Alignment of λ-DNA on Organic Monolayer Surface Patterned by Scanning Probe Lithography

Abstract

With the combination of a molecular combing technique and scanning probe lithographic patterning,-DNA wires were stretched and aligned to form parallel lines on a patterned organic monolayer surface. The patterned organic monolayer was composed of hydrophilic aminopropyltriethoxysilane (APS) in the middle of hydrophobic octadecyltrichlorosilane (OTS) on a silicon surface. The stretching and alignment of-DNA wires were induced along the lines of the APS layer which attracted-DNA through a coulombic interaction at an early stage of the combing. Weaker van der Waals interaction with the OTS layer induced a settlement of the wire after the sample was dried. The aligned structures were confirmed by tapping-mode atomic force microscope images, aided by positively-charged gold nanoparticles exclusively attached to the DNA backbone.

Selective Formation of a Latticed Nanostructure with the Precise Alignment of DNA-Templated Gold Nanowires

“…This is called a combing process. 23,24 The patterned silicon substrate is immersed in 1.5 mL of a λ-DNA (Bio Basic Inc., 16 μm-long 48 502 bp) solution at a concentration of 1 ng/μL using a TE buffer (10 mM tris-HCl and 1 mM EDTA, pH 8.0). While the sample is immersed in the DNA solution, DNA molecules are strongly bound to the APS region.…”

“…The process of attaching DNA onto the patterned polymer is carried out using a custom-made dipping/pulling machine in which the translation is directed parallel to the patterned lines on the silicon substrate. This is called a combing process. , The patterned silicon substrate is immersed in 1.5 mL of a λ-DNA (Bio Basic Inc., 16 μm-long 48 502 bp) solution at a concentration of 1 ng/μL using a TE buffer (10 mM tris-HCl and 1 mM EDTA, pH 8.0). While the sample is immersed in the DNA solution, DNA molecules are strongly bound to the APS region.…”

“…After the first combed sample is dried for 60 min, a second combing is processed perpendicularly to the first one as patterned (“2nd” in Figure e). Following the alignment process, DNA molecules are treated with a solution of 60 μL of aniline-capped gold nanoparticles (AN-AuNP’s) for 30 min; this solution is prepared on the basis of the conventional reduction of HAuCl 4 (Sigma-Aldrich) using aniline (Sigma-Aldrich) as a reducer; − that is, 0.5 mL of 0.1 mM aniline and 25 mL of 0.03 wt % HAuCl 4 were mixed together, and then the mixture was cooled to 5 °C after being heated to 80 °C for 20 min and was centrifuged at 15 000 rpm for 30 min.…”

Single molecule transcription profiling with AFM

“…The CD44v cDNA sequence corresponds to Genbank accession number BC052287.1. Stretching DNA on surfaces has been researched extensively [170][171][172][173][174][175][176][177][178][179][180][181]. We used fluid flow to stretch cDNAs, a standard technique.…”

Surface Modification of Plasma Polymer Thin Films for DNA Fixation by Atmospheric Pressure Plasma Treatment

“…These methods have employed coatings of patterned aminopropyltriethoxysilane (APS) for attaching the DNA, and octadecyltrichlorosilane (OTS) for passivating the DNA. 1,10) However, such coatings are easily affected by humidity since ethoxysilyl and chlorosilyl groups are easily hydrolyzed, so that it is hard to control precisely the function of the surface. [3][4][5][6][7][8][9] In this work, the plasma polymer thin films and the atmospheric pressure plasma treatment, which were ex-pected to be hardly affected by humidity, was investigated to control the surface density of amine groups and to optimize the surface condition with respect to the subsequent alignment of DNA molecules: lower surface densities make insufficient attachment of DNA and higher surface densities make DNA not to be distributed well on the substrate resulting in lumps of DNA.…”