Session W9: Invited Session: Physics of Next Generation DNA Sequencing

Detection and interrogation of biomolecules via nanoscale probes: From fundamental physics to DNA sequencing

A rapid and low-cost method to sequence DNA would revolutionize personalized medicine [1], where genetic information is used to diagnose, treat, and prevent diseases. There is a longstanding interest in nanopores as a platform for rapid interrogation of single DNA molecules. I will discuss a sequencing protocol based on the measurement of transverse electronic currents during the translocation of single-stranded DNA through nanopores. Using molecular dynamics simulations coupled to quantum mechanical calculations of the tunneling current, I will show that the DNA nucleotides are predicted to have distinguishable electronic signatures in experimentally realizable systems. Several recent experiments support our theoretical predictions. In addition to their possible impact in medicine and biology, the above methods offer ideal test beds to study open scientific issues in the relatively unexplored area at the interface between solids, liquids, and biomolecules at the nanometer length scale [1]. \\[4pt] [1] M. Zwolak and M. Di Ventra, ``Physical Approaches to DNA Sequencing and Detection,'' Rev. Mod. Phys. 80, 141 (2008).   

Single Molecule Electrical Sequencing of DNA and RNA

Gating nanopore devices are composed of nanopores with embedded nanoelectrodes, and they are expected to be one of the core devices used to realize label-free, low-cost DNA sequencing, subsequently leading to {\$}1000-genome sequencing technologies. The operating principle of these nanodevices is based on identifying single base molecules of single DNA passing through a nanopore using a tunneling current between nanoelectrodes. We successfully identified single base molecules of DNA and RNA using tunneling currents. To make gating nanopore devices fit for practical use, core technologies should be integrated on one device chip. One core technology is the identification of single DNA and RNA composed of many base molecules using tunneling currents. We have succeeded in the single-molecule electrical sequencing of DNA and RNA formed by 3 and 7 base molecules, respectively, using a hybrid method of identifying single base molecules via a tunnelling current and random sequencing. A method that controls the speed of a single DNA passing through a nanopore is one core technology that determines the speed and accuracy of sequencing. We successfully developed a method that controls the translocation speed of a single DNA by three orders of magnitude using a voltage between nanoelectrodes.   

DNA Electronic Fingerprints by Local Spectroscopy on Graphene

Working and scalable alternatives to the conventional chemical methods of DNA sequencing that are based on electronic/ionic signatures would revolutionize the field of sequencing. The approach of a single molecule imaging and spectroscopy with unprecedented resolution, achieved by Scanning Tunneling Spectroscopy (STS) and nanopore electronics could enable this revolution. We use the data from our group [1] and others in applying this local scanning tunneling microscopy and illustrate possibilities of electronic sequencing of freeze dried deposits on graphene. We will present two types of calculated fingerprints: first in Local Density of States (LDOS) of DNA nucleotide bases (A,C,G,T) deposited on graphene[2]. Significant base-dependent features in the LDOS in an energy range within few eV of the Fermi level were found in our calculations. These features can serve as electronic fingerprints for the identification of individual bases in STS. In the second approach we present calculated base dependent electronic transverse conductance as DNA translocates through the graphene nanopore. Thus we argue that the fingerprints of DNA-graphene hybrid structures may provide an alternative route to DNA sequencing using STS.\\[4pt] [1] Yarotski DA, Kilina SV, Talin AA, Tretiak S, Prezhdo OV, Balatsky AV, Taylor AJ., ``Scanning tunneling microscopy of DNA-wrapped carbon nanotubes.'' Nano Lett. 2009 Jan;9(1):12-7\\[0pt] [2] Ahmed T, Kilina S, Das T, Haraldsen JT, Rehr JJ,~Balatsky~AV, ``Electronic Fingerprints of DNA Bases on Graphene,'' Nano Lett., 2012, v 12 ~~Issue: 2 ~~Pages: 927-931 ~~DOI: 10.1021/nl2039315   

Edge-functionalization aspects in DNA sequencing with graphene nano-electrodes

Slowing down DNA translocation and achieving single-nucleobase resolution are major issues for the realization of nanopore-based sequencing [see, e.g., our review in J Mater Sci 47, 7439 (2012)]. On the one hand, complex functionalization of nanopore-embedded gold electrodes with one [J Phys Chem C 112, 3456 (2008)] or two types of molecules [Appl Phys Lett 100, 023701 (2012)] might address both these issues simultaneously, but is difficult to implement in practice. On the other hand, the fabrication process of nano-gaps or -pores in graphene could readily introduce more simple edge-functionalization in the form of hydrogen atoms saturating the dangling bonds resulting from cutting the carbon network. --- A range of computational tools can be used to theoretically determine the electronic structure and quantum transport properties of individual nucleotides or short DNA strands in realistic models of nanopore-based sequencing device setups. In this manner, we were able to explore the effects of the temporary formation of weak H-bonds between hydrogenated graphene edges and suitable atomic sites in the nucleotides on the dynamical [Adv Funct Mater 21, 2674 (2011)] and static [Nano Lett 11, 1941 (2011)] properties of this system. Recently also more ambitious functionalization schemes for graphene edges [arXiv:1202.3040] as well as a promising bilayer graphene setup [arXiv:1206.4199] were investigated by us. Finally, there might be a particular appeal to use graphene edges terminated with nitrogen atoms, and we have studied some of the benefits that this type of edge-functionalization could offer for the purpose of DNA sequencing. --- Funding provided by the Swedish Research Council (VR), the Swedish Foundation for International Cooperation in Research and Higher Education (STINT), and the Carl Trygger Foundation for Scientific Research.