Nano-Analysis of DNA Conformation Changes Induced by Transcription Factor Complex Binding Using Plasmonic Nanodimers

Abstract

The plasmon resonant wavelength for a pair of gold nanoparticles, or gold nanodimer, increases inversely with the gap distance between the two nanoparticles. Taking advantage of this property, we performed nanoscale measurements of DNA conformation changes induced by transcription factor binding. Gold nanoparticles were bridged by double-stranded DC5 DNA that included binding sequences for the transcription factors SOX2 and PAX6, which interact on the DC5 enhancer sequence and activate transcription. The gold nanodimers bound by SOX2 shifted the plasmon resonant wavelength from 586.8 to 604.1 nm, indicating that SOX2 binding induces DNA bending. When the SOX2 formed a ternary complex with PAX6 on DC5, the plasmon resonant wavelength showed a further shift to 611.6 nm, indicating additional bending in the DC5 sequence. Furthermore, we investigated DNA conformation changes induced by SOX2 and PAX6 on the DC5-con sequence, which is a consensus sequence of DC5 for the PAX6 binding region that strengthens the PAX6 binding but at the same time disrupts SOX2-PAX6-dependent transcriptional activation. When the PAX6 binding sequence in DC5 was altered to DC5-con, the plasmon resonant wavelength shifted much less to 606.5 nm, which is more comparable to the 603.9 nm by SOX2 alone. These results demonstrate that SOX2-PAX6 cobinding induces a large conformation change in DC5 DNA.

DNA-mediated cooperativity facilitates the co-selection of cryptic enhancer sequences by SOX2 and PAX6 transcription factors

“…A recent study on Sox2 and Pax6 cooperativity used plasmon resonance and gold nanoparticles tethered to the end of DC5 and DC5con sequences. While Sox2 alone induced indistinguishable bends, it was reported that the DC5 is more markedly deformed by Sox2–Pax6 dimers than the DC5con element ( 65 ). Apparently, Sox2–Pax6 binding induces structural changes to DNA in a sequence-dependent manner.…”

Increasing the Morphological Stability of DNA-Templated Nanostructures with Surface Hydrophobicity

“…The programmed assembly of gold nanoparticles (AuNPs) on DNA scaffolds is a powerful technique to design metamaterials for applications such as plasmon‐enhanced spectroscopy, chemical sensing, and molecular rulers, as well as for the development of novel imaging and therapeutic agents . All of these examples rely on the collective optical response of AuNP groupings and therefore on distance‐dependent plasmon coupling.…”

Nanoparticle sizing method based on fluorescence anisotropy analysis

“…We used DNA strands with 23 bases. Given the lengths of particlethiol and DNA-fluorophore linkers (%1.8 nm) [18][19][20], the distance between the fluorophore and metal particles is about 9.6 nm, which is longer than the Forster distance, 9 nm, calculated by Yun for case of energy transfer from an organic fluorophore to a gold nanoparticle [17]. Therefore, the energy transfer efficiency is below 50%, and sufficient fluorescence intensity can be obtained for performing measurements.…”