Sizing up DNA nanostructure assembly with native mass spectrometry and ion mobility

Interest in oligonucleotide nanostructures has recently surged in basic and applied research. Here, the authors use native mass spectrometry and ion mobility to elucidate a prototypical hexameric DNA barrel structure as well as intermediates and byproducts of the assembly reaction. Recent interest in biological and synthetic DNA nanostructures has highlighted the need for methods to comprehensively characterize intermediates and end products of multimeric DNA assembly. Here we use native mass spectrometry in combination with ion mobility to determine the mass, charge state and collision cross section of noncovalent DNA assemblies, and thereby elucidate their structural composition, oligomeric state, overall size and shape. We showcase the approach with a prototypical six-subunit DNA nanostructure to reveal how its assembly is governed by the ionic strength of the buffer, as well as how the mass and mobility of heterogeneous species can be well resolved by careful tuning of instrumental parameters. We find that the assembly of the hexameric, barrel-shaped complex is guided by positive cooperativity, while previously undetected higher-order 12- and 18-mer assemblies are assigned to defined larger-diameter geometric structures. Guided by our insight, ion mobility-mass spectrometry is poised to make significant contributions to understanding the formation and structural diversity of natural and synthetic oligonucleotide assemblies relevant in science and technology.

Automated summary

Recent interest in oligonucleotide nanostructures has led to the use of mass spectrometry and ion mobility to study their assembly. In this study, the authors use these techniques to characterize the structure of a hexameric DNA barrel and its intermediates and byproducts. They demonstrate the ability of these methods to determine the mass, charge state, and size of noncovalent DNA assemblies and reveal the role of ionic strength in their assembly. They also identify previously undetected higher-order assemblies and assign them to larger geometric structures.