Skip to main content
SpringerLink
Log in

Adsorption of DNA binding proteins to functionalized carbon nanotube surfaces with and without DNA wrapping

  • Original Article
  • Published:
European Biophysics Journal Aims and scope Submit manuscript

Abstract

We examined the adsorption of DNA binding proteins on functionalized, single-walled carbon nanotubes (SWNTs). When SWNTs were functionalized with polyethylene glycol (PEG-SWNT), moderate adsorption of protein molecules was observed. In contrast, nanotubes functionalized with CONH2 groups (CONH2-SWNT) exhibited very strong interactions between the CONH2-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 candidates to realize DNA nanodevices involving protein reactions on DNA-SWNT surfaces. In addition, the DNA binding protein RecA was more adhesive than single-stranded DNA binding proteins to the functionalized SWNT surfaces.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Becerril HA, Woolley AT (2009) DNA-templated nanofabrication. Chem Soc Rev 38:329–337

    Article  CAS  PubMed  Google Scholar 

  • Chen RJ, Zhang YG, Wang DW, Dai HJ (2001) Noncovalent sidewall functionalization of single-walled carbon nanotubes for protein immobilization. J Am Chem Soc 123:3838–3839

    Article  CAS  PubMed  Google Scholar 

  • Cheung W, Chiu PL, Parajuli RR, Ma YF, Ali SR, He HX (2009) Fabrication of high performance conducting polymer nanocomposites for biosensors and flexible electronics: summary of the multiple roles of DNA dispersed and functionalized single walled carbon nanotubes. J Mater Chem 19:6465–6480

    Article  CAS  Google Scholar 

  • Daniel S, Rao TP, Rao KS, Rani SU, Naidu GRK, Lee HY, Kawai T (2007) A review of DNA functionalized/grafted carbon nanotubes and their characterization. Sens Actuators B Chem 122:672–682

    Article  CAS  Google Scholar 

  • Fu KF, Huang WJ, Lin Y, Zhang DH, Hanks TW, Rao AM, Sun YP (2002) Functionalization of carbon nanotubes with bovine serum albumin in homogeneous aqueous solution. J Nanosci Nanotechnol 2:457–461

    Article  CAS  PubMed  Google Scholar 

  • Gao JB, Zhao B, Itkis ME, Bekyarova E, Hu H, Kranak V, Yu AP, Haddon RC (2006) Chemical engineering of the single-walled carbon nanotube-nylon 6 interface. J Am Chem Soc 128:7492–7496

    Article  CAS  PubMed  Google Scholar 

  • Gigliotti B, Sakizzie B, Bethune DS, Shelby RM, Cha JN (2006) Sequence-independent helical wrapping of singles-walled carbon nanotubes by long genomic DNA. Nano Lett 6:159–164

    Article  CAS  PubMed  Google Scholar 

  • Hayashida T, Umemura K (2013) Surface morphology of hybrids of double-stranded DNA and single-walled carbon nanotubes studied by atomic force microscopy. Colloids Surf B Biointerfaces 101:49–54

    Article  CAS  PubMed  Google Scholar 

  • Hayashida T, Kawashima T, Nii D, Ozasa K, Umemura K (2013) Kelvin probe force microscopy of single-walled carbon nanotubes modified with DNA or poly(ethylene glycol). Chem Lett 42:666–668

    Article  CAS  Google Scholar 

  • Huang WJ, Taylor S, Fu KF, Lin Y, Zhang DH, Hanks TW, Rao AM, Sun YP (2002) Attaching proteins to carbon nanotubes via diimide-activated amidation. Nano Lett 2:311–314

    Article  CAS  Google Scholar 

  • Li HL, Sun XP (2011) Fluorescence-enhanced nucleic acid detection: using coordination polymer colloids as a sensing platform. Chem Commun 47:2625–2627

    Article  CAS  Google Scholar 

  • Li H, Tian J, Wang L, Zhang Y, Sun X (2011) Multi-walled carbon nanotubes as an effective fluorescent sensing platform for nucleic acid detection. J Mater Chem 21:824–828

    Article  CAS  Google Scholar 

  • Liu S, Wang L, Luo YL, Tian JQ, Li HL, Sun XP (2011) Polyaniline nanofibres for fluorescent nucleic acid detection. Nanoscale 3:967–969

    Article  CAS  PubMed  Google Scholar 

  • Martin CR, Kohli P (2003) The emerging field of nanotube biotechnology. Nat Rev Drug Discov 2:29–37

    Article  CAS  PubMed  Google Scholar 

  • Nakashima N, Okuzono S, Murakami H, Nakai T, Yoshikawa K (2003) DNA dissolves single-walled carbon nanotubes in water. Chem Lett 32:456–457

    Article  CAS  Google Scholar 

  • Nii D, Hayashida T, Umemura K (2013) Controlling the adsorption and desorption of double-stranded DNA on functionalized carbon nanotube surface. Colloids Surf B Biointerfaces 106:234–239

    Article  CAS  PubMed  Google Scholar 

  • Nii D, Hayashida T, Yamaguchi Y, Ikawa S, Shibata T, Umemura K (2014) Selective binding of single-stranded DNA-binding proteins onto DNA molecules adsorbed on single-walled carbon nanotubes. Colloids Surf B Biointerfaces 121:325–330

    Article  CAS  PubMed  Google Scholar 

  • Oura S, Umemura K (2016) Optimal conditions for decorating outer surface of single-walled carbon nanotubes with RecA proteins. Jpn J Appl Phys 55:03DF04

    Article  Google Scholar 

  • Oura S, Ito M, Nii D, Homma Y, Umemura K (2015) Biomolecular recognition ability of RecA proteins for DNA on single-walled carbon nanotubes. Colloids Surf B Biointerfaces 126:496–501

    Article  CAS  PubMed  Google Scholar 

  • Pan B, Xing BS (2008) Adsorption mechanisms of organic chemicals on carbon nanotubes. Environ Sci Technol 42:9005–9013

    Article  CAS  PubMed  Google Scholar 

  • Pividori MI, Alegret S (2005) DNA adsorption on Carbonaceous materials. Immobil DNA Chips I 260:1–36

    Article  CAS  Google Scholar 

  • Tian JQ, Liu Q, Shi JL, Hu JM, Asiri AM, Sun XP, He YQ (2015) Rapid, sensitive, and selective fluorescent DNA detection using iron-based metal-organic framework nanorods: synergies of the metal center and organic linker. Biosens Bioelectron 71:1–6

    Article  PubMed  Google Scholar 

  • Tournus F, Latil S, Heggie MI, Charlier JC (2005) pi-stacking interaction between carbon nanotubes and organic molecules. Phys Rev B 72:075431

    Article  Google Scholar 

  • Tu XM, Zheng M (2008) A DNA-based approach to the carbon nanotube sorting problem. Nano Res 1:185–194

    Article  CAS  Google Scholar 

  • Umemura K (2015) Hybrids of nucleic acids and carbon nanotubes for nanobiotechnology. Nanomaterials 5:321–350

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Umemura K, Izumi K, Oura S (2016a) Probe microscopic studies of DNA molecules on carbon nanotubes. Nanomaterials 6:180

    Article  PubMed Central  Google Scholar 

  • Umemura K, Ishibashi Y, Oura S (2016b) Physisorption of DNA molecules on chemically modified single-walled carbon nanotubes with and without sonication. Eur Biophys J 45:483–489

    Article  CAS  PubMed  Google Scholar 

  • Wang L, Zhang YW, Tian JQ, Li HL, Sun XP (2011) Conjugation polymer nanobelts: a novel fluorescent sensing platform for nucleic acid detection(dagger). Nucl Acids Res 39:e37

    Article  CAS  PubMed  Google Scholar 

  • Williams KA, Veenhuizen PTM, de la Torre BG, Eritja R, Dekker C (2002) Nanotechnology–carbon nanotubes with DNA recognition. Nature 420:761

    Article  CAS  Google Scholar 

  • Yang R, Tang Z, Yan J, Kang H, Kim Y, Zhu Z, Tan W (2008) Noncovalent assembly of carbon nanotubes and single-stranded DNA: an effective sensing platform for probing biomolecular interactions. Anal Chem 80:7408–7413

    Article  CAS  PubMed  Google Scholar 

  • Zhao B, Hu H, Yu AP, Perea D, Haddon RC (2005) Synthesis and characterization of water soluble single-walled carbon nanotube graft copolymers. J Am Chem Soc 127:8197–8203

    Article  CAS  PubMed  Google Scholar 

  • Zheng M, Jagota A, Semke ED, Diner BA, McLean RS, Lustig SR, Richardson RE, Tassi NG (2003) DNA-assisted dispersion and separation of carbon nanotubes. Nat Mater 2:338–342

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This work was supported by a Grant-in-Aid for Scientific Research (26400436) of the Japan Society for the Promotion of Science (JSPS).

Author information

Authors and Affiliations

  1. Biophysics Section, Department of Physics, Graduate School of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku, Tokyo, 1628601, Japan

    Yu Ishibashi, Shusuke Oura & Kazuo Umemura

Authors
  1. Yu Ishibashi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Shusuke Oura
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Kazuo Umemura
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Kazuo Umemura.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PPTX 1150 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Ishibashi, Y., Oura, S. & Umemura, K. Adsorption of DNA binding proteins to functionalized carbon nanotube surfaces with and without DNA wrapping. Eur Biophys J 46, 541–547 (2017). https://doi.org/10.1007/s00249-017-1200-3

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00249-017-1200-3

Keywords

Search

Navigation