Real-Time Label-Free Direct Electronic Monitoring of Topoisomerase Enzyme Binding Kinetics on Graphene.

Monolayer graphene field-effect sensors operating in liquid have been widely deployed for detecting a range of analyte species often under equilibrium conditions. Here we report on the real-time detection of the binding kinetics of the essential human enzyme, topoisomerase I interacting with substrate molecules (DNA probes) that are immobilized electrochemically on to monolayer graphene strips. By monitoring the field-effect characteristics of the graphene biosensor in real-time during the enzyme-substrate interactions, we are able to decipher the surface binding constant for the cleavage reaction step of topoisomerase I activity in a label-free manner. Moreover, an appropriate design of the capture probes allows us to distinctly follow the cleavage step of topoisomerase I functioning in real-time down to picomolar concentrations. The presented results are promising for future rapid screening of drugs that are being evaluated for regulating enzyme activity.

[1]  E. T. Carlen,et al.  Real-time measurements of PNA:DNA hybridization kinetics with silicon nanowire biosensors , 2013, 2013 Transducers & Eurosensors XXVII: The 17th International Conference on Solid-State Sensors, Actuators and Microsystems (TRANSDUCERS & EUROSENSORS XXVII).

[2]  Rory Stine,et al.  Real‐Time DNA Detection Using Reduced Graphene Oxide Field Effect Transistors , 2010, Advanced materials.

[3]  K. Novoselov,et al.  Detection of individual gas molecules adsorbed on graphene. , 2006, Nature materials.

[4]  J. Krieg,et al.  Tuning the isoelectric point of graphene by electrochemical functionalization , 2015, Scientific Reports.

[5]  J. Krieg,et al.  Chemical vapor deposition of graphene on a "peeled-off" epitaxial Cu(111) foil: a simple approach to improved properties. , 2014, ACS nano.

[6]  Jason J. Davis,et al.  Graphene-based protein biomarker detection. , 2015, Bioanalysis.

[7]  N. Zaffaroni,et al.  Camptothecin resistance in cancer: insights into the molecular mechanisms of a DNA-damaging drug. , 2013, Current medicinal chemistry.

[8]  Philip G. Collins,et al.  Single-Molecule Lysozyme Dynamics Monitored by an Electronic Circuit , 2012, Science.

[9]  Yi-Ping Ho,et al.  DNA-Based Sensor for Real-Time Measurement of the Enzymatic Activity of Human Topoisomerase I , 2013, Sensors.

[10]  R. Schasfoort,et al.  Handbook of surface plasmon resonance , 2008 .

[11]  W G Hol,et al.  A model for the mechanism of human topoisomerase I. , 1998, Science.

[12]  Qiyuan He,et al.  Real-time DNA detection using Pt nanoparticle-decorated reduced graphene oxide field-effect transistors. , 2012, Nanoscale.

[13]  Wei Zhou,et al.  General strategy for biodetection in high ionic strength solutions using transistor-based nanoelectronic sensors. , 2015, Nano letters.

[14]  Y. Ho,et al.  Quantum dot based DNA nanosensors for amplification-free detection of human topoisomerase I , 2014 .

[15]  O. Westergaard,et al.  Characterization of intra- and intermolecular DNA ligation mediated by eukaryotic topoisomerase I. Role of bipartite DNA interaction in the ligation process. , 1994, The Journal of biological chemistry.

[16]  R. T. Hill,et al.  Plasmonic biosensors. , 2015, Wiley interdisciplinary reviews. Nanomedicine and nanobiotechnology.

[17]  Jaulang Hwang,et al.  Immobilizing topoisomerase I on a surface plasmon resonance biosensor chip to screen for inhibitors , 2010, Journal of Biomedical Science.

[18]  M. Burghard,et al.  Tuning the functional interface of carbon nanotubes by electrochemistry: Toward nanoscale chemical sensors and biosensors , 2012 .

[19]  A. Shtil,et al.  Topoisomerase I and II inhibitors: chemical structure, mechanisms of action and role in cancer chemotherapy , 2014 .

[20]  K. Balasubramanian,et al.  Rolling circle amplification-based detection of human topoisomerase I activity on magnetic beads. , 2014, Analytical biochemistry.

[21]  Lan Yang,et al.  Review Label-free detection with high-Q microcavities: a review of biosensing mechanisms for integrated devices , 2012 .

[22]  J. Champoux,et al.  Reconstitution of Enzymatic Activity by the Association of the Cap and Catalytic Domains of Human Topoisomerase I* , 2002, The Journal of Biological Chemistry.

[23]  Y. Pommier Topoisomerase I inhibitors: camptothecins and beyond , 2006, Nature Reviews Cancer.

[24]  G. Jenkins,et al.  Graphene field-effect transistor and its application for electronic sensing. , 2014, Small.

[25]  Ashraf Ahmad,et al.  Label-free detection of few copies of DNA with carbon nanotube impedance biosensors. , 2011, Angewandte Chemie.

[26]  A. Desideri,et al.  Interaction between natural compounds and human topoisomerase I , 2012, Biological chemistry.

[27]  K. Balasubramanian,et al.  25th Anniversary Article: Label‐Free Electrical Biodetection Using Carbon Nanostructures , 2014, Advanced materials.

[28]  K. Balasubramanian,et al.  Tunable Enhancement of Raman Scattering in Graphene‐Nanoparticle Hybrids , 2014 .

[29]  K. Balasubramanian,et al.  Identifying chemical functionalization on individual carbon nanotubes and graphene by local vibrational fingerprinting. , 2015, ACS nano.

[30]  Yves Pommier,et al.  Topoisomerase I inhibitors: selectivity and cellular resistance. , 1999, Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy.

[31]  J. Champoux DNA topoisomerases: structure, function, and mechanism. , 2001, Annual review of biochemistry.

[32]  P. Tiwari,et al.  A surface plasmon resonance study of the intermolecular interaction between Escherichia coli topoisomerase I and pBAD/Thio supercoiled plasmid DNA. , 2014, Biochemical and biophysical research communications.

[33]  V. Nagaraja,et al.  Functional cooperation between topoisomerase I and single strand DNA-binding protein. , 2001, Journal of molecular biology.

[34]  R. Sundaram,et al.  Electrochemical Modification of Graphene , 2008 .

[35]  M. Sehested,et al.  Interaction of Human DNA Topoisomerase II α with DNA: Quantification by Surface Plasmon Resonance† , 2002 .

[36]  M. Sehested,et al.  Interaction of human DNA topoisomerase II alpha with DNA: quantification by surface plasmon resonance. , 2002, Biochemistry.

[37]  Klaus Kern,et al.  Self-assembled electrical biodetector based on reduced graphene oxide. , 2012, ACS nano.

[38]  A. Andersen,et al.  Topoisomerase I has a strong binding preference for a conserved hexadecameric sequence in the promoter region of the rRNA gene from Tetrahymena pyriformis. , 1985, Nucleic acids research.

[39]  Eroica Soans,et al.  Topoisomerase Assays , 2012, Current protocols in pharmacology.

[40]  Wenrong Yang,et al.  Molecularly engineered graphene surfaces for sensing applications: A review. , 2015, Analytica chimica acta.

[41]  James R Heath,et al.  Quantitative real-time measurements of DNA hybridization with alkylated nonoxidized silicon nanowires in electrolyte solution. , 2006, Journal of the American Chemical Society.

[42]  Peng Chen,et al.  Biological and chemical sensors based on graphene materials. , 2012, Chemical Society reviews.

[43]  P. Unwin,et al.  Structural correlations in heterogeneous electron transfer at monolayer and multilayer graphene electrodes. , 2012, Journal of the American Chemical Society.

[44]  J. Holden,et al.  Surface plasmon resonance analysis of topoisomerase I-DNA binding: effect of Mg2+ and DNA sequence. , 1997, Anti-cancer drugs.

[45]  H. Craighead,et al.  Micro- and nanomechanical sensors for environmental, chemical, and biological detection. , 2007, Lab on a chip.

[46]  G. Weiss,et al.  Electronic measurements of single-molecule catalysis by cAMP-dependent protein kinase A. , 2013, Journal of the American Chemical Society.

[47]  J. Wang,et al.  Expression of human DNA topoisomerase I in yeast cells lacking yeast DNA topoisomerase I: restoration of sensitivity of the cells to the antitumor drug camptothecin. , 1989, Cancer research.

[48]  Yi-Ping Ho,et al.  Droplet microfluidics platform for highly sensitive and quantitative detection of malaria-causing Plasmodium parasites based on enzyme activity measurement. , 2012, ACS nano.

[49]  T. Hsieh,et al.  New mechanistic and functional insights into DNA topoisomerases. , 2013, Annual review of biochemistry.

[50]  Y. Pommier DNA Topoisomerase I Inhibitors: Chemistry, Biology, and Interfacial Inhibition , 2009 .

[51]  Gregory A Weiss,et al.  Electronic measurements of single-molecule processing by DNA polymerase I (Klenow fragment). , 2013, Journal of the American Chemical Society.

[52]  I. Brooks,et al.  Determination of rate and equilibrium binding constants for macromolecular interactions using surface plasmon resonance: use of nonlinear least squares analysis methods. , 1993, Analytical biochemistry.

[53]  Mark A. Reed,et al.  Direct, rapid, and label-free detection of enzyme-substrate interactions in physiological buffers using CMOS-compatible nanoribbon sensors. , 2014, Nano letters.

[54]  M. Norton,et al.  Interactions of DNA with graphene and sensing applications of graphene field-effect transistor devices: a review. , 2015, Analytica chimica acta.

[55]  A. Andersen,et al.  Eukaryotic topoisomerase I-mediated cleavage requires bipartite DNA interaction. Cleavage of DNA substrates containing strand interruptions implicates a role for topoisomerase I in illegitimate recombination. , 1993, The Journal of biological chemistry.

[56]  A. Desideri,et al.  The human topoisomerase 1B Arg634Ala mutation results in camptothecin resistance and loss of inter-domain motion correlation. , 2013, Biochimica et biophysica acta.

[57]  Y. Ho,et al.  Real-time investigation of human topoisomerase I reaction kinetics using an optical sensor: a fast method for drug screening and determination of active enzyme concentrations. , 2015, Nanoscale.

[58]  J. Champoux,et al.  Structural flexibility in human topoisomerase I revealed in multiple non-isomorphous crystal structures. , 1999, Journal of molecular biology.

[59]  Giovanni Chillemi,et al.  Single Mutation in the Linker Domain Confers Protein Flexibility and Camptothecin Resistance to Human Topoisomerase I* , 2003, Journal of Biological Chemistry.

[60]  Mohammad Yusuf Mulla,et al.  Detection Beyond Debye's Length with an Electrolyte‐Gated Organic Field‐Effect Transistor , 2015, Advanced materials.

[61]  J. Robinson,et al.  Fabrication, optimization, and use of graphene field effect sensors. , 2013, Analytical chemistry.

[62]  Feng Yan,et al.  Solution‐Gated Graphene Transistors for Chemical and Biological Sensors , 2014, Advanced healthcare materials.

[63]  Xuexin Duan,et al.  Quantification of the affinities and kinetics of protein interactions using silicon nanowire biosensors. , 2012, Nature nanotechnology.

[64]  K. Balasubramanian,et al.  Enhancing the Electrochemical and Electronic Performance of CVD‐Grown Graphene by Minimizing Trace Metal Impurities , 2014 .

[65]  M. Otyepka,et al.  Functionalization of graphene: covalent and non-covalent approaches, derivatives and applications. , 2012, Chemical reviews.