Systems NMR: single-sample quantification of RNA, proteins and metabolites for biomolecular network analysis

Nat Methods. 2019 Aug;16(8):743-749. doi: 10.1038/s41592-019-0495-7. Epub 2019 Jul 29.


Cellular behavior is controlled by the interplay of diverse biomolecules. Most experimental methods, however, can only monitor a single molecule class or reaction type at a time. We developed an in vitro nuclear magnetic resonance spectroscopy (NMR) approach, which permitted dynamic quantification of an entire 'heterotypic' network-simultaneously monitoring three distinct molecule classes (metabolites, proteins and RNA) and all elementary reaction types (bimolecular interactions, catalysis, unimolecular changes). Focusing on an eight-reaction co-transcriptional RNA folding network, in a single sample we recorded over 35 time points with over 170 observables each, and accurately determined five core reaction constants in multiplex. This reconstruction revealed unexpected cross-talk between the different reactions. We further observed dynamic phase-separation in a system of five distinct RNA-binding domains in the course of the RNA transcription reaction. Our Systems NMR approach provides a deeper understanding of biological network dynamics by combining the dynamic resolution of biochemical assays and the multiplexing ability of 'omics'.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Gene Regulatory Networks*
  • HEK293 Cells
  • Humans
  • Metabolome*
  • Nuclear Magnetic Resonance, Biomolecular / methods*
  • Nucleic Acid Conformation
  • Protein Conformation
  • Proteins / analysis*
  • Proteins / chemistry
  • RNA / analysis*
  • RNA / chemistry
  • RNA Folding


  • Proteins
  • RNA