Download journalclub

Liquid Crystal Phases of DNA and
Implications for the origin of life
Yang Yang, Xianfeng Song
Advisor: Sima Setayeshgar
Journal Club
April 11th, 2008
Outline
o Part I: Introduction to liquid crystals
o Part II: Introduction to DNA
o Part III: Background on theories of origin of life
o Part IV: Liquid crystal condensation of 6-to-20-base pair
DNA duplexes
Part I: Introduction to liquid crystals
Introduction to Liquid Crystal
o Phases between liquid and solid
o Can be divided into two types:
o Thermotropic: exhibit phase transition into the LC phase as temperature is changed
o Lyotropic: exhibit phase transition into the LC phase as a function of concentration
of the mesogen
o Mesogen is the fundamental unit of a liquid crystal that induces structural
order in the crystals.
Birefringence (Double Refraction)
o A typical behavior due to anisotropy
o Two different refraction index
o no is the refractive indices for o-ray (polarization direction is
perpendicular to the optical axis, called director)
o ne is the refractive indices for e-ray (polarization direction is parallel to the
optical axis)
o Utilized to view the texture of different phases of LC.
Optical Devices: Crossed polarizers
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 director’s direction, LC’s thickness, ray’s
frequency.
Liquid Crystal Phases: Nematic phase
o Nematic phase
o The mesogens have no
positional order, but exhibits
long-range orientational
order.
o Most nematics are uniaxial,
but some liquid crystals are
biaxial nematics.
The Schlieren texture, is characteristic of the nematic
phase. The dark regions that represent alignment parallel
or perpendicular to the director are called brushes.
Liquid Crystal Phases: Chiral Nematic Phase
o The chiral nematic (cholesteric) liquid crystal phase is typically composed of
nematic mesogenic molecules containing a chiral center which produces
intermolecular forces that favor alignment between molecules at a slight
angle to one another.
o 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.
The structure of chiral
nematic liquid crystals
A typical texture of chiral nematic liquid
crystal with long pitch helix. Network-like
defect lines are oily-streak lines.
Liquid Crystal Phases: Smectic Phase
Picture of the
smectic A phase
Texture of the smectic A
phase
Picture of the
smectic C phase
o Form well-defined layers that can slide over one another
o Smectic A phase: the mesogen are oriented along the layer normal
o Smectic C phase: the mesogen are tilted away from the layer normal
Liquid Crystal Phases: Columnar Phases
A class of liquid crystal phases in which molecules assemble
into cylindrical structures
Columnar phase
formed by discotic
molecules
Columnar phase
formed by rod-like
molecules
100× of texture exhibited by
the hexagonal columnar
mesophase
Part II: Introduction to DNA
DNA
In 1952, Rosalind Franklin took the first X-ray
diffraction image of DNA , photo 51, which was
critical evidence in identifying the structure of DNA.
In 1953, James D. Watson and Francis Crick
described the double helix structure of DNA .
oDNA is a double helix, with the sugar and
phosphate parts of nucleotides forming the two
strands of the helix, and the nucleotide bases
pointing into the helix and stacking on top of each
other.
oThe nucleotide bases use hydrogen bonds to pair
specifically, with an A always opposing a T, and a C
always opposing a G.
oThe two strands of the double helix run in opposite
directions.
DNA and RNA Structure
A, B , Z form of DNA
A
B
Z
Helix sense
Right handed
Right-handed Left handed
Repeating unit
1 bp
1bp
2 bp
Rotation/bp
33.6°
35.9°
60°/2
Mean bp/turn
10.7
10.0
12
Inclination of bp to +19°
axis
-1.2°
-9°
Rise/bp along axis 2.3Å
3.32Å
3.8Å
Pitch/turn of helix 24.6Å
33.2Å
45.6Å
Mean propeller
twist
+18°
+16°
0°
Glycosyl angle
anti
anti
C: anti, G: syn
Sugar pucker
C3'-endo
C2'-endo
C: C2'-endo, G:
C2'-exo
Diameter
26Å
20Å
18Å
Genetic Information Flow
o 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).
o In transcription, the codons of a gene are copied into messenger RNA by RNA
polymerase.
o 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.
Part III: Theories of origin of life
Origin of Life
o Before the mid-17th century, most people believed that God had
created humankind and other higher organisms and that insects,
frogs and other small creatures could arise spontaneously in mud
or decaying matter.
o Scientific theory
o Origin of organic molecules
o From organic molecules to protocells
Origin of organic molecules
o Miller's experiments (The Primordial Soup Theory): using a highly
reduced mixture of gases – methane, ammonia and hydrogen – to form basic organic
monomers, such as amino acids.
o The Deep Sea Vent Theory: hydrogen-sulfide and hydrogen coming out from the
vent in contact with a suitable oxidant, such as carbon dioxide can release chemical
energy.
o Wächtershäuser's hypothesis: In 1997, Wächtershäuser and Claudia Huber mixed
carbon monoxide, hydrogen sulfide, nickel sulfide, and iron sulfide particles at 100°C and
demonstrated that amino acids could form.
o Radioactive beach theory: stronger tidal processes from a much closer moon may
have concentrated radioactive grains of uranium and other radioactive elements at the high
water mark on primordial beaches where they may have been responsible for generating life's
building blocks.
Origin of Organic Molecules:
Miller's experiments
In 1953 a graduate student, Stanley Miller, and his
professor, Harold Urey, performed an experiment
that proved organic molecules could have
spontaneously formed on early Earth from inorganic
precursors. The now-famous “Miller-Urey
experiment” used a highly reduced mixture of gases
– methane, ammonia and hydrogen – to form basic
organic monomers, such as amino acids.
The Miller-Urey experiment attempted to recreate
the chemical conditions of the primitive Earth in the
laboratory, and synthesized some of the building
blocks of life.
How the relatively simple organic building
blocks polymerase and form more
complex structures?
From Organic Molecules to Protocells
o "Genes first" models-the RNA world: the nucleic acids comes first.
o "Metabolism first" models-iron-sulfur world : the evolution of
biochemical reactions and pathways comes first
o Bubble Theory: Bubble on the shore is a hypothetical precursor to the
modern cell membrane. If protein appears in the bubble, it will spread when
bubble burst. When the material accumulate enough, protocell may be
occur.
From Organic Molecules to Protocells:
RNA Word hypothesis
In the late 1960s Carl R. Woese present this
independent RNA idea.
The phrase "RNA World" was first used by
Nobel laureate Walter Gilbert in 1986, in a
commentary on recent observations of the
catalytic properties of various forms of RNA.
This is a world in which RNA catalyzed all the
reactions necessary for a precursor of life's last
common ancestor to survive and replicate.
Difficulties
o The formation of molecular chains as uniform as DNA by
random chemistry is essentially impossible.
The paper gives us
an idea how the
small molecule s
tend to self-organize
themselves to larger
molecule
Part IV: Liquid crystal condensation
of 6-to-20-base pair DNA duplexes
Background
o Duplex lDNA can form liquid crystal phases when hydrated:
o Four phases: isotropic phase (I), chiral nematic (N), uniaxial columnar
(CU)
o 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)
o Onsager-Bolhuis-Frenkel(OBF) criterion
o Model: Monodisperse repulsive hard rods (length L, diameter D)
o Conclusions: If the rods are sufficiently anisotropic in shape, the
appearance of nematic phase require: L/D>4.7 (N>28bp). If
L/D<4.7, there should be no LC phases at any volume fraction.
Experiments
o
Subject: The solutions which
contains a series of selfcomplementary sDNA duplexforming “palindromic” oligomers,
along with a variety of
noncomplementary and partially
complementary oligomers
o
Result: Short complementary Bform 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
Phase Diagram
o 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 < 20, phase transitions
from our data are marked by
red open symbols (I-N,
triangles; N-CU, circles; CUC2, squares), and the range of
each phase is indicated by
colored columns (I, magenta;
N, cyan, CU, yellow), at T =
20°C for 20 > N > 8 and T
= 10°C for N = 6.
LC Ordering from Mixed Solutions of Complementary and
Non-complementary Oligomers
o The addition of unpaired bases at the
sDNA duplex ends, eliminates LC
ordering by weakening end-to-end
adhesion. This interplay of sequence
and LC ordering leads to a remarkable
means of condensation of
complementary sDNA duplexes from
mixed solutions of complementary
and noncomplementary oligomers.
o Experiment show if there is a large
excess of noncomplementary
oligomers, the LC phase appears as
isolated drops.
Discussion & Conclusion
o The observation of nematic and columnar LC phase provides clear
evidence for end-to-end stacking of sDNA into rod-shaped aggregates.
o The end-to-end stacking makes the DNA concentration is much higher
than in the surrounding isotropic, which has potential implications for
the prebiotic chemical generation of complementarily H-bonded
molecular assemblies, which will promote ligation in the LC phase.
o Additionally, every ligation in the LC phase produces an extended
complementary oligomer. Thus, the formation of the LC phase by the
complementary duplexes has the autocatalytic effect of establishing
conditions that would strongly promote their own growth into longer
complementary chains relative to the non-LC-forming oligomers.
Thanks!