dna sequencing via transverse transport: possibilities and

Massimiliano Di VentraDepartment of Physics, University of California, San Diego

Group

Matt Krems

Yoni DubiH. AppelS. 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)

DNA sequencing via transverse transport:possibilities and fundamental issues

M. Zwolak and M. Di Ventra, Physical approaches to DNA sequencing and

detection, Rev. Mod. Phys. 80, 141 (2008).

Outline

� Sequencing via transverse transport

� Quantum transport + Molecular Dynamics

A primer on DNA

Adenine GuanineThymine Cytosine

Backbone

Humans ~ 3 Billion base pairs

• Driven by biased electrodes, DNA can

be analyzed as it translocates a nanopore

Kasianowicz et al Proc. Natl. Acad. Sci. 1996

Pore

Mathe, et al. PNAS 2005

Idea: ionic current in nanopores

α-hemolysin nanopore

Idea: Transverse TransportM

icro

cha

nn

els

Micro

cha

nn

els

FIB Milled Channels

(10-50-nm width)

(a)

AFM Formed Channel

(1-5-nm width and length)

STM Formed Nanoelectrodes

2-nm width

-A-C-T-G-

A C T G

DNAVoltage Biased

translocaton

M. Zwolak and M. Di Ventra,

Nano Lett. 5, 421 (2005)Ramsey et al., unpublished

e-

||Er

⊥Er

Transverse Transport

( )btDNAHE

EGΣ−Σ−−

=1

( ) ( ) ( )[ ]∫ −= EfEfETdEh

eI bt

2

M. Zwolak and M. Di Ventra,

Nano Lett. 5, 421 (2005)

Use ratio of currents as a

measure of their difference

Transverse Transport (static)

0 0.05 0.1Voltage (V)

101

102

103

I A/I

XG

C

T

Electrode Surface

Single Nucleotides

M. Zwolak and M. Di Ventra,

Nano Lett. 5, 421 (2005)

0 0.05 0.1Voltage (V)

101

102

103

I A/I

XG

C

T

Single Nucleotides

M. Zwolak and M. Di Ventra,

Nano Lett. 5, 421 (2005)

Transverse Transport (static)

Transverse Transport (static)

Nearest neighbors

Electrode “size” ~ 1 nm

Transverse Transport (static)

Transverse Transport (static)

Transverse Transport (static)

What about variations of orientation?

Transverse Transport (static)

Transverse Transport (static)

Consider 6 different changes:

Translations:

Rotations:

x y z

x y z

Electrode Surface

Transverse Transport (static)

Transverse Transport (static)

Electrode Surface

100

101

102

103

104

I A/I

X

GC

T

Variations of orientation

Transverse Transport (static)

Noise

• Thermal noise:

V= 1 V; I= 1 nA; ∆f= 10 kHz ⇒ ith= 0.4 pA

• Shot noise:ishot< ith

• 1/f noise:operate at f > 0

• Structural noise

R

fTki Bth

∆=

4

Electronic Noise

Experimental Pores

� Use 4 probes to collect more info (not necessary though)

5 µm

500 nm

Fujimori, et al. Nanotech. 2004.

Molecular Dynamics

� Thousands of atoms

� Full quantum mechanical treatment not possible

NAMD, UIUC

Molecular Dynamics

12.5 Å

25 Å

� Inner diameter 12.5 Å

� Outer diameter 25 Å

� Potassium chloride concentration 1M

� Room Temperature

pore

Top view

E

Molecular DynamicsAdenine

Molecular Dynamics

Adenine

Field effects:� Bending� Stretching

||Er

Transverse Transport (dynamics)

J. Lagerqvist, M. Zwolak, and M. Di Ventra, Nano Letters 2006

Transverse Transport (dynamics)

Transverse Transport (dynamics)

15 bases

Transverse Transport (dynamics)

Driving electric field

� As the field strength increases, the minimum diameter can be decreased

� Decreasing field, bases bend less

0.2x electric field

⊥<< EErr

||

⊥Er

||Er

Controlling the dynamics

J. Lagerqvist, M. Zwolak, and M. Di Ventra, Nano Letters 2006

⊥Er

Current Distributions

{ } ∏∏∏∏

∏∑ ∑

====

=

= +++

=−=N

n

n

G

N

n

n

C

N

n

n

T

N

n

n

A

N

n

n

X

GCTAX PPPP

PX

PError

1111

1

I ,,,n4

1

J. Lagerqvist, M. Zwolak, and M. Di Ventra, Nano Letters 2006

Accuracy 99.9 %

107 measurements/ s

Genome seq. time < 7 hours

No parallelization

Current distributions1 Volt, 12.5 Å spacing

Lagerqvist et al., Nano Lett. 2006

Current distributions1 Volt, 12.5 Å spacing

Lagerqvist et al., Nano Lett. 2006

• Large bias, risk of electrolysiseven though not obvious at nano scale

Current distributions

1 V

Lagerqvist et al., Nano Lett. 2006 Lagerqvist et al., BioPhys. J. 2007

0.1 V

Stabilizing field

Lagerqvist et al., BJ 2007

Adenine, 15 Å spacing

• Stabilizing field helps increase the conductance

Finite bandwidth

Lagerqvist et al., BJ 2007

0.1 V

Finite bandwidth

Lagerqvist et al., BJ 2007

Average:

100 / 1,000 / 10^7 times

Sample at:

10 GHz / 1 GHz / 100 kHz

0.1 V

Effect of probes and environment

1) Electrical probes help distinguish bases due to averaging over configurations

2) Water is not the main source of noise

Without water

With water

3) Main sources of noise: thermal andion fluctuations

� May lead to decoherence

0.1 V

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.

⊥<< EErr

||

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.

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, 013901 (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