In-depth investigation of the interaction between DNA and nano-sized graphene oxide

Abstract Graphene oxide (GO) has been harnessed in diverse biomedical applications such as drug delivery, biomolecule detection and enzymatic activity assay for a decade. In specific, optical biosensors have been developed based on the preferential binding of single stranded nucleic acid on GO and fluorescence quenching capability of GO. Recently, nano-size GO (NGO), which is smaller than micro-sized large GO (LGO), was employed for live cell imaging of various biomarkers and intracellular RNA. However, in contrast to the expanded applications of size controlled NGO, in-depth study on the interaction between DNA and NGO was not sufficiently carried out. Here, we investigated the DNA length dependent interaction between DNA and NGO. By using three DNA strands having different lengths, we observed (1) kinetics and capacity of DNA adsorption, (2) kinetics and sensitivity of sequence specific desorption of DNA and (3) relative strength of DNA interaction with NGO compared to LGO. Present study will give useful information on the effect of GO size to its interaction with DNA, which are important in developing robust biosensors based on GO and DNA.

[1]  W. Kabsch,et al.  Three‐dimensional structure of bovine pancreatic DNase I at 2.5 A resolution. , 1984, The EMBO journal.

[2]  G. Eda,et al.  Chemically Derived Graphene Oxide: Towards Large‐Area Thin‐Film Electronics and Optoelectronics , 2010, Advanced materials.

[3]  Younghoon Lee,et al.  Direct, sequence-specific detection of dsDNA based on peptide nucleic acid and graphene oxide without requiring denaturation. , 2014, Biosensors & bioelectronics.

[4]  Xiaogang Qu,et al.  Using Graphene Oxide High Near‐Infrared Absorbance for Photothermal Treatment of Alzheimer's Disease , 2012, Advanced materials.

[5]  K. L. Sebastian,et al.  Long range resonance energy transfer from a dye molecule to graphene has (distance)(-4) dependence. , 2009, The Journal of chemical physics.

[6]  Xiaogang Qu,et al.  Graphene Oxide: Intrinsic Peroxidase Catalytic Activity and Its Application to Glucose Detection , 2010, Advanced materials.

[7]  Byong-Seok Choi,et al.  Deoxyribozyme-loaded nano-graphene oxide for simultaneous sensing and silencing of the hepatitis C virus gene in liver cells. , 2013, Chemical communications.

[8]  Bengt Fadeel,et al.  Classification framework for graphene-based materials. , 2014, Angewandte Chemie.

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

[10]  Bong Jin Hong,et al.  Tunable biomolecular interaction and fluorescence quenching ability of graphene oxide: application to "turn-on" DNA sensing in biological media. , 2012, Small.

[11]  Jiye Shi,et al.  Size-dependent programming of the dynamic range of graphene oxide-DNA interaction-based ion sensors. , 2014, Analytical chemistry.

[12]  Huang-Hao Yang,et al.  A graphene platform for sensing biomolecules. , 2009, Angewandte Chemie.

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

[14]  V. Dravid,et al.  Graphene oxide as an enzyme inhibitor: modulation of activity of α-chymotrypsin. , 2011, Journal of the American Chemical Society.

[15]  Nianqiang Wu,et al.  Fluorescent aptamer-functionalized graphene oxide biosensor for label-free detection of mercury(II). , 2013, Biosensors & bioelectronics.

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

[17]  Jiayan Luo,et al.  Graphene oxide nanocolloids. , 2010, Journal of the American Chemical Society.

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

[19]  M. Israel,et al.  A rapid method for detecting and mapping homology between heterologous DNAs. Evaluation of polyomavirus genomes. , 1979, The Journal of biological chemistry.

[20]  Hongje Jang,et al.  A Graphene‐Based Platform for the Assay of Duplex‐DNA Unwinding by Helicase† , 2010, Angewandte Chemie.

[21]  Franklin Kim,et al.  Graphene Oxide: Surface Activity and Two‐Dimensional Assembly , 2010, Advanced materials.

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

[23]  J. Gang.  Graphene Oxide-based Direct Measurement of DNase I Activity with Single Stranded DNA , 2014 .

[24]  Dong-Eun Kim,et al.  Discovery of Hepatitis C Virus NS3 Helicase Inhibitors by a Multiplexed, High‐Throughput Helicase Activity Assay Based on Graphene Oxide† , 2013, Angewandte Chemie.

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

[26]  Yong Liu,et al.  Biocompatible graphene oxide-based glucose biosensors. , 2010, Langmuir : the ACS journal of surfaces and colloids.

[27]  R. Ruoff,et al.  Graphene and Graphene Oxide: Synthesis, Properties, and Applications , 2010, Advanced materials.

[28]  Young-Kwan Kim,et al.  Laser desorption/ionization mass spectrometric assay for phospholipase activity based on graphene oxide/carbon nanotube double-layer films. , 2010, Journal of the American Chemical Society.

[29]  Hong-Wu Tang,et al.  Low background signal platform for the detection of ATP: when a molecular aptamer beacon meets graphene oxide. , 2011, Biosensors & bioelectronics.

[30]  Young-Kwan Kim,et al.  The Structural Influence of Graphene Oxide on Its Fragmentation during Laser Desorption/Ionization Mass Spectrometry for Efficient Small-Molecule Analysis. , 2015, Chemistry.

[31]  Sang Woo Han,et al.  Quantitative and multiplexed microRNA sensing in living cells based on peptide nucleic acid and nano graphene oxide (PANGO). , 2013, ACS nano.

[32]  Young-Kwan Kim,et al.  A new assay for endonuclease/methyltransferase activities based on graphene oxide. , 2011, Analytical chemistry.

[33]  Juewen Liu,et al.  Mechanisms of DNA sensing on graphene oxide. , 2013, Analytical chemistry.

[34]  Xi Chen,et al.  Graphene oxide-protected DNA probes for multiplex microRNA analysis in complex biological samples based on a cyclic enzymatic amplification method. , 2012, Chemical communications.

[35]  Martin Pumera,et al.  Electrochemistry of graphene, graphene oxide and other graphenoids: Review , 2013 .

[36]  Xiaogang Qu,et al.  3D Graphene Oxide–Polymer Hydrogel: Near‐Infrared Light‐Triggered Active Scaffold for Reversible Cell Capture and On‐Demand Release , 2013, Advanced materials.

[37]  X. Qu,et al.  Cancer biomarker detection: recent achievements and challenges. , 2015, Chemical Society reviews.

[38]  B. Hong,et al.  Biomedical applications of graphene and graphene oxide. , 2013, Accounts of chemical research.

[39]  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.

[40]  Min Jae Lee,et al.  A New Helicase Assay Based on Graphene Oxide for Anti-Viral Drug Development , 2013, Molecules and cells.

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

[42]  C. Fan,et al.  Uniform ultrasmall graphene oxide nanosheets with low cytotoxicity and high cellular uptake. , 2013, ACS applied materials & interfaces.

[43]  Po-Jung Jimmy Huang,et al.  DNA-length-dependent fluorescence signaling on graphene oxide surface. , 2012, Small.