Investigations on DNA intercalation and surface binding by SYBR Green I, its structure determination and methodological implications

Nucleic Acids Res. 2004 Jul 12;32(12):e103. doi: 10.1093/nar/gnh101.


The detection of double-stranded (ds) DNA by SYBR Green I (SG) is important in many molecular biology methods including gel electrophoresis, dsDNA quantification in solution and real-time PCR. Biophysical studies at defined dye/base pair ratios (dbprs) were used to determine the structure-property relationships that affect methods applying SG. These studies revealed the occurrence of intercalation, followed by surface binding at dbprs above approximately 0.15. Only the latter led to a significant increase in fluorescence. Studies with poly(dA)* poly(dT) and poly(dG)* poly(dC) homopolymers showed sequence-specific binding of SG. Also, salts had a marked impact on SG fluorescence. We also noted binding of SG to single-stranded (ss) DNA, although SG/ssDNA fluorescence was at least approximately 11-fold lower than with dsDNA. To perform these studies, we determined the structure of SG by mass spectrometry and NMR analysis to be [2-[N-(3-dimethylaminopropyl)-N-propylamino]-4-[2,3-dihydro-3-methyl-(benzo-1,3-thiazol-2-yl)-methylidene]-1-phenyl-quinolinium]. For comparison, the structure of PicoGreen (PG) was also determined and is [2-[N-bis-(3-dimethylaminopropyl)-amino]-4-[2,3-dihydro-3-methyl-(benzo-1,3-thiazol-2-yl)-methylidene]-1-phenyl-quinolinium]+. These structure-property relationships help in the design of methods that use SG, in particular dsDNA quantification in solution and real-time PCR.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cations / pharmacology
  • DNA / analysis
  • DNA / metabolism
  • DNA, Single-Stranded / metabolism
  • Electrophoresis, Agar Gel
  • Fluorescent Dyes / analysis
  • Fluorescent Dyes / chemistry*
  • Fluorescent Dyes / metabolism
  • Intercalating Agents / chemistry*
  • Intercalating Agents / metabolism
  • Macromolecular Substances
  • Organic Chemicals / analysis
  • Organic Chemicals / chemistry*
  • Organic Chemicals / metabolism
  • Polymerase Chain Reaction
  • Spectrophotometry


  • Cations
  • DNA, Single-Stranded
  • Fluorescent Dyes
  • Intercalating Agents
  • Macromolecular Substances
  • Organic Chemicals
  • PicoGreen
  • SYBR Green I
  • DNA