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Scanning Tunneling Microscopy of DNA Scanning Tunneling Microscopy of DNA molecules. molecules.
DNA Nanoelectronics: sequencing and DNA Nanoelectronics: sequencing and Imaging of single moleculesImaging of single molecules
Dzmitry YarotskiDzmitry YarotskiS. Kilina, S. Tretiak, A. Taylor, AV Balatsky(Center for Intergrated Nanotechnology, Los Alamos)
A. Talin(CINT, SANDIA)
CINT is one of five Department of Energy Nanoscience Centers.Centers.
Center for Nanophase Materials Sciences
Center for Functional Nanomaterials
Center for Integrated Nanotechnologies
Center for Nanoscale MaterialsMolecular Foundry
http://cint.lanl.gov; http://cint.sandia.gov
LANL Gateway Facility, LANL Gateway Facility, opened Aug 2006opened Aug 2006
3D Active Stereo Scientific VisualizationWe have developed visualization capabilities for simulation, theory and experiment for users. Our focu areas are:
Scanning Tunneling Microscopy and Spectroscopy of high temperature cuprates, heavy fermions and DNA
Heterogeneous structures of foams, poly-xtal, poly-meric and HE materials
Molecular Dynamics simulationsof phase transitions
3D active stereo demo of a large molecule in the graphics room at CINT.
Fakespace rear projection system with a 6’x8’ soft screen (behind screen sits a Christie Digital Mirage S+4K stereo projector with 3-chip DLP technology that delivers 5000 lumens (1 kW lamp) and SXGA+ 1400x1050 resolution).
Data by Kawai group
Raw data Same data using viz software
Potential for STM tunneling as an alternative sequencing and imagingtechnique. Fingerprints of molecules.
STM tunneling through DNA on a metallic substrate.
Historical review, Scanning Tunneling Spectrroscopy, Inelastic Tunneling
DNA nanoelectronics
Nanotechnology: Science and Engineering ofthe 21st Century
Size of structureExamples of Size
Year
NA
NO
MIC
RO
MA
CR
O
Top down
Syste
m Creatio
n
Bottom up
0.1 m
1 cm
1 mm
0.1 mm
10 μm
1 μm
0.1 μm
10 nm
1 nm
0.1 nm1940 1960 1980 2000 2020 2040
Tools, Pens, ---
Wire, Screws,
Fibre GlassOptics, MicroprobesThick Film, Microsensors
Hair, Skin
Bacteria, CD-bits64Mb-256Mb-ChipThickness of Gold foil,G bit-Chip
ProteinNanoparticels, widthOf DNAMolecule/FullerenesAtom Size
Utilization ofBiological principles
Physical lawsAnd
Chemical properties
Boundaries between nano/micro domains
(Still) Looking for a few new sequencing technologiesNanopore Sequencing
(Sequence-specific detection of single molecules)
Our casePossible?
Nature Biotech. Vercoutere et al. 2001
STM Tip
D.Branton et al. 2001
Tipsample
LDOSDOS
ε
eV
z
It
Scanning tunneling microscopy/spectroscopy
It ∝∫LDOSsample (ε) dεεF
εF + eV
∝
LDOSsample (ε)dIt dV
Spectroscopic map (LDOS map) can be obtained.
High Resolution STM Imaging of Single Molecular DNA
STM Tip
AG
T
A
CPS
PS
P PS S
S SS
SS
SS
S
SS
S
P
PP
PP P
P PP
P
SS
S
SS
SP
P
PPP
SS
SP
PP
PP
S SS
S
SS
PP
PS
C
GC
CG
A
A GC
CG T
T
GC
TA
G
GGC
CS S S
3.4nm
Surface
3.4nm
2nm
Fragile and large Bio-molecules!
• Pros and cons for single molecule sequencing•Is it competitive?•Bottleneck: sample preparation- slow – hour to 30 min•Once the STM starts scanning, takes ~ 1-100 microsec•This is not a live culture. True. •But a lot of conventionalapproaches do cut and destroy assayed material. All we are looking is a table : ATGC…• Clear alternative to the optical detection schemes dominating landscape of sequecing now.
STM: DNA on graphiteHighest resolution images of the timeHighest resolution images of the time
R.J. Driscoll et al., Nature 346, 294 (1990) P.G. Arscott et al., Nature 339, 484 (1989) G. Lee et al., Science 244, 475 (1989)
Steps on the graphite surface crossing domain boundary mimic DNASteps on the graphite surface crossing domain boundary mimic DNA molecule, rendering molecule, rendering HOPG unsuitable as reliable substrate for biomolecule depositionHOPG unsuitable as reliable substrate for biomolecule deposition
C.R. Clemmer et al., Science 251, 640 (1991)
W.M. Heckl et al, Ultramicroscopy 42-44, 1073 (1992)
Motivation for DNA nanoelectronics
Recently developed pulse injection method opens new perspectivesRecently developed pulse injection method opens new perspectives for STM studies of for STM studies of broad range of biological objects, especially of DNA molecule broad range of biological objects, especially of DNA molecule
• Single nstructure of individual nucleotide?
• Nucleotides has been differentiated by their size thus far. Need for further investigations of electronic response of various nucleotides.
• STM tunneling spectroscopy may become a new sequencing technique applicable to short single DNA molecules if theoretical predictions of difference in frequencies of vibrational modes of A-T and G-C bond are confirmed ucleotides has been imaged in the unfolded DNA. Is it possible to resolve the experimentally.
Ever decreasing size of electronic devices calls for fabricationEver decreasing size of electronic devices calls for fabrication approaches inspired by approaches inspired by biobio--selfself--assembly. STM may prove to be the tool for characterization of sassembly. STM may prove to be the tool for characterization of such structures.uch structures.
• In particular, optimization of the process of metallization of DNA-based wires can be achieved by exploration of the relation between geometrical arrangement of nanoparticles and electronic properties of the wire.
Pulse injection method
H. Tanaka and T. Kawai, JVST B15(3) 602-604 1997
Pulse valve opens for short period of time and injects DNA Pulse valve opens for short period of time and injects DNA solution into the vacuum chamber. During such solution into the vacuum chamber. During such ““freezefreeze--drydry”” procedure water evaporates faster than DNA aggregates, thus procedure water evaporates faster than DNA aggregates, thus
leaving a single DNA molecule on the substrateleaving a single DNA molecule on the substrate
Pulse injection method
Hiroyuki Tanaka et al, Surface Science, 432 (1999) L611-L616. Hiroyuki Tanaka et al, Surface Science 539, L531 (2003).
Show viz for these data
Experiments at Los Alamos
• New STM • DNA- Carbon Nanotube Hybrid
structures: preliminary results
WORKING!!Upgraded experimental setup
D. YarotskiLANL
DNADNA--Carbon Nanotube composite:Sample PreparationCarbon Nanotube composite:Sample Preparation
Surfactant‐based
nanotube
suspensions
were
prepared
by
sonicating
purified
SWCNT
powder
obtained
from
SES
Research
in
1%
by
weight
of
Triton
X‐100
in
water
for
several
hours. The final concentration of SWCNTs in Triton X‐100 suspensions was ,0.1 mg/ ml.To
form
DNA‐based
nanotube
suspensions,
a
20‐mer
DNA
sequence
of
5’NH2
(C‐
6)GAGAAGAGAGCAGAAGGAGA‐3’ was
prepared
to
approximately
5
mg/ml
in
phosphate
buffer
solution
with
pH
7.4
(PBS
7.4).
One
mg
of
SWCNT
was
brought
to
approximately
250
microliters with the DNA solution, and then diluted to approximately 0.75 ml with PBS 7.4.The resulting mixture was sonicated at 0 °C for at least 90 min, and then centrifuged at 14
000 rpm for 90 min.Small drop of the resulting solution has been deposited onto p‐doped Si(110) substrate and
let dry. A.A. Talin et al., J. Vac. Sci. Technol. B 22(6), Nov/Dec 2004
Sample
was
heated
to
550oC for 30 min.
Sample
was
heated
to
550oC for 60 min.
Sample
was
heated
to
300oC for 40 min.
Surface structure is very sensitive to the annealing temperature
and duration
1.6 1.8 2.0 2.2 2.4 2.6 2.80
2
4
6
8
Cou
nt
Period Across CNT (nm)
2.5 3.0 3.5 4.0 4.5 5.0 5.50
2
4
6
8
Cou
nt
Period along CNT (nm)
AA
BB
DNA‐CNT: Periods of the structure along and across the CNT direction
Angle between A and B = 63.4o
Imaging conditions:Ub
=3 V; It
=10 pA; T=50 K
Peak at this position is also present when there is
no obvious periodic modulation along CNT exists. It
is due to shape of the structure itslef?
Sample
was
heated
to
550oC
for
30
min.
before
imaging
to
remove
organic
residue
from
the
surface
Current prospectsCurrent prospects
Deposit the DNADeposit the DNA--CNT solution onto Au(111) or HOPG surface to CNT solution onto Au(111) or HOPG surface to eliminate heating in sample preparation and improve spatial resoeliminate heating in sample preparation and improve spatial resolutionlution
Acquire spatially resolved dI/dV spectroscopy on new samples ofAcquire spatially resolved dI/dV spectroscopy on new samples of the the DNADNA--CNT hybrids and look for correlation with structural informationCNT hybrids and look for correlation with structural information
Compare the results to the bare CNT samplesCompare the results to the bare CNT samples
Calculate hybrid structural and electronic properties (TCalculate hybrid structural and electronic properties (T--11 team) and 11 team) and compare to experimentcompare to experiment
Theory and modeling
• Realistic ab initio calculations• Comparison with the data• Future directions
Molecular Orbitals of C and C-derivatives
(HOMO)
Cytidine (LUMO)
Cytiside (LUMO)
(HOMO)
Eg=2.44 (2.49) eVEg=2.99eVEg=5.08eV
Eg=4.98 eVEg=5.56 eVEg=7.59 eV
Cytosine (LUMO)
(HOMO)
Eg=5.11 (5.28) eVEg=5.54 eVEg=7.57eV
B3LYPPBE1PBE
BHandHLYPEg=9.49 eV Eg=11.94 eVEg=11.8 eVHF
Eg=3.62 eV (3.56)PW91
DOS of DNA-bases
- 1 5
- 1 2
- 9
- 6
- 3
0
3
6
9T h y m in e
Ene
rgy,
eV
A d e n in e C y to s in e G u a n in e
Eg=5.28(4.47)
Eg=5.54 (4.86)
Eg=5.59(5.03)
Eg=5.41(4.45)(TDDFT)
Experimental Eg: 4.51-4.63 4.4-4.7 4.31-4.59 4.44-4.8
B3LYP
Electronic fingerprint of Guanine
• Electronic detection of a single Guanine• Work on other bases• Potential to image proteins.
0
0 . 2
0 . 4
0 . 6
0 . 8
1
- 3 - 2 - 1 0 1 2
0 4 8 2 0 5 0 _ 1 6 C h 4 . c s v0 4 8 2 0 5 0 _ 1 4 C h 4 . c s v
dI/dV / nS
V s / V
Top:
Tanaka
data on GuaninBottom
:
Theory
calculat
ionOn
LDOS
of G on
Cu(111
)
Backed out full sequence for the observed chunk
aaaacgcgctacagtctgacgxxxxxgxgxxxxxgxxxgxxg
---xxxxxgxgxxxxxgxxxgxxg-- -----
aaaacgcgctacagtctgacg------
This shows that one can back out the dI/dV
features
on other bases in the sameMolecule.
Step A : identify portion you tunnel ing in g‐specific map
Step B: identify other bases in the same chunk.
DNA nanoelectronics and STM
• Community building and growing• Biology vs Physics: view as physical system• Very exciting possibilities at the interface of
Bio and Nano.• Be aware about standard: doped Si. This is a
very tough comparison. Reproducibility, lack of understanding. Nowhere near sequence reliability of PCR. Obvious strength: single molecule.
• Future is bright and full of challenges.