title: 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.
authors.affiliation: Department of Applied Physics, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan, ‡Graduate School of Frontier Biosciences, 1-3 Yamada-oka, Suita, Osaka 565-0871, Japan, and §Photonics Advanced Research Center, Osaka University , 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Morimura
authors.forename: Shin-Ichi
authors.initials: S
authors.lastname: Tanaka
authors.forename: Hidekazu
authors.initials: H
authors.lastname: Ishitobi
authors.forename: Tomoyuki
authors.initials: T
authors.lastname: Mikami
authors.forename: Yusuke
authors.initials: Y
authors.lastname: Kamachi
authors.forename: Hisato
authors.initials: H
authors.lastname: Kondoh
authors.forename: Yasushi
authors.initials: Y
authors.lastname: Inouye
mesh_terms: D000818:Animals; D004247:DNA / Q000737:chemistry*; D019281:Dimerization; D005136:Eye Proteins / Q000737:chemistry; D006046:Gold / Q000737:chemistry; D018398:Homeodomain Proteins / Q000737:chemistry; D007313:Insecta; D053768:Metal Nanoparticles / Q000737:chemistry; D053758:Nanoparticles / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D000071841:PAX6 Transcription Factor; D051761:Paired Box Transcription Factors / Q000737:chemistry; D011485:Protein Binding; D011487:Protein Conformation; D012097:Repressor Proteins / Q000737:chemistry; D055748:SOXB1 Transcription Factors / Q000737:chemistry; D055672:Static Electricity; D020349:Surface Plasmon Resonance; D014157:Transcription Factors / Q000737:chemistry*
chemical_list: D005136:Eye Proteins; D018398:Homeodomain Proteins; D000071841:PAX6 Transcription Factor; D051761:Paired Box Transcription Factors; D012097:Repressor Proteins; D055748:SOXB1 Transcription Factors; D014157:Transcription Factors; D006046:Gold; D004247:DNA