Nucleic Acid Supercoiling as a Means for Ionic Switching of DNA–Nanoparticle Networks

Abstract

Oligomeric nanoparticle networks, generated by the self-assembly of bis-biotinylated double-stranded DNA fragments and streptavidin, have been studied by scanning force microscopy (SFM). SFM imaging revealed the presence within the networks of irregular thick DNA molecules, which were often associated with distinct, Y-shaped structural elements. Closer analysis revealed that the Y structures are formed by condensation (thickening and shortening) of two DNA fragments, most likely through the supercoiling of two DNA molecules bound to adjacent binding sites of the streptavidin particle. The frequency of supercoiling was found to be dependent on the ionic strength applied during the immobilization of the oligomeric networks on mica surfaces. Potential applications of the structural changes as a means for constructing ion-dependent molecular switches in nanomaterials are discussed.

Real-time imaging of DNA–streptavidin complex formation in solution using a high-speed atomic force microscope

“…2(c), yellow arrows). We rarely found streptavidin with four DNA fragments attached, which is consistent with a previous report [3].…”

Real-time imaging of DNA–streptavidin complex formation in solution using a high-speed atomic force microscope

“…2(c), yellow arrows). We rarely found streptavidin with four DNA fragments attached, which is consistent with a previous report [3].…”

Rapid Detection of Drugs in Human Plasma Using a Small-Molecule-Linked Hybridization Chain Reaction

“…Although streptavidin has four binding sites enabling quadruple biotin binding, it is wellknown that the affinity decreases after two binding sites of streptavidin have been occupied. 29 Therefore, 2 equiv of antibody is employed in the following experiments. As such, the optimal setup for small molecule detection is 200 nM hairpins, an initiator/hairpin ratios of 0.35 for Dig and 0.5 for MTX, and the use of 2 equiv of protein at 25 °C.…”

Detection of Staphylococcus aureus toxins using immuno-PCR

“…For DNA tags we used supramolecular complexes [(biotin)DNA(biotin) streptavidin] n [16,19], the conditions for preparation of these complexes were developed in this study. For this purpose single stranded oligodeoxynucleotides (oligo(N)) with lengths of 60 bp with one (Bt oligo(N) and two mole cules of biotin (Bt 2 oligo (N)) were synthesized.…”

Real-time imaging of DNA–streptavidin complex formation in solution using a high-speed atomic force microscope

“…2(c), yellow arrows). We rarely found streptavidin with four DNA fragments attached, which is consistent with a previous report [3].…”

Rapid Detection of Drugs in Human Plasma Using a Small-Molecule-Linked Hybridization Chain Reaction

“…Although streptavidin has four binding sites enabling quadruple biotin binding, it is wellknown that the affinity decreases after two binding sites of streptavidin have been occupied. 29 Therefore, 2 equiv of antibody is employed in the following experiments. As such, the optimal setup for small molecule detection is 200 nM hairpins, an initiator/hairpin ratios of 0.35 for Dig and 0.5 for MTX, and the use of 2 equiv of protein at 25 °C.…”

Detection of Staphylococcus aureus toxins using immuno-PCR

“…For DNA tags we used supramolecular complexes [(biotin)DNA(biotin) streptavidin] n [16,19], the conditions for preparation of these complexes were developed in this study. For this purpose single stranded oligodeoxynucleotides (oligo(N)) with lengths of 60 bp with one (Bt oligo(N) and two mole cules of biotin (Bt 2 oligo (N)) were synthesized.…”

Real-time imaging of DNA–streptavidin complex formation in solution using a high-speed atomic force microscope

“…2(c), yellow arrows). We rarely found streptavidin with four DNA fragments attached, which is consistent with a previous report [3].…”

Rapid Detection of Drugs in Human Plasma Using a Small-Molecule-Linked Hybridization Chain Reaction

“…Although streptavidin has four binding sites enabling quadruple biotin binding, it is wellknown that the affinity decreases after two binding sites of streptavidin have been occupied. 29 Therefore, 2 equiv of antibody is employed in the following experiments. As such, the optimal setup for small molecule detection is 200 nM hairpins, an initiator/hairpin ratios of 0.35 for Dig and 0.5 for MTX, and the use of 2 equiv of protein at 25 °C.…”

Detection of Staphylococcus aureus toxins using immuno-PCR

“…For DNA tags we used supramolecular complexes [(biotin)DNA(biotin) streptavidin] n [16,19], the conditions for preparation of these complexes were developed in this study. For this purpose single stranded oligodeoxynucleotides (oligo(N)) with lengths of 60 bp with one (Bt oligo(N) and two mole cules of biotin (Bt 2 oligo (N)) were synthesized.…”