Title: Multiscale model of electronic behavior and localization in stretched dry DNA
1Multiscale model of electronic behavior and
localization in stretched dry DNA
- R. L. Barnett, P. Maragakis, A. Turner, M. Fyta ,
E. Kaxiras - J Mater Sci (2007) 42 8894 - 8903
- Presented by
- Pooja Shrestha
2Introduction
- The mechanism of charge transport has been
subject of numerous studies in past few years.
These works address the problem of DNA stretching
effects on the electronic states and the electron
localization. - Eley and Spivey 1 introduced the notion of
efficient charge transport along the stacked
pi-orbitals of the DNA bases. - More recent electron transport experiments on DNA
have widely varying results showing alternatively
insulating behavior, semi-conducting behavior,
ohmic conductivity and proximity induced
superconductivity. - There is a large diversity of the DNA forms in
terms of its composition, length and structure.
The electronic and transport properties of DNA
are directly influenced by its different
conformations as well as by environmental factors
such as counterions, impurities or temperature.
DNA electrode contact and rich variety of
structures that it assume are cause of
variability in experimental measurements. - (1). Eley DD, Spivey DI
(1961) Trans Faraday Soc 58 411
3DNA can be used to
- Build nanostructure
- Guide material synthesis
- Construct nanomaterial device
- Perform computations
4A short introduction to DNA
- DNA is a nucleic acid that contains the genetic
information used in development and functioning
of all known living organism and some virus. - Nucleic acid is a macromolecule composed of
chains of monomeric nucleotide which is a
chemical compound that consists of three
portions nitrogenous base, sugar and phosphate
groups. - Chemically, DNA is long polymer made from
repeating units called nucleotides, with a
backbone made of sugars and phosphate groups.
Single strand DNA
http//www.nanoroadmap.it/events/first_conference/
presentations/simmel.pdf
5Continued..
-
- DNA exist as the pair of molecule in the shape
of double helix which is stabilized by hydrogen
bonds between base attached to two stands
Form of double helix
http//www.nanoroadmap.it/events/first_conference/
presentations/simmel.pdf
6Continued..
- Each types of base on one strand forms a bond
with just one type of base in other strand which
is called complementary base pairing. Eg - A-T
- C-G
- T-A
- G-C
- where, A Adenine
- C Cytosine
- G Guanine
- T Thymine
Base pairing
http//www.nanoroadmap.it/events/first_conference/
presentations/simmel.pdf
7Continued..
- Double helix is also stabilized by hydrophobic
effect and pi stacking. - An aromatic interaction (or pi-pi interaction) is
a noncovalent interaction between organic
compounds containing aromatic moieties. - pi-pi interaction is caused by intermolecular
overlapping of p-orbitals. - In DNA pi stacking occurs between adjacent
nucleotides. Aromatic ring are positioned nearly
perpendicular to the length of the DNA strands
and arranged parallel to each other allowing the
bases to participate in aromatic interaction. -
http//www.quantumconsciousness.org/images/DNA02.g
if
8Theoretical methods
- Theoretical efforts to understand the electronic
behavior and transport in DNA can be divided into
two general categories -
- Model calculations using effective Hamiltonian
and master equations to describe the dynamics of
electrons and holes in DNA 4. The main
limitation of such approach lies in the
difficulty of determining accurate values for the
parameters in effective Hamiltonian. - Ab initio calculations can provide an accurate
and detailed description of the electronic
features but this approach is typically limited
to a small number of atoms due to computational
cost and cannot handle the full complexity of DNA
molecule in various conformations. -
- (4). Caetano RA, Schulz PA (2005) Phys Rev Lett
95 126601
9Continued..
- The calculations are based on density-functional
theory and some approximations are employed to
handle computational demands. The results have
been compared to an efficient and realistic
semi-empirical model 2 in order to establish
the validity of the latter approach. - The poly(CG)-poly(CG) structures obtained in the
pioneering study of Lebrun and Lavery 3 are
used as representative structure for stretching
effects which models two different modes of
stretching - pulling on opposite 3- 3 ends unwound helix
leading to ribbon like structure and - pulling on opposite 5- 5 ends leads helix
contraction - Dry and neutral DNA structure has been taken
where the negatively charged groups on the
backbone are passivated by protons water
molecules or counterions (such as Na ion) are not
considered in the calculations. -
(2). Elstner M, et.al. (1998) Phys Rev B 58
7260 (3). Lebrun A, Lavery R (1996) Nucl Ac Res
24 2260
10Ab initio calculations
- Three different implementations of
density-functional theory have been used to study
the nature of electronic states in individual
bases and in base pairs a method that uses
atomic-like orbitals as the basis, one that uses
plane waves and third that uses a real-space
grid. - For consistency and simplicity same
exchange-correlation functional has been used in
local-density approximation 5. - In each methods pseudopotentials are represented
by the Trouiller-Martins type in SIESTA, the
Vanderbilt ultrasoft type in VASP and the
Hammann-Schluter-Chiang type in HARES with
computational parameters that ensure high level
of convergence. - (5). Perdew JP. Zunger A, (1981) Phys Rev B
23 7260
11SIESTA a linear scaling density functional method
- Siesta (Spanish Initiative for Electronic
Simulations with Thousands of Atoms) is both a
method and its computer program implementation,
to perform electronic structure calculations and
ab initio molecular dynamics simulations of
molecules and solids. - It uses the standard Kohn-Sham selfconsistent
density functional method in the local density
(LDA-LSD) or generalized gradient (GGA)
approximations. - It uses norm-conserving pseudopotentials in its
fully nonlocal form. - The basis set is a very general and flexible
linear combination of numerical atomic orbitals
(LCAO). - It projects the electron wavefunctions and
density onto a real-space grid in order to
calculate the Hartree and exchange-correlation
potentials and their matrix elements.
12Continued..
- It allows the use of localized linear
combinations of the occupied orbitals
(valence-bond or Wannier-like functions), making
the computer time and memory scale linearly with
the number of atoms. Simulations with several
hundred atoms are feasible with modest
workstations. - It also provides
- Total and partial energies.
- Atomic forces.
- Stress tensor.
- Electric dipole moment.
- Atomic, orbital and bond populations (Mulliken).
- Electron density
http//www.uam.es/departamentos/ciencias/fismateri
ac/siesta/
13Semi-empirical model
- 18 base pairs of poly(CG)-poly(CG) DNA sequence
is used which has been stretched by 30, 60 and
90. Within the semi-empirical scheme the
electronic eigenfunctions are expressed as -
- where the basis set includes the s and p atomic
orbitals for each atom in the system. The
coefficients are numerical constants. - This method uses second order expansion in the
electronic density to obtain the total energy. - The result for band gaps is in excellent
agreement with those of the ab initio simulation.
14Results and discussion
- The structure of base pairs is shown with
labeled atoms in each base Figure (1).
Figure (1) The DNA base pairs AT (top) and CG
(bottom), with the atoms labeled. The purines (A,
G) are on the right, the pyrimidines (T, C) on
the left. Atom labeling follows standard notation
convention.
15Continued..
- The HOMO (highest occupied molecular orbital)
state of AT pair is exactly the same as that of
the HOMO state of the isolated A and the LUMO
(lowest unoccupied molecular orbital) state of AT
is same as that of the isolated T. - The HOMO state of CG pair is exactly the same as
that of the HOMO state of the isolated G and the
LUMO state of CG is same as that of the isolated
C. - This shows that purines (A or G) give rise to the
HOMO state, while the pyrimidines (C or T) are
responsible for the LUMO states of each pair.
Thus it is clear that all p-orbitals which
belongs to purine or pyrimidine contribute to
respective HOMO or LUMO state of base pair.
This is in agreement with calculation with
absorption spectra of DNA base and base pairs 6 - (6). Varsano D, Felice RI, Marques MAL, Rubio A
(2006) J Phys Chem B 110 7129
Figure (2) The frontier states in the base pairs
and their identification with corresponding
orbitals in the isolated bases. The middle figure
in each panel shows the total charge density on
the plane of the base pair, with higher values of
the charge density in red and lower values in
blue. The figure on the left shows the HOMO state
and the figure on the right shows the LUMO state,
where red and blue isosurfaces correspond to
positive and negative values of the wave
functions. The labels on the left denote the type
of bases and base pairs.
16Continued..
- HOMO and LUMO states are slightly affected when
the two components of base pair are separated
along the direction of hydrogen-bond. - Only in the reason where the backbone distance is
significantly smaller than equilibrium value,
interaction between the two bases shifts the
eigenvalues of electronic state appreciably but
the shift is relatively small for the HOMO and
LUMO states. - Band gap of the AT pair is significantly larger
(3 eV) than that of CG pair (2 eV) and the HOMO
and LUMO states of CG pair lie within band gap of
AT pair.
Figure (3) Eigenvalues of states in the AT and
CG base pairs as a function of backbone distance.
In each case three states are included above and
below the band gap. Lines are results from SIESTA
calculations, points are results from HARES
calculations (see text). The frontier orbitals in
both pairs are related to one component of the
pair as indicated by the labels. The equilibrium
backbone distance is denoted by a vertical dashed
line.
17Continued..
- Eigenvalue shows slight dependence on axial
distance and the angle of rotation except for
small values of the axial distance which
correspond to unphysical small separation between
two base pairs.
Figure (4) Eigenvalues of states in the AT-AT,
CG-CG and ATCG base pair combinations as a
function of the distance along the helical axis
(at zero angle of rotation) and the rotation
angle around the helical axis (at the equilibrium
axial distance).
18Continued..
- The radius of the sphere centered on a particular
atom is proportional to the magnitude of the
dominant coefficient at this site which is
essentially proportional to the local electronic
density. - As DNA becomes more elongated, orbitals overlap
is less and become localized for high stretching.
Figure (5) The DNA structures for the
unstretched (top) and the different amounts of
stretching in the 3-3 and the 5-5 modes with
features of the frontier orbitals described by
the blue (HOMO) and red (LUMO) spheres. For both
modes theamount of stretching is (a) 30, (b)
60, and (c) 90 relative to the unstretched
structure, which is the BDNA form. The 3-5
orientations of the poly(CG)-poly(CG) sequence
are shown in the left panel at 90 stretching,
whereth ese the structure is easier to visualize.
19Conclusions
- The external force subjected to DNA double helix
stretch elastically and have a dramatic effect on
electronic properties at the atomic scale and on
electrical transport along DNA. - Purines are found to be associated with the HOMO
states while the pyrimidines with the LUMO
states. - In the AT-CG combination the HOMO and LUMO states
are identified with those of CG pair. - For all combinations of bases and base pairs the
nature of these states is not affected by
separation of bases or base pairs along different
directions or rotation along the helical axis. - Electron hopping along DNA molecule is the
function of stretching which is stronger for 3-
3 mode than 5- 5 mode.
20ANY QUESTION ?
21THANK YOU !