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

Area of Science:

• Biochemistry
• Nanotechnology
• Analytical Chemistry

Background:

• Growing interest in biological and synthetic DNA nanostructures necessitates advanced characterization techniques.
• Understanding the formation and structure of multimeric DNA assemblies is crucial for their applications.

Purpose of the Study:

• To establish native mass spectrometry coupled with ion mobility as a method for characterizing noncovalent DNA assemblies.
• To elucidate the structural composition, oligomeric state, size, and shape of DNA nanostructures.

Main Methods:

• Utilized native mass spectrometry (MS) combined with ion mobility (IM).
• Determined mass, charge state, and collision cross section (CCS) of DNA assemblies.
• Analyzed a prototypical six-subunit DNA nanostructure assembly process.

Main Results:

• Characterized the influence of ionic strength on DNA nanostructure assembly.
• Resolved heterogeneous species by optimizing instrumental parameters.
• Identified positive cooperativity in hexameric complex formation.
• Discovered and assigned previously undetected 12- and 18-mer assemblies to specific geometric structures.

Conclusions:

• Native MS-IM is effective for detailed structural analysis of DNA nanostructures.
• The study provides insights into the assembly mechanisms and structural diversity of DNA assemblies.
• This technique holds significant potential for advancing research in natural and synthetic oligonucleotide assemblies.