Transcript journalclub-v4 - Indiana University

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: Background on theories of origin of life
o Part III: 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 Theories of
Origin of Life
Origin of Life
o Religion theory
o Creation of humankind and other higher organisms by God
o Spontaneous Generation
o non-living objects giving rise to living organisms
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)
o The Deep Sea Vent Theory
o Wächtershäuser’s hypothesis
“Miller-Urey” experiments
o Performed by Stanley Miller, and his
professor, Harold Urey in 1953
o Recreating the chemical conditions of
the primitive earth in the laboratory
oUsing a highly reduced mixture of
gases – methane, ammonia and
hydrogen – to form basic organic
monomers, such as amino acids.
o Proving the spontaneously forming of
organic molecule on early earth from
inorganic precursor
From NASA
How the relatively simple organic building
blocks polymerase and form more
complex structures?
Deep Sea Vent Theory
o The hot environs of undersea hydrothermal vents being the
birthplace for life
o Dr. Gold Thomas clamming the upwelling petroleum acting
as a nutrient for deep-dwelling microorganisms that are the
source of the biological molecules found in crude oil
o Synthesizing peptides around an artificial deep-sea vent by
Japanese researchers in 1999 (Ei-ichi Imai, et al. Science,1999)
Wächtershäuser's hypothesis
o Early chemistry of life starting on
ajdubre.tripod.com/.../OriginLifeSci-82500.html
mineral surfaces (e.g. iron pyrites)
near deep hydrothermal vents
o Bubbles on the mineral surfaces
acting as the first ‘cell’
o Demonstrating amino acids could
form by mixing carbon,
monoxide, hydrogen sulfide,
nickel sulfide and iron sulfide by
Wächtershäuser and Claudia
Huber, in 1997
From Organic Molecules to
Protocells
o"Genes first" models-the RNA world
o"Metabolism first" models-iron-sulfur world
oOther theory: Bubble Theory
RNA Word Hypothesis
o Carl R. Woese first presented this independent
RNA idea in late 1960s
o Walter Gilbert first used the phrase "RNA World"
in 1986
o DNA replication need proteins and enzymes while
at the origin of life there is no present of any protein
o RNA catalyzed all the reactions necessary for a
precursor of life’s last common ancestor to survive
and replicate
o New enzymes replicate DNA and make RNA
copies
o DNA took the role as the genetic information
storage
DNA Structure
o First X-ray diffraction image of DNA, photo 51
o Taken by Rosalind Franklin in 1952
o Critical evidence in identifying the structure of DNA
Franklin R, Gosling RG , Nature 171,1953
o First and still-using structure model of DNA
o Presented by James D. Watson and Francis
Crick in 1953
o Double helix with sugar and phosphate parts
of the nucleotides forming the two strand
o Using hydrogen bonds to pair specifically
with A opposing to T, and C opposing to G
o Opposite directions of the two strands of
double helix
"Metabolism first" Models:
Iron-Sulfur World
o Early form of metabolism predated genetics
o steps for producing proteins:
o Produce acetic acid through metallic ion catalysis
o Add carbon to the acetic acid molecule to produce three-carbon
pyruvic acid(CH3COCO2H)
o Add ammonia to form amino acids
o Produce peptides and then proteins.
Other theory: Bubble Theory
o Solving the problem where the cell membrane comes from
o Bubble on the shore acting as a hypothetical precursor to the
modern cell membrane
o Spreading the protein inside the bubble when the bubble
burst as cell division
o Protocell starting to form when accumulating enough
‘material’
Pending Problem
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
A, B , Z Form of Double strand DNA
Notes form Prof. Cherbas, Dept. of Biology,
Indiana University
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
Terms Using in The Paper
o DNA ligation: joining linear DNA fragments together with
o
o
o
o
o
covalent bonds.
Self-complementary DNA: each of the single strand of the
duplex-DNA can form double helix, ex: CCTCAATTGAGG
Non self-complementary DNA: neither of the single strand of
the duplex-DNA can form double helix ex: CCTCAAAACTCC
Oligomer:
sDNA: short DNA double helix (not single strand DNA)
Onsager rigid-rod limit:
Part III: Liquid Crystal
Condensation of sDNA Duplexes
Background on lDNA Liquid Crystal
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 on sDNA
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
DNA 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!