Transcript Manohar_6May2008_NIRT

Force
Binding Energy between a Nucleotide and
Graphite: Single Molecule Force Microscopy
(SMFM) – AFM Approach
Tip-Surface Distance
Introduction
•
ssDNA wraps around CNT to form
the hybrid.
• Purpose:
Zheng, M. et. al., Nat. Mat. 2003,2,338-342
1. Dispersion, sorting and patterned
placement of CNTs.
2. Transportation of DNA into cells
3. Thermal ablation to kill cancer cells
• Motivation:
1. Binding strength decides stability, dispersion and sorting ability
of the hybrid
2. Interaction of DNA with hydrophobic surfaces
Single Base Binding Energy
G,A,T,C (kBT)
Reference
23.55, 18.91, 18.91, 18.91
Gowtham, S. et. Al. Phys Rev B 2007, 76,
033401-033403
(with graphite)
25.09, 23.16, 21.23, 18.53
(with CNT)
50, 45, 43, 40
Johnson, R. R. et. Al. Nano Lett 2008, 8, 1, 6975
Shi, X. et. Al. Acta Mech Sinica 2005, 21, 249-256
(with graphite)
12.1, 13, 10.5, 10.8
(with CNT)
18.9 for Thymine
Manohar, S. et. Al. J Phys Chem C 2007, 111,
17835-17845
Manohar, S. et. Al. ACS Nano (submitted)
(with graphite)
8 for Adenine (base only)
Sowerby, S. J. Astrobiology 2001, 1, 4, 481-487
(with graphite)
11.5 for Thymidine (SMFM)
Manohar, S. et. Al. ACS Nano (submitted)
(with graphite)
Current Work
Experimental Scheme
AFM Cantilever
–
MHA –
–
Free ssDNA
n Kuhn links
f
MHA – Mercaptohexanoic acid
ssDNA – 5’-T50-3’-O-(CH2)3-SH
AFM Tip
–
–
Separation, Rz
z
y
Adsorbed ssDNA
x
(N-n) Kuhn links
Graphite
Main Results
1000
Approach
Retract
• Control Experiments: No tip
adhesion
Force (pN)
Force (pN)
800
600
400
10
10
Experiment
Line Fit
2
1
200
2
• Gold tip with poly-(dT)50 and
MHA:
4
6
8
10
Distance (nm)
0
0
20
40
60
Tip-Surface Distance (nm)
Desorption forces show plateau force jumps.
Force (pN)
200
a
0
-200
b
155 pN
15
-400
10
1
20
30
Piezo Displacement (nm)
Counts
Force (nN)
2
86 pN
0
-1
10
5
Approach
Retract
-2
0
10
20
30
40
Tip-Surface Distance (nm)
50
0
50
75
100
Force (pN)
125
150
Main Results (contd …)
• Force jump was independent of:
1.
2.
3.
4.
•
•
•
Location on the graphite surface
Rate of peeling or AFM tip velocity
AFM tip used
Ionic Strength of buffer used. Electrostatic contribution to binding energy
is negligible.
Mean value of force jump = 84.2 ± 8.4 pN
Analytical model to relate the measured plateau forces to the
binding energy of DNA bases. This gave single base binding
energy for Thymidine to be 11.5 ± 0.6 kBT.
MD: Estimated single base pull off from graphite surface for
thymine is 18.9 kBT.
Results from the Model:
PfgT ensemble
Dimensionless free energy of adhesion
AFM Cantilever
Partition Function
 4 sinh F 
X  ln 

F


k BT
f
fb
F
k BT
Z
gb
200
AFM Tip
<Rz>/b
<n>
150
1  exp  X   N  1
Free ssDNA
1  exp  X    Separation, R
F
z
n Kuhn links
peel
Force (pN)
Dimensionless Force

z
50
Free Energy G  k B T ln Z
Adsorbed ssDNA
y
0
0
5
10
15
N 20
Dimensionless Average Extension <Rz>/b, Desorbed Links <n>
x
Average Number of Desorbed links


N  1
1

n  








 1  Kuhn links
 exp   X  1 exp N  1   X (N-n)
Graphite
Average end-to-end
distance of
desorbed chain
1

R z  b coth F   n
F

Fpeel = 85 pN, b = 1.6 nm, T = 300
K, N = 18
Condition for Desorption
n  N /2 X  
Results from MD:
Thermodynamic Integration Method
 1
A 

0
 (p, r,  )


d   F h dh  18.9 k B T
where <F>h is the average force to hold the base at a distance, h
from the graphite surface
-5
B
Energy (k T)
0
-10
-15
-20
0.8
1
1.2
1.4
Distance from graphite (nm)
1.6