Inferred large-scale DNA microscopy image

Individual RNA molecules (coloured dots) in a cell culture. An algorithm picked out the molecules by analysing the products of a chemical reaction and identifying their relative position. Credit: Joshua Weinstein/Broad Institute

Molecular biology

‘Microscope’ made of DNA reveals a cell’s hidden structures

DNA tags can be used to assemble a diagram of the genetic material inside a cell.

An imaging technique that uses chemical reactions instead of light can reveal the spatial organization and sequences of DNA molecules inside cells.

Joshua Weinstein at the Broad Institute in Cambridge, Massachusetts, and his colleagues generated small DNA tags known as unique molecular identifiers (UMIs) and inserted them into cells, where the tags bound to complementary DNA or RNA sequences. The researchers then carried out a process that makes numerous copies of these tagged sequences.

The resulting DNA fragments diffuse between cells and interact with other UMIs, forming DNA or RNA complexes that the researchers can then sequence. The resulting data is fed into a computer algorithm, which uses this information to piece together UMI positions in the cells.

The process allows the researchers to see the arrangement of DNA and RNA in cells, which they say could be helpful in identifying cell types and understanding how cells interact with one another.