Duplex DNA/Graphene Oxide Biointerface: From Fundamental Understanding to Specific Enzymatic Effects

The exploration and fabrication of nano-biointerfaces have fundamental significance and practical importance in many fields including chemistry, biology, and materials science. Recently, the integration of DNA with graphene has been substantially advanced. It is well known that single-stranded (ss) DNA can interact with graphene (or graphene oxide) via π–π stacking. However, for the case of DNA duplex/graphene, the studies are still not conclusive. Most work does not address the question of whether or how dsDNA is attracted to graphene oxide (GO). Here the interaction of DNA/GO is systematically investigated and its nanobiological effects, molecular recognition, and biosensing are explored. It is demonstrated that GO can adsorb DNA duplexes, which is possibly facilitated by partial deformation of the double helix on GO. Additionally dsDNA on GO shows specific effects on enzymatic degradation, which could be effectively cleaved by DNA enzyme I and restriction endonucleases as EcoR I, whereas it is highly resistant to degradation by Exo III. An improved understanding of the behavior of these GO/DNA entities will facilitate the development of applications in biomedicine, biosensing, and bionanotechnology.

[1]  Ronghua Yang,et al.  Noncovalent assembly of carbon nanotubes and single-stranded DNA: an effective sensing platform for probing biomolecular interactions. , 2008, Analytical chemistry.

[2]  Chad A. Mirkin,et al.  Oligonucleotide-Modified Gold Nanoparticles for Intracellular Gene Regulation , 2006, Science.

[3]  Efthimios Kaxiras,et al.  Carbon nanotube interaction with DNA. , 2005, Nano letters.

[4]  M. Dresselhaus,et al.  Structure-Based Carbon Nanotube Sorting by Sequence-Dependent DNA Assembly , 2003, Science.

[5]  Jannik C. Meyer,et al.  The structure of suspended graphene sheets , 2007, Nature.

[6]  G. N. Sastry,et al.  Quantum Mechanical Study of Physisorption of Nucleobases on Carbon Materials: Graphene versus Carbon Nanotubes , 2011 .

[7]  Jian-hui Jiang,et al.  Graphene fluorescence resonance energy transfer aptasensor for the thrombin detection. , 2010, Analytical chemistry.

[8]  A. Patil,et al.  Aqueous Stabilization and Self‐Assembly of Graphene Sheets into Layered Bio‐Nanocomposites using DNA , 2009 .

[9]  Ying Wang,et al.  Preparation, Structure, and Electrochemical Properties of Reduced Graphene Sheet Films , 2009 .

[10]  G. Jiang,et al.  C60 affects DNA replication in vitro by decreasing the melting temperature of DNA templates , 2009 .

[11]  Shouwu Guo,et al.  Adsorption of double-stranded DNA to graphene oxide preventing enzymatic digestion. , 2011, Nanoscale.

[12]  Herman O. Sintim,et al.  Junction probes - sequence specific detection of nucleic acids via template enhanced hybridization processes. , 2008, Journal of the American Chemical Society.

[13]  X. Qu,et al.  Triplex inducer-directed self-assembly of single-walled carbon nanotubes: a triplex DNA-based approach for controlled manipulation of nanostructures , 2011, Nucleic acids research.

[14]  Jinghong Li,et al.  Sensitive and rapid screening of T4 polynucleotide kinase activity and inhibition based on coupled exonuclease reaction and graphene oxide platform. , 2011, Analytical chemistry.

[15]  V. Maheshwari,et al.  Adsorption and desorption of DNA on graphene oxide studied by fluorescently labeled oligonucleotides. , 2011, Langmuir : the ACS journal of surfaces and colloids.

[16]  Kemin Wang,et al.  Bioconjugated nanoparticles for DNA protection from cleavage. , 2003, Journal of the American Chemical Society.

[17]  Longhua Tang,et al.  DNA-directed self-assembly of graphene oxide with applications to ultrasensitive oligonucleotide assay. , 2011, ACS nano.

[18]  Juewen Liu,et al.  Functional nucleic acid sensors. , 2009, Chemical reviews.

[19]  Xiongce Zhao Self-Assembly of DNA Segments on Graphene and Carbon Nanotube Arrays in Aqueous Solution: A Molecular Simulation Study , 2011 .

[20]  N. Mohanty,et al.  Graphene-based single-bacterium resolution biodevice and DNA transistor: interfacing graphene derivatives with nanoscale and microscale biocomponents. , 2008, Nano letters.

[21]  Zhuang Liu,et al.  PEGylated nanographene oxide for delivery of water-insoluble cancer drugs. , 2008, Journal of the American Chemical Society.

[22]  H. Dai,et al.  Carbon nanotubes as multifunctional biological transporters and near-infrared agents for selective cancer cell destruction. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[23]  Chunhai Fan,et al.  A Graphene Nanoprobe for Rapid, Sensitive, and Multicolor Fluorescent DNA Analysis , 2010 .

[24]  S. Nie,et al.  Self-assembled nanoparticle probes for recognition and detection of biomolecules. , 2002, Journal of the American Chemical Society.

[25]  Jun Liu,et al.  Constraint of DNA on functionalized graphene improves its biostability and specificity. , 2010, Small.

[26]  Mary E. Hughes,et al.  Optical absorption of DNA-carbon nanotube structures. , 2007, Nano letters.

[27]  R. Kaner,et al.  Honeycomb carbon: a review of graphene. , 2010, Chemical reviews.

[28]  Yuehe Lin,et al.  Aptamer/graphene oxide nanocomplex for in situ molecular probing in living cells. , 2010, Journal of the American Chemical Society.

[29]  Andre K. Geim,et al.  Electric Field Effect in Atomically Thin Carbon Films , 2004, Science.

[30]  K. L. Sebastian,et al.  Resonance energy transfer from a dye molecule to graphene. , 2008, The Journal of chemical physics.

[31]  Klaus Kern,et al.  Electronic transport properties of individual chemically reduced graphene oxide sheets. , 2007, Nano letters.

[32]  Jian-hui Jiang,et al.  Terminal protection of small-molecule-linked DNA for sensitive electrochemical detection of protein binding via selective carbon nanotube assembly. , 2009, Journal of the American Chemical Society.

[33]  C. Niemeyer REVIEW Nanoparticles, Proteins, and Nucleic Acids: Biotechnology Meets Materials Science , 2022 .

[34]  Itamar Willner,et al.  Biomolecule-functionalized carbon nanotubes: applications in nanobioelectronics. , 2004, Chemphyschem : a European journal of chemical physics and physical chemistry.