Eur Biophys J (2017) 46:541–547
Adsorption of DNA binding proteins to functionalized carbon
nanotube surfaces with and without DNA wrapping
· Shusuke Oura
· Kazuo Umemura
Received: 29 September 2016 / Revised: 12 December 2016 / Accepted: 2 February 2017 / Published online: 15 February 2017
© European Biophysical Societies’ Association 2017
from the differing perspectives of materials science and
biosciences (Martin and Kohli 2003; Nakashima et al.
2003; Umemura 2015; Umemura et al. 2016a; Williams
et al. 2002; Zheng et al. 2003). In the former discipline,
hybridization techniques were established for solubiliza-
tion of SWNTs because wrapping SWNT surfaces with
DNA molecules allows the preparation of mono-disperse
SWNT suspensions (Gigliotti et al. 2006; Hayashida et al.
2013; Hayashida and Umemura 2013; Nii et al. 2013). In
bioscience applications, DNA wrapped SWNTs can be
employed as nanobiodevices (Becerril and Woolley 2009;
Cheung et al. 2009; Daniel et al. 2007; Oura and Umemura
2016; Pividori and Alegret 2005; Tu and Zheng 2008).
Several authors have proposed novel methods for detect-
ing single-mismatches between two DNA molecules using
DNA-SWNT hybrids (Li et al. 2011; Yang et al. 2008). In
these applications, an SWNT surface was coated with a
single-stranded DNA (ssDNA), and a second ssDNA was
reacted with the ssDNA-SWNT hybrid. Interestingly, Li
et al. found that multi-walled carbon nanotubes (MWNTs)
also have advantages for detection. Furthermore, single-
mismatch detection techniques using various nanomaterials
such as polymer nanoﬁbers have been reported recently (Li
and Sun 2011; Liu et al. 2011; Tian et al. 2015; Wang et al.
2011). The progress of DNA detection technology using
nanomaterials in the past 5 years is remarkable.
We have previously studied the interaction of DNA bind-
ing proteins with DNA molecules on SWNT surfaces (Nii
et al. 2014; Oura et al. 2015; Oura and Umemura 2016).
There are many types of DNA binding proteins e.g., DNA
polymerase, topoisomerase, single-stranded DNA binding
(SSB) proteins, and RecA proteins. If biochemical reac-
tions can be controlled on SWNT surfaces, the technique
might be useful for analysis of single-molecule behavior, as
well as single-mismatch detection in DNA studies.
Abstract We examined the adsorption of DNA binding
proteins on functionalized, single-walled carbon nanotubes
(SWNTs). When SWNTs were functionalized with polyeth-
ylene glycol (PEG-SWNT), moderate adsorption of protein
molecules was observed. In contrast, nanotubes functional-
ized with CONH
-SWNT) exhibited very
strong interactions between the CONH
-SWNT and DNA
binding proteins. Instead, when these SWNT surfaces were
wrapped with DNA molecules (thymine 30-mers), protein
binding was a little decreased. Our results revealed that DNA
wrapped PEG-SWNT was one of the most promising can-
didates to realize DNA nanodevices involving protein reac-
tions on DNA-SWNT surfaces. In addition, the DNA bind-
ing protein RecA was more adhesive than single-stranded
DNA binding proteins to the functionalized SWNT surfaces.
Keywords DNA · Single-walled carbon nanotubes · DNA
binding proteins · Atomic force microscopy · Polyethylene
The hybridization of single-walled carbon nanotubes
(SWNTs) and DNA molecules has been intensively studied
Electronic supplementary material The online version of this
article (doi:10.1007/s00249-017-1200-3) contains supplementary
material, which is available to authorized users.
* Kazuo Umemura
Biophysics Section, Department of Physics, Graduate School
of Science, Tokyo University of Science, 1-3 Kagurazaka,
Shinjuku, Tokyo 1628601, Japan