Journal: Nucleic Acids Research

Article Title: Selection of DNA nanoparticles with preferential binding to aggregated protein target

doi: 10.1093/nar/gkw136

Figure Lengend Snippet: Selection of streptavidin-binding DeNAno. ( A ) Schematic of selection process. ( B ) Staining of streptavidin selection rounds 1–5. Probe-only, library and positive control (biotinylated library) are also shown. ( C ) Staining of four selected streptavidin clones on streptavidin beads and BSA-coated beads. Negative control clone (G10neg) and biotinylated positive control clone (G10bio) also shown.

Article Snippet: Streptavidin-coated magnetic beads (NEB) were used for selections/staining for streptavidin-specific DeNAno with no modifications.

Techniques: Selection, Binding Assay, Staining, Positive Control, Clone Assay, Negative Control

Journal: Nucleic Acids Research

Article Title: Selection of DNA nanoparticles with preferential binding to aggregated protein target

doi: 10.1093/nar/gkw136

Figure Lengend Snippet: Streptavidin clones

Article Snippet: Streptavidin-coated magnetic beads (NEB) were used for selections/staining for streptavidin-specific DeNAno with no modifications.

Techniques:

Journal: Nucleic Acids Research

Article Title: Selection of DNA nanoparticles with preferential binding to aggregated protein target

doi: 10.1093/nar/gkw136

Figure Lengend Snippet: Imaging of DeNAno and staining different size DeNAno. ( A ) Atomic force micrograph (AFM) of dried DeNAno SA-D8 on poly-L-lysine-coated mica. Scale = 400 nm. ( B ) SA-D8 DeNAno roughly 75 nm in diameter as observed by transmission electron microscopy (TEM) using negative staining. Scale = 100 nm. ( C ) TEM of small SA-D8 DeNAno roughly 58 nm in diameter. Scale = 100 nm. ( D ) Binding of streptavidin DeNAno of different sizes made by alteration of dNTP concentration. DeNAno particles were made with 3 nmol dNTPs for 30 m at 30°C (the standard conditions), or 93.8 pmol dNTPs for 30 m at 30°C. A control DeNAno from a different library was also made for both of these conditions and used as an internal control in the staining and subsequent PCR. The ratio of the bound particles (streptavidin DeNAno:control DeNano) to total particles (streptavidin DeNAno:control DeNAno) is graphed.

Article Snippet: Streptavidin-coated magnetic beads (NEB) were used for selections/staining for streptavidin-specific DeNAno with no modifications.

Techniques: Imaging, Staining, Transmission Assay, Electron Microscopy, Negative Staining, Binding Assay, Concentration Assay

Journal: Nucleic Acids Research

Article Title: Selection of DNA nanoparticles with preferential binding to aggregated protein target

doi: 10.1093/nar/gkw136

Figure Lengend Snippet: Dissociation of streptavidin-binding DeNAno over time. Streptavidin-coated magnetic beads were stained with DeNAno particles. The stained beads were then incubated in 10 ml buffer for 35 days. Aliquots were taken every week of the total sample (supernatant plus beads) and supernatant only (beads were removed by magnet). PCR was done on all samples/timepoints and percentage release is graphed (DeNAno in supernatant/DeNAno in total * 100%).

Article Snippet: Streptavidin-coated magnetic beads (NEB) were used for selections/staining for streptavidin-specific DeNAno with no modifications.

Techniques: Binding Assay, Magnetic Beads, Staining, Incubation

Journal: Nucleic Acids Research

Article Title: Selection of DNA nanoparticles with preferential binding to aggregated protein target

doi: 10.1093/nar/gkw136

Figure Lengend Snippet: Competitive titration and competitive release of streptavidin-binding DeNAno with biotin/biotin derivatives or streptavidin. ( A ) Schematic of competitive titration using biotin/biotin derivatives. ( B ) Free biotin (top), desthiobiotin (middle) and 2-iminobiotin (bottom) competition titrations were done by pre-incubating streptavidin beads with one of the biotin/biotin derivatives (or buffer for the baseline), then adding DeNAno particles. ( C ) Schematic of competitive release using biotin/biotin derivatives. ( D ) Biotin (top), desthiobiotin (middle) and 2-iminobiotin (bottom) competitive release assays were done by staining streptavidin beads with DeNAno particles, then adding biotin/biotin derivative (or buffer for baseline). ( E ) Schematic of streptavidin competitive titration. ( F ) Free streptavidin competition titration of SA-D7 and SA-D8 clones and G10bio positive control. Fluorescently-labeled DeNAno particles were pre-incubated with varying concentrations of free streptavidin, then streptavidin beads were added.

Article Snippet: Streptavidin-coated magnetic beads (NEB) were used for selections/staining for streptavidin-specific DeNAno with no modifications.

Techniques: Titration, Binding Assay, Staining, Clone Assay, Positive Control, Labeling, Incubation