Analytical and Bioanalytical Chemistry

, Volume 390, Issue 6, pp 1595–1603 | Cite as

Binding of hairpin polyamides to DNA studied by fluorescence correlation spectroscopy for DNA nanoarchitectures

  • Chayan K. Nandi
  • Partha P. Parui
  • Thorsten L. Schmidt
  • Alexander Heckel
  • Bernhard Brutschy
Original Paper


We have recently constructed a “DNA strut” consisting of two DNA-binding hairpin polyamides of Dervan-type connected via a long flexible linker and were able to show that this strut can be used to sequence-selectively connect DNA helices. This approach provides a second structural element (besides the Watson–Crick base pairing) for the assembly of higher-order DNA nanoarchitectures from smaller DNA building blocks. Since none of the existing analytical techniques for studying this kind of system were found suitable for detection and quantification of the formation of the resulting complexes, we chose fluorescence correlation spectroscopy (FCS). In the present study we show that FCS allowed us in a versatile and fast way to investigate the binding of Dervan polyamides to DNA. In particular it also shows its power in the quantitative detection of the formation of multimeric complexes and the in investigation of binding under nonphysiological conditions.


Fluorescence correlation spectroscopy DNA-binding polyamides DNA nanoarchitectures Single molecule spectroscopy Multimeric complexes 



CKN is grateful for a scholarship from the Alexander von Humboldt-Foundation. This work was supported by the DFG (SFB 624, SFB 579 and Cluster of Excellence “Macromolecular Complexes” EXC115).

Supplementary material

216_2008_1852_MOESM1_ESM.doc (439 kb)
ESM 1 (DOC 439 kb)


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Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  1. 1.Institute for Physical and Theoretical ChemistryUniversity of FrankfurtFrankfurtGermany
  2. 2.Cluster of Excellence Macromolecular Complexes, c/o Institute for Organic Chemistry and Chemical BiologyUniversity of FrankfurtFrankfurtGermany

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