Yang%20Yang,%20Xianfeng%20Song

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Liquid Crystal Phases of DNA and Implications for
The Origin of Life

• Yang Yang, Xianfeng Song
• Advisor Sima Setayeshgar
• Journal Club
• April 11th, 2008

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Outline

• Part I Introduction to liquid crystals
• Part II Background on theories of origin of life
• Part III Liquid crystal condensation of
  6-to-20-base pair DNA duplexes

Liquid crystal condensation of short DNA duplexes
provides a means to form long DNA, which is an
essential process in origin of life.
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Part I Introduction to liquid crystals
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Introduction to Liquid Crystal
http//dept.kent.edu/spie/liquidcrystals

• Phases between liquid and solid
• Can be divided into two types
• Thermotropic exhibit phase transition into the
  LC phase as temperature changed, due to the
  anisotropy of molecules.
• Lyotropic exhibit phase transition into the LC
  phase as a function of concentration of the
  mesogen, formed by amphiphilic molecules in
  solution.
• Mesogen is the fundamental unit of a liquid
  crystal that induces structural order in the
  crystals.

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Birefringence (Double Refraction)
http//plc.cwru.edu/tutorial/enhanced/files/lc/bir
ef/graphics/birefringence.JPG

• Two different refraction index
• no is the refractive indices for o-ray
  (polarization direction is perpendicular to the
  optical axis, so called director)
• ne is the refractive indices for e-ray
  (polarization direction is parallel to the
  optical axis)
• A typical behavior due to anisotropy, can be
  affected by temperature, electrical field, etc
• Can twist linear polarization into elliptical
  polarization if the polarization direction is not
  parallel or perpendicular to the optical axis.

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Optical Devices Crossed Polarizers
http//bly.colorado.edu/lcphysics/lcintro/tnlc.htm
l
When the polarizers are arranged so that their
planes of polarization are perpendicular to each
other, the light is blocked. When the second
filter (called the analyzer) is parallel to the
first, all of the light passed by the first
filter is also transmitted by the second.
When putting LC in between two polarizers, the
polarization state is modified by LC. Now there
will be light come through depends on the
directors direction, LCs thickness, rays
frequency.
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Liquid Crystal Phases Nematic Phase

• The mesogens exhibit long-range orientational
  order
• Have no positional order

http//dept.kent.edu/spie/liquidcrystals/
From Nature 430, 413-414(22 July 2004)
The Schlieren texture, is characteristic of the
nematic phase. The dark regions that represent
director alignment parallel or perpendicular to
the polarizers are called brushes.
Schematic of nematic phase
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Liquid Crystal Phases Chiral Nematic Phase

• The chiral nematic (cholesteric) liquid crystal
  phase is typically composed of chiral molecules
  which produces intermolecular forces that favor
  alignment between molecules at a slight angle to
  one another.
• This leads to the formation of a structure which
  can be visualized as a stack of very thin 2-D
  nematic-like layers with the director in each
  layer twisted with respect to those above and
  below.

http//plc.cwru.edu/tutorial/enhanced/files/lc/pha
se/phase.htm
http//bly.colorado.edu/lcphysics/textures/
A typical texture of chiral nematic liquid
crystal with long pitch helix, chracterized by
network-like defect lines.
The structure of chiral nematic liquid crystals
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Liquid Crystal Phases Smectic Phase
http//plc.cwru.edu/tutorial/enhanced/files/lc/pha
se/phase.htm
Texture of the smectic A phase
Picture of the smectic A phase
Picture of the smectic C phase

• Form well-defined layers that can slide over one
  another
• Smectic A phase the mesogen are oriented along
  the layer normal
• Smectic C phase the mesogen are tilted away from
  the layer normal

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Liquid Crystal Phases Columnar Phases
A class of liquid crystal phases in which
molecules assemble into cylindrical structures
http//www.rsc.org/ej/JM/2001/b008904o/b008904o-f2
.gif
From Nature 406, 868-871, 2000
From Science 318, 1276 (2007)
100 of texture exhibited by the hexagonal
columnar mesophase
Columnar phase formed by discotic molecules
Columnar phase formed by rod-like molecules
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Application of liquid crystals

• Liquid crystal displays (LCDs) relying on the
  optical properties of certain liquid crystals in
  the presence or absence of an electric field.
• Thermotropic chiral LCs whoses pitch varies
  strongly with temperature can be used as crude
  thermometers, since the color of the material
  will change as the pitch is changed.

LCD display
The liquid crystal on the base changes color with
temperature change. From http//demo.physics.uiuc.
edu/
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Part II Introduction to Theories of Origin of
Life
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Origin of Life

• Scientific theory
• Origin of organic molecules
• From organic molecules to protocells
• Other theories
• Religion theory humankind and other organisms
  are created by God.
• Spontaneous Generation small organisms like
  bacterium and frogs are spontaneously generated
  in the mud.
• Aliens organisms were brought to earth by
  aliens

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DNA Structure

• First X-ray diffraction image of DNA, photo 51
• Taken by Rosalind Franklin in 1952
• Critical evidence in identifying the structure
  of DNA

• Structure model of DNA
• Presented by James D. Watson and Francis Crick
  in 1953
• Double helix with sugar and phosphate parts of
  the nucleotides forming the two strand
• Using hydrogen bonds to pair specifically with A
  opposing to T, and C opposing to G
• Opposite directions of the two strands of double
  helix

Franklin R, Gosling RG , Nature ,1953
Watson J.D. and Crick F.H.C. Nature, 1953
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Genetic Information Flow

• A gene is a sequence of DNA that contains genetic
  information and can influence the phenotype of an
  organism. The genetic code consists of
  three-letter 'words' called codons formed from a
  sequence of three nucleotides (e.g. ACT, CAG,
  TTT).
• In transcription, the codons of a gene are copied
  into messenger RNA by RNA polymerase(protein).
• In translation, messenger RNA (mRNA) is decoded
  to produce a specific polypeptide according to
  the rules specified by the genetic code. This
  uses an mRNA sequence as a template to guide the
  synthesis of a chain of amino acids that form a
  protein.

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Origin of Organic Molecules

• Miller's experiments (The Primordial Soup Theory)
• The Deep Sea Vent Theory
• Wächtershäusers experiment

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Miller-Urey Experiments

• Performed by Stanley Miller, and his advisor,
  Harold Urey in 1953
• Recreating the chemical conditions of the
  primitive earth in the laboratory
• Using a highly reduced mixture of gases
  methane, ammonia and hydrogen to form basic
  organic monomers, such as amino acids.
• Proving the spontaneously forming of organic
  molecule on early earth from inorganic precursor

Miller S. L., Science ,1953. Miller S. L., and
Urey, H. C . Science, 1959
How the relatively simple organic building blocks
polymerize and form more complex structures?
From NASA
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Deep Sea Vent Theory

• The hot environs of undersea hydrothermal vents
  were the birthplace for life.
• In 1999, Japanese researchers synthesized
  peptides around an artificial deep-sea vent.
• Balter, M. Science, 1998
• Imai E., et al. ,Science,1999

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Wächtershäuser's experiment

• Early chemistry of life started on mineral
  surfaces (e.g. iron pyrites) near deep
  hydrothermal vents
• Bubbles on the mineral surfaces acted as the
  first cell
• Amino acids and peptides could be formed by
  mixing simple chemical compounds (carbonmonoxide,
  hydrogen sulfide, nickel sulfide and iron
  sulfide)h
• Huber, C. and Wächterhäuser, G. , Science, 1998
• Wächtershäuser, G. , Science 2000. 

ajdubre.tripod.com/.../OriginLifeSci-82500.html
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From Organic Molecules to Protocells

• "Genes first" models-the RNA world
• "Metabolism first" models-iron-sulfur world

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RNA World Hypothesis

• Carl R. Woese first presented this independent
  RNA idea in late 1960s .
• Walter Gilbert first used the phrase "RNA World"
  in 1986
• DNA replication need proteins and enzymes while
  at the origin of life there is no present of any
  protein
• RNA catalyzed all the reactions necessary for a
  precursor to survive and replicate
• Relatively short RNA molecules which can
  duplicate others have been artificially produced
  in the lab
• New enzymes replicate DNA and make mRNA copies
• DNA took the role as the genetic information
  storage
• Woese, C. The Genetic Code, Harper
  Row, New York, 1967
• Gilbert, Walter, Nature, 1986
• Johnston W. K. ,et al. Science, 2001

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"Metabolism first" Models Iron-Sulfur World

• Early form of metabolism predated genetics
• Metabolism here means a cycle of chemical
  reactions that produce energy in a form that can
  be harnessed by other processes
• Steps for producing proteins
• Produce acetic acid through metallic ion
  catalysis
• Add carbon to the acetic acid molecule to produce
  three-carbon pyruvic acid(CH3COCO2H)
• Add ammonia to form amino acids
• Produce peptides and then proteins.
• Once protein had been formed, DNA can be
  replicated and make RNA copies, and followed by
  translation to proteins

Huber, C. and Wächterhäuser, G. , Science,
1998 Wächtershäuser, G. , Science, 2000.
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Pending Problem

• Once having the building blocks (small RNAs,
  small DNAs, small proteins) to the protocell, it
  is still essentially hard to form larger and more
  complex ones which needed by the protocell for
  other purpose.
• For example, even one of the simplest organism,
  E. coli, has approximately 4,639,221 base pairs
  of the genome contain 4,403 genes. The entire
  genome of humankind occupies over 3 billion DNA
  base pairs.
• The formation of long DNA chains by random
  chemistry predicted by those theories is
  essentially impossible.

The paper gives us an idea how the small
molecules tend to self-organize themselves to
larger molecule
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Part III Liquid Crystal Condensation of sDNA
Duplexes
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Terminology in the Paper

• Oligomer A molecule formed from a small number
  of monomers.
• Self-complementary Each single strand of the
  duplex-DNA can form double helix with itself. For
  example
• CCTCAATTGAGG gtgt
• ltltGGAGTTAACTCC
• Non self-complementary Not self-complementary.
  For example CCTCAAAACTCC
• sDNA Short DNA double helix (different than
  single stranded DNA), with less than 28bps.
• lDNA Long DNA, refers to DNA with more than 28
  bps.
• DNA ligation sDNA join together end-to-end to
  form lDNA.

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A, B , Z Form of Double strand DNA

• B-DNA Common form in all living creatures. Make
  a turn every 3.4nm and 10 base pairs.
• A-DNA Similar to B, but with increase in the
  number of base pairs per rotation.
• Z-DNA Left handed form.

Notes form Prof. Cherbas, Dept. of Biology,
Indiana University
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Background on lDNA Liquid Crystal

• Duplex lDNA can form liquid crystal phases when
  hydrated
• Four phases isotropic phase (I), chiral nematic
  (N), uniaxial columnar (CU), crystal phase (X)
• Ranging from mega base pair (bp) semi-flexible
  polymers down to approximately 100 bp rigid
  rod-like segments (B-DNA has bend persistence
  length 50nm)
• Onsager-Bolhuis-Frenkel(OBF) criterion
• Model Monodisperse repulsive hard rods (length
  L, diameter D)
• Conclusions If the rods are sufficiently
  anisotropic in shape, the appearance of nematic
  phase require L/Dgt4.7 (Ngt28bp). If L/Dlt4.7,
  there should be no LC phases at any volume
  fraction. .

Onsager, Ann. N.Y. Acad. Sci. 51, 627 (1949)
Bolhuis etc, J. Chem. Phys. 106, 666 (1997)
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Experiments on sDNA

• Subject The solutions which contains a series of
  self-complementary sDNA duplex-forming
  palindromic oligomers, along with a variety of
  noncomplementary and partially complementary
  oligomers
• Result Short complementary B-form DNA oligomers,
  6 to 20 base pairs in length, are found to
  exhibit nematic and columnar liquid crystal
  phases, even though such duplexes lack the shape
  anisotropy required for liquid crystal ordering

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DNA Phase Diagram

• The phase diagram includes the phase boundaries
  measured for sDNA with those obtained from the
  literature for lDNA, along with the predictions
  from the Onsager and other models of interacting
  semi-flexible rod-shaped particle and aggregate
  solutes.

For N lt 20, phase transitions from experiments
are marked by red open symbols (I-N, triangles
N-CU, circles CU-C2, squares), and the range of
each phase is indicated by colored columns (I,
magenta N, cyan, CU, yellow), at T 20C for 20
gt N gt 8 and T 10C for N 6.

• The phase diagram presents evidence that the
  origin of the LC phases in sDNA is the
  equilibrium end-to-end physical aggregation of
  short duplexes into extended duplex units that
  are long and rigid enough to order.
• Estimates of the stacking energy between duplexes
  are consistent with end-to-end attraction
  resulting from the hydrophobicity of the faces of
  their terminal base pairs.

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LC Ordering from Mixed Solutions of Complementary
and Non-complementary Oligomers

• In the mixed solutions of complementary and
  non-complementary DNA oligomers, the
  complementary ologomers form ridgid duplexes that
  have a tendency to aggregate end-to-end and form
  LC phase, whereas the non-complementary oligomers
  remain as flexible single strands.
• Experiment show if there is a large excess of
  noncomplementary oligomers, the LC phase appears
  as isolated drops.

Experiment procedure
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Discussion Conclusion

• The observation of nematic and columnar LC phase
  provides clear evidence for end-to-end stacking
  of sDNA into rod-shaped aggregates.

• The observation of nematic and columnar LC phase
  provides clear evidence for end-to-end stacking
  of sDNA into rod-shaped aggregates.
• The end-to-end stacking makes the terminal groups
  on neighboring oligomers close to each other and
  the effective concentration much higher than in
  the surrounding isotropic, thus should strongly
  promote ligation in the LC phase.
• Additionally, every ligation in the LC phase
  produces an extended complementary oligomer.

LC phase acts as the positive feedback for
establishing conditions that would strongly
promote their own growth into longer
complementary chains relative to the
non-LC-forming oligomers.
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• Thanks!