DNA SEQUENCING

1
Ramin roohi

Prof. V.Ahmadi
INDEX

 Introduction
 DNA
 DNA sequencing

 History
 3rd Generation sequencing
 Single-molecule real-time sequencing (SMRT)
 Nanopore sequencing using synthetic dna and optical
readout
 DNA sequencing with carbon nanotube electrodes

 conclusion
2
INTRODUCTION
DNA
 Deoxyribonucleic acid (DNA)
is a molecule that encodes the
genetic instructions used in
the development and
functioning of all known living
organisms and many viruses.

 each nucleotide is composed of

a nucleobase (guanine,
adenine, thymine, and
cytosine), recorded using the
letters G, A, T, and C 3

[1] http://en.wikipedia.org/wiki/DNA
INTRODUCION
DNA SEQUENCING
 DNA Sequencing is the process of determining the order of
nucleotides (A,T,C and G) within a DNA.
 A human genome is constructed from about 3 billion
basepairs.

M. Morey et al, Molecular Genetics and Metabolism,2013

DNA SEQUENCING HISTORY
 First Generation
 Sanger Sequencing
 Maxam and Gilbert Sequencing

 Second Generation
 454 Pyrosequencing
 Qiagen-intelligent bio-systems sequencing-by-
synthesis
 Illumina sequencing-by-synthesis
 Polony sequencing–Danaher Motion Polonator
 Sequencing-by-ligation: SOLiD
 Ion-torrent semiconductor sequencing
5
 DNA nanoball sequencing
DNA SEQUENCING HISTORY
 Third Generation
 Single-molecule real-time sequencing (SMRT)
 Real-Time DNA sequencing using fluorescence resonance
energy transfer
 Direct imaging of DNA using electron microscopy
 Direct imaging of DNA sequences using scanning
tunneling microscope tips
 DNA sequencing with nanopores
 Strand-sequencing using ionic current blockage through an
alpha hemolysin pore
 Exonuclease sequencing by modulation of the ionic current
 Nanopore sequencing using synthetic DNA and optical readout
 Strand-sequencing using transverse electron currents
 Sequencing using solid-state graphene nanopores
 Nanopore sequencing-bysynthesis 6
 Transistor-mediated DNA sequencing
SINGLE-MOLECULE REAL-TIME
SEQUENCING (SMRT)

 Zero mode wave (ZMW) guide is utilized to

eliminate the light from the background

J. Eid et al, Science,2009

NANOPORE SEQUENCING USING
SYNTHETIC DNA AND OPTICAL READOUT

 The Molecular conversion is available by 99.9

percent accuracy

B. McNallyet al, Nano Lett, 2010.

NANOPORE SEQUENCING USING
SYNTHETIC DNA AND OPTICAL READOUT

B. McNallyet al, Nano Lett, 2010.

DNA SEQUENCING
WITH CARBON NANOTUBE ELECTRODES

 Si3N4 nanopore and CNT electrodes

10

X.Chen et al, Phys. Rev. B, 2012.

DNA SEQUENCING
WITH CARBON NANOTUBE ELECTRODES

 Molecular Dynamic simulation for Highest

occupied and lowest unoccupied states

11

X.Chen et al, Phys. Rev. B, 2012.

DNA SEQUENCING
WITH CARBON NANOTUBE ELECTRODES

12

X.Chen et al, Phys. Rev. B, 2012.

DNA SEQUENCING
WITH CARBON NANOTUBE ELECTRODES

 Reading sequence by measuring the current at a

fixed voltage

13

X.Chen et al, Phys. Rev. B, 2012.

DNA SEQUENCING
WITH CARBON NANOTUBE ELECTRODES

 Effect of displacement along x

14

X.Chen et al, Phys. Rev. B, 2012.

DNA SEQUENCING
WITH CARBON NANOTUBE ELECTRODES

 Effect of displacement along y-axis and rotation

about z-axis

15

X.Chen et al, Phys. Rev. B, 2012.

DIRECT IMAGING OF DNA SEQUENCES
USING STM TIPS

16
CONCLUSION
 Possibility of chemical methods
 Importance of single molecule resolution in
nanopores
 Fertile ground for optical based sequencing

 Fertile ground for semiconductor technology

17
18