A general design strategy for protein-responsive riboswitches in mammalian cells

Nat Methods. 2014 Nov;11(11):1154-60. doi: 10.1038/nmeth.3136. Epub 2014 Oct 5.


RNAs are ideal for the design of gene switches that can monitor and program cellular behavior because of their high modularity and predictable structure-function relationship. We have assembled an expression platform with an embedded modular ribozyme scaffold that correlates self-cleavage activity of designer ribozymes with transgene translation in bacteria and mammalian cells. A design approach devised to screen ribozyme libraries in bacteria and validate variants with functional tertiary stem-loop structures in mammalian cells resulted in a designer ribozyme with a protein-binding nutR-boxB stem II and a selected matching stem I. In a mammalian expression context, this designer ribozyme exhibited dose-dependent translation control by the N-peptide, had rapid induction kinetics and could be combined with classic small molecule-responsive transcription control modalities to construct complex, programmable genetic circuits.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alkaline Phosphatase / biosynthesis*
  • Alkaline Phosphatase / genetics*
  • Animals
  • Binding Sites / genetics
  • CHO Cells
  • Cricetulus
  • GPI-Linked Proteins / biosynthesis
  • GPI-Linked Proteins / genetics
  • Gene Expression
  • Gene Regulatory Networks*
  • Green Fluorescent Proteins / genetics
  • HEK293 Cells
  • HeLa Cells
  • Humans
  • Isoenzymes / biosynthesis*
  • Isoenzymes / genetics*
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Protein Biosynthesis*
  • RNA, Catalytic / chemistry
  • RNA, Catalytic / genetics
  • RNA, Catalytic / metabolism*
  • RNA, Messenger / biosynthesis
  • RNA, Messenger / genetics
  • Riboswitch*
  • Structure-Activity Relationship
  • Transgenes*
  • Viral Proteins / genetics
  • Viral Proteins / metabolism


  • GPI-Linked Proteins
  • Isoenzymes
  • NutR protein, bacteriophage lambda
  • RNA, Catalytic
  • RNA, Messenger
  • Riboswitch
  • Viral Proteins
  • enhanced green fluorescent protein
  • Green Fluorescent Proteins
  • Alkaline Phosphatase
  • alkaline phosphatase, placental

Associated data

  • GENBANK/KM403566
  • GENBANK/KM403567
  • GENBANK/KM403568
  • GENBANK/KM403569