Tribological effects on DNA translocation in a nanochannel coated with a self-assembled monolayer.
A biomimetic nanochannel coated with a self-assembled monolayer (SAM) can be used for sensing and analyzing biomolecules. The interaction between a transported biomolecule and a SAM governs the mechanically or electrically driven motion of the molecule. To investigate the translocation dynamics of a biomolecule, we performed all-atom molecular dynamics simulations on a single-stranded DNA in a solid-state nanochannel coated with a SAM that consists of octane or octanol polymers. Simulation results demonstrate that the interaction between DNA and a hydrophobic or a hydrophilic SAM is effectively repulsive or adhesive, respectively, resulting in different translocation dynamics of DNA. Therefore, with proper designs of SAMs coated on a channel surface, it is possible to control the translocation dynamics of a biomolecule. This work also demonstrates that traditional tribology methods can be deployed to study a biological or biomimetic transport process.
IBM T. J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, New York 10598, USA. bluan@us.ibm.com
Binquan
B
Luan
Ali
A
Afzali
Stefan
S
Harrer
Hongbo
H
Peng
Philip
P
Waggoner
Stas
S
Polonsky
Gustavo
G
Stolovitzky
Glenn
G
Martyna
D040761:Biomimetic Materials / Q000737:chemistry; D004277:DNA, Single-Stranded / Q000737:chemistry* / Q000378:metabolism; D057927:Hydrophobic and Hydrophilic Interactions; D056004:Molecular Dynamics Simulation; D049329:Nanostructures / Q000737:chemistry*
D004277:DNA, Single-Stranded