rely upon data gathered from similar samples in order to correlate genetic information.

What is DNA Microscopy?

In a June 2019 Cell paper, a group of researchers from the Massachusetts Institute of Technology (MIT) proposed a novel technique they refer to as DNA microscopy. This distinct imaging modality is capable of capturing physical images of specimens and encoding this information for the reconstruction of DNA molecules and their respective positions. Similar to the way in which light microscopy utilizes the interaction between specimens and photons to generate an image, DNA microscopy relies upon the interaction between the imaging molecules and the genetic material of interest.

DNA Microscopy Methodology

The methodology behind this DNA microscopy technique begins with fixing the cells and synthesizing their cDNA for beacon and target transcripts with randomized nucleotides (UMIs) that will tag individual DNA or RNA molecules. UMIs are comprised of randomized bases that tag a genetic molecule, like RNA or DNA, prior to any copies of the genetic material that are made. The UMIs developed by these researchers have been specifically designed to ensure that the tagging of a DNA or RNA molecule by a UMI will not be repeated in the event that these markers come into contact with another genetic molecule.

Following this process, each UMI-tagged cDNA molecule is uniquely labeled and amplified in order to allow for their communication with neighboring molecules. Each of these concatenation events, which is achieved through the use of overlap extension polymerase chain reaction (PCR), is subsequently labeled with randomized nucleotides in order to generate unique event identifiers (UEIs).

Depending upon the degree of diffusion that exists between the centers, each UMI-tagged DNA molecule determines the frequency by which UEIs will appear. These frequencies will ultimately be determined by DNA sequencing, followed by insertion into a UEI matrix that is used to infer their original UMI positions. Local investigations can also be performed by utilizing a “zoom” function, which involves the application of a recursive graph-cut algorithm that separates subsets of UMIs for sub-region visualization.


In order to test the efficacy of their DNA microscopy technique, the researchers of this study attempted to image the genetic transcripts that belonged to two co-cultured human cell lines of GFP-expressing MDA-MBN-231 cells and RFP-expressing BT-549 cells. When utilizing the methodology of their DNA microscopy technique, the researchers were able to observe both cellular and local supra-cellular resolution of their tagged molecules.


Overall, the revolutionary imaging technique developed by this MIT group successfully tagged biomolecules with UMIs in order to gain meaningful and spatial information on a specimen’s genetic material. Some improvements that must still be made in order to enhance the applicability of this technique is to produce high-quality reconstructions of samples over larger lengths in order to reduce the occurrence of any molecular density gaps. While both analytical and experimental solutions to this problem have been proposed, their incorporation into the original DNA microscopy technique must still be considered.


  • Weinstein, J. A., Regev, A., & Zhang, F. (2019). DNA Microscopy: Optics-free Spatio-genetic Imaging by a Stand-Alone Chemical Reaction. Cell 178(1); 229-241. DOI: 10.1016/j.cell.2019.05.019.

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Benedette Cuffari

Written by

Benedette Cuffari

After completing her Bachelor of Science in Toxicology with two minors in Spanish and Chemistry in 2016, Benedette continued her studies to complete her Master of Science in Toxicology in May of 2018. During graduate school, Benedette investigated the dermatotoxicity of mechlorethamine and bendamustine; two nitrogen mustard alkylating agents that are used in anticancer therapy.


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