Counting the number of magnesium ions bound to the surface-immobilized thymine oligonucleotides that comprise spherical nucleic acids

Stephanie R. Walter, Kaylie L. Young, Joseph G. Holland, Richard L. Gieseck, Chad A. Mirkin, Franz M. Geiger*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

13 Scopus citations

Abstract

Label-free studies carried out under aqueous phase conditions quantify the number of Mg2+ ions binding to surface-immobilized T40 sequences, the subsequent reordering of DNA on the surface, and the consequences of Mg2+ binding for DNA-DNA interactions. Second harmonic generation measurements indicate that, within error, 18-20 Mg2+ ions are bound to the T40 strand at saturation and that the metal-DNA interaction is associated with a near 30% length contraction of the strand. Structural reordering, evaluated using vibrational sum frequency generation, atomic force microscopy, and dynamic light scattering, is attributed to increased charge screening as the Mg2+ ions bind to the negatively charged DNA, reducing repulsive Coulomb forces between nucleotides and allowing the DNA single strands to collapse or coil upon themselves. The impact of Mg 2+ binding on DNA hybridization and duplex stability is assessed with spherical nucleic acid (SNA) gold nanoparticle conjugates in order to determine an optimal working range of Mg2+ concentrations for DNA-DNA interactions in the absence of NaCl. The findings are consistent with a charge titration effect in which, in the absence of NaCl, (1) hybridization does not occur at room temperature if an average of 17.5 or less Mg2+ ions are bound per T40 strand, which is not reached until the bulk Mg 2+ concentration approaches 0.5 mM; (2) hybridization proceeds, albeit with low duplex stability having an average Tm of 31(3) C, if an average of 17.5-18.0 Mg2+ ions are bound; and (3) highly stable duplexes having a Tm of 64(2) C form if 18.5-19.0 Mg2+ ions are bound, corresponding to saturation of the T40 strand.

Original languageEnglish (US)
Pages (from-to)17339-17348
Number of pages10
JournalJournal of the American Chemical Society
Volume135
Issue number46
DOIs
StatePublished - Nov 20 2013

ASJC Scopus subject areas

  • Catalysis
  • Chemistry(all)
  • Biochemistry
  • Colloid and Surface Chemistry

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