Electronic Detection of DNA-nicks Using 2D Solid-state Nanopore - PowerPoint PPT Presentation

Electronic Detection of DNA-nicks Using 2D Solid-state Nanopore Transistor I use Blue Waters to devise novel 2D nanopore systems for genetic and epigenetic detection Presented by Nagendra Athreya PI: Jean-Pierre Leburton

DNA: The Blue Print of Life Applications of Decoding the Genome Personalized Medicine Pharmaceutical Research Nelson MR et. al., Nature Genetics , 47(8):856-60. 2015 Point-of-care Genomic Testing Tonna, Stephen, Assam El-Osta, Mark E. Cooper, and Chris Tikellis. Nature Reviews Nephrology (2010) 2

Sequencing Technologies Illumina Sequencer New target < $100 Nanopore Sequencing is a potential solution 3

Principle of Nanopore Sensing • δ I: Average amplitude • t d : Dwell time • δ t: Waiting time between two events Wanunu, M. (2012, June). Physics of Life Reviews . Biological Nanopores Solid-state Nanopores Oxford Nanopore Technologies 4

Towards Electronic Detection of Bio-molecules Sheet Current 1. Tunable sensitivity of detection. 2. Easily integrated into semiconductor 3. Massively parallel detection. Image Courtesy: Bayley , Nature, 467 ,164-65, 2010 Previous Work Radenovic Group, EPFL, 2013 Leburton Group, UIUC, 2013 5

Modeling Ionic Currents using BW Nodes MD System Setup System Model Molecular Dynamics Simulation (NAMD) DNA Trajectory Ionic Current • ~500k atoms • 5-10 Nodes/simulation Ionic Current Calculations • 2-4 weeks/simulation summed over all K + , Cl - ions A. Aksimentiev, et. al, Biophysical Journal, 2004 6

Modeling Electronic Sheet Currents using BW Nodes DNA Trajectory 2 DNA charge model Electrostatics of nanopore system Self-Consistent Poisson Equation Solver Potentials induced around pore Electronic Transport Calculations using Non-Equilibrium Green’s Function Formalism/Boltzmann transport Electron Current/Conductance Transverse Electronic Current Response • Poisson Solver • 50 Nodes/simulation • ~6 hours/job • Electronic Transport • ~4000 Nodes!!! • ~6 hours/job 7

DNA-nick Detection in 2D Nanopore Membranes Human Cell is subjected to ~70,000 lesions/day. Majority of them • arise from DNA backbone breaks . These breaks in critical gene cause the cell to undergo apoptosis . • Contrarily, if repair mechanism fails, the DNA breaks cause • chromosomal instability leading to tumorigenesis . No existing technology can efficiently detect these DNA-nicks. • Our efforts are directed towards unraveling the potential of Two- • dimensional solid-state nanopore membranes to detect and map these site-specific nicks along the genome with single-base resolution . 8

Site of the nick: A-A Potential Profile of Damaged dsDNA translocation 9

Site Specificity of the nick positions SITE OF THE DNA DAMAGE CURRENT TRACES T-T C-C Not recognizable by ionic currents G-G 10

Voltage (V cis-Trans ) dependence Normal translocation Denaturing of the DNA 11

Voltage (V cis-Trans ) dependence Breaking point! 12

Future Work § Cross-base pairs (A-C, A-G, A-T, C-G, C-T, T-G) § Different electrically active 2D materials: Semi-conductor (MoS 2 ) § Complete voltage dependence analysis 13

ACKNOWLEDGEMENTS Jean-Pierre Leburton & Aditya Sarathy Olgica Milenkovic 14

THANK YOU 15

Appendix 16

Multigrid Solution of Semiconductor PBE 𝐿 , (𝐬, 𝜒) − 𝐷𝑚 0 (𝐬, 𝜒 ) ) 𝛼 · 𝜁(𝐬)𝛼𝜒(𝐬 = −𝑓 − 𝜍 234 − 𝜍 56 , (𝐬) − 𝑂 0 (𝐬) + 𝑞(𝐬) − 𝑜(𝐬) ] 𝜍 56 (𝐬) = 𝑓[𝑂 2 4 89 089 𝐷𝑚 0 (𝐬, 𝜒) = 𝐷 7 𝑓 𝐿 , (𝐬, 𝜒) = 𝐷 7 𝑓 : ; < : ; < 𝐹 K + 𝑓𝜒(𝐬) + 𝐹 OPQ 2 𝑜(𝐬) = 𝑂 6 𝜌 𝐺 ⁄ 2 −𝑓𝜒(𝐬) − 𝐹 K H I 𝑙 M 𝑢 𝑞(𝐬) = 𝑂 C 𝜌 𝐺 ⁄ H I 𝑙 M 𝑈 Half Order Fermi-Dirac Function Need to solve 3D Poisson Boltzmann Equation with Newton Multigrid FMV cycle Multigrid gives O(N) performance Gracheva, Maria E., et al. "Simulation of the electric response of DNA translocation through a semiconductor nanopore–capacitor." Nanotechnology 17.3 (2006): 622. 17

Graphene Nanopore Sheet Conductance Model Graphene honeycomb lattice Tight-binding Hamiltonian Non-Equilibrium Green’s Function Landauer-Buttiker Formula Conductance A. Girdhar, C. Sathe, K. Schulten, and J. P. Leburton PNAS (2013) 18

Graphene Nanoribbon Transverse Conductance Fisher-Lee Relation Transmission T(E) G: Transverse conductance of the sheet; T(E): Transmission coefficient f(E): Fermi-Dirac distribution Non-equilibrium Green's function (NEGF) Carrier Energy (eV) Conductance (G) 0H 𝐹 + 𝑗η W 𝑱 − 𝐼 1 𝑊 1𝐷 𝐻 1 𝐻 1𝐷 = 𝐹 + 𝑗η W 𝐻 𝐷1 𝐻 𝐷 𝑊 𝐷1 𝑱 − 𝐼𝐷 Fermi Energy (eV) b 𝐹 + 𝑗η W 𝑱 − 𝐼 1 0H 𝑊 𝛵 = 𝑊 ^ 𝐽 = 2𝑓 6H H6 W ℎ ] 𝑈 (𝐹)[𝑔 H (𝐹) − 𝑔 I (𝐹)]𝑒𝐹 ^ 19

All-atom MD Simulations 20

Detection of DNA molecule: Ionic Currents Diameter (nm) 3 140 c b 120 2.5 100 2 z (Å) 80 1.5 60 1 40 0.5 20 0 20 40 60 80 20 40 60 80 (V) x (Å) 2 nm 7 nm Potential profile Note the sharp non-linear potential profile! 0.8 V 2.5 V 4.3 V Current blockade is stronger for lower applied bias! C. Sathe, X. Zou, J. P. Leburton, and K. Schulten. ACS Nano 2011. 21

Detecting Stepwise ssDNA Translocation Conductance in the 2D Membranes due to change in electrostatic potential Permeated bases (#) 10 Sheet current (nA) 0.94 8 0.92 6 4 1 2 3 4 0.90 2 0.88 0 0 10 20 30 40 Simulation time (ns) H. Qiu A. Sarathy, J-P Leburton and K. Schulten Nanoletters (2015) 22

Large Scale Parallel DNA Detection in Multi-pore Systems 23

Large Scale Parallel DNA Detection in Multi-pore Systems 24

25