DNA sequencing via transverse transport: possibilities and fundamental issues

Transcription

1 DNA sequencing via transverse transport: possibilities and fundamental issues Massimiliano Di Ventra Department of Physics, University of California, San Diego M. Zwolak and M. Di Ventra, Physical approaches to DNA sequencing and detection, Rev. Mod. Phys. 80, 141 (2008). Group Matt Krems Yoni Dubi H. Appel S. La Fontaine Former Members Johan Lagerqvist (London) Mike Zwolak (LANL) Yuriy Pershin (USC) Roberto D Agosta (Spain) Neil Bushong (NC) Na Sai (U. Texas, Austin) Tony Schindler (UNM) John Gamble (Wooster) Yu-Chang Chen (Chiao Tung U.) Zhongqin Yang (Fudan Univ.) Mairbek Chshiev (UA)

2 Outline Sequencing via transverse transport Quantum transport + Molecular Dynamics

3 A primer on DNA Backbone Adenine Thymine Cytosine Guanine Humans ~ 3 Billion base pairs

4 Idea: ionic current in nanopores Driven by biased electrodes, DNA can be analyzed as it translocates a nanopore Kasianowicz et al Proc. Natl. Acad. Sci Pore α-hemolysin nanopore Mathe, et al. PNAS 2005

5 Idea: Transverse Transport e - E r STM Formed Nanoelectrodes 2-nm width A C T G Microchannels Voltage Biased translocaton DNA AFM Formed Channel (1-5-nm width and length) -A-C-T-G- FIB Milled Channels (10-50-nm width) Microchannels E r (a) Ramsey et al., unpublished M. Zwolak and M. Di Ventra, Nano Lett. 5, 421 (2005)

6 Transverse Transport G I ( E) = E H DNA 1 Σ t Σ 2e = det t b E h ( E) [ f ( E) f ( )] Use ratio of currents as a measure of their difference b M. Zwolak and M. Di Ventra, Nano Lett. 5, 421 (2005)

7 Transverse Transport (static) Electrode Surface Single Nucleotides 10 3 T I A /I X 10 2 C G Voltage (V) M. Zwolak and M. Di Ventra, Nano Lett. 5, 421 (2005)

8 Transverse Transport (static) Single Nucleotides 10 3 T I A /I X 10 2 C G Voltage (V) M. Zwolak and M. Di Ventra, Nano Lett. 5, 421 (2005)

9 Transverse Transport (static) (static) Nearest neighbors Electrode size ~ 1 nm

10 Transverse Transport (static)

11 Transverse Transport (static) (static) What about variations of orientation?

12 Transverse Transport (static) (static) Consider 6 different changes: Electrode Surface Translations: x y z Rotations: x y z

13 Transverse Transport (static) (static) Variations of orientation Electrode Surface I A /I X T G C

14 Noise Thermal noise: i th k = 4 T f R V= 1 V; I= 1 na; f= 10 khz i th = 0.4 pa B Electronic Noise Shot noise: i shot < i th 1/f noise: operate at f > 0 Structural noise

15 Experimental Pores Use 4 probes to collect more info (not necessary though) 5 µm Fujimori, et al. Nanotech nm

16 Molecular Dynamics Thousands of atoms Full quantum mechanical treatment not possible NAMD, UIUC

17 Molecular Dynamics Inner diameter 12.5 Å Outer diameter 25 Å Potassium chloride concentration 1M Room Temperature E Top view 12.5 Å 25 Å pore

18 Molecular Dynamics Adenine

19 Molecular Dynamics Adenine E r Field effects: Bending Stretching

20 Transverse Transport (dynamics) J. Lagerqvist, M. Zwolak, and M. Di Ventra, Nano Letters 2006

21 Transverse Transport (dynamics)

22 Transverse Transport (dynamics) 15 bases

23 Transverse Transport (dynamics)

24 Driving electric field As the field strength increases, the minimum diameter can be decreased r r Decreasing field, bases bend less E << E E r E r 0.2x electric field

25 Controlling the dynamics E r J. Lagerqvist, M. Zwolak, and M. Di Ventra, Nano Letters 2006

26 Current Distributions Accuracy 99.9 % 10 7 measurements/ s Genome seq. time < 7 hours No parallelization Error J. Lagerqvist, M. Zwolak, and M. Di Ventra, Nano Letters 2006 N n PX X n= 1 = 1 P = N N N N { I } X = A, T, C, G 4 n n n n PA + PT + PC + n= 1 n= 1 n= 1 n= 1 P n G

27 1 Volt, 12.5 Å spacing Current distributions Lagerqvist et al., Nano Lett. 2006

28 1 Volt, 12.5 Å spacing Current distributions Large bias, risk of electrolysis even though not obvious at nano scale Lagerqvist et al., Nano Lett. 2006

29 Current distributions 1 V 0.1 V Lagerqvist et al., Nano Lett Lagerqvist et al., BioPhys. J. 2007

30 Stabilizing field Adenine, 15 Å spacing Stabilizing field helps increase the conductance Lagerqvist et al., BJ 2007

31 Finite bandwidth 0.1 V Lagerqvist et al., BJ 2007

32 Finite bandwidth Average: 0.1 V 100 / 1,000 / 10^7 times Sample at: 10 GHz / 1 GHz / 100 khz Lagerqvist et al., BJ 2007

33 Effect of probes and environment 1) Electrical probes help distinguish bases due to averaging over configurations 0.1 V 2) Water is not the main source of noise 3) Main sources of noise: thermal and ion fluctuations May lead to decoherence Without water With water

34 Conclusion: Sequencing protocol 1) Bases can be distinguished statistically if some control is exerted: transverse field. 2) Need to slow down DNA translocation so that more measurements per base can be performed. r E r << E 3) Need to calibrate the device with polybase strands. Re-calibration is probably necessary at intervals of time due to possible atomic rearrangements of the nanopore/electrodes.

35 References 1) M. Zwolak and M. Di Ventra, Physical approaches to DNA sequencing and detection, Rev. Mod. Phys. 80, 141 (2008). 2) J. Lagerqvist, M. Zwolak, and M. Di Ventra, Influence of the environment and probes on rapid DNA sequencing via transverse electronic transport, Biophys. J. 93, 2384 (2007). 3) J. Lagerqvist, M. Zwolak, and M. Di Ventra, Comment on Characterization of tunneling conductance across DNA bases, Phys. Rev. E 76, (2007). 4) J. Lagerqvist, M. Zwolak, and M. Di Ventra, Fast DNA sequencing via transverse electronic transport, 6, 779 (2006). 5) M. Zwolak and M. Di Ventra, Electronic signature of DNA nucleotides via transverse transport, Nano Lett. 5, 421 (2005). Thanks