title: Counting the number of magnesium ions bound to the surface-immobilized thymine oligonucleotides that comprise spherical nucleic acids.
abstract: Label-free studies carried out under aqueous phase conditions quantify the number of Mg(2+) ions binding to surface-immobilized T40 sequences, the subsequent reordering of DNA on the surface, and the consequences of Mg(2+) binding for DNA-DNA interactions. Second harmonic generation measurements indicate that, within error, 18-20 Mg(2+) 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 Mg(2+) 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 Mg(2+) 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 Mg(2+) 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 Mg(2+) ions are bound; and (3) highly stable duplexes having a Tm of 64(2)°C form if 18.5-19.0 Mg(2+) ions are bound, corresponding to saturation of the T40 strand.
authors.affiliation: Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States.
authors.forename: Stephanie R
authors.initials: SR
authors.lastname: Walter
authors.forename: Kaylie L
authors.initials: KL
authors.lastname: Young
authors.forename: Joseph G
authors.initials: JG
authors.lastname: Holland
authors.forename: Richard L
authors.initials: RL
authors.lastname: Gieseck
authors.forename: Chad A
authors.initials: CA
authors.lastname: Mirkin
authors.forename: Franz M
authors.initials: FM
authors.lastname: Geiger
mesh_terms: D004247:DNA / Q000737:chemistry*; D007477:Ions / Q000737:chemistry; D008274:Magnesium / Q000737:chemistry*; D015394:Molecular Structure; D009841:Oligonucleotides / Q000737:chemistry*; D013499:Surface Properties; D013941:Thymine / Q000737:chemistry*
chemical_list: D007477:Ions; D009841:Oligonucleotides; D004247:DNA; D008274:Magnesium; D013941:Thymine