Transcript 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: 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
http://dept.kent.edu/spie/liquidcrystals
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)
http://plc.cwru.edu/tutorial/enhanced/files/lc/biref/graphics/birefringence.JPG
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
http://bly.colorado.edu/lcphysics/lcintro/tnlc.html
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.
From Nature 430, 413-414(22 July 2004)
The Schlieren texture, is characteristic of the nematic
phase. The dark regions that represent alignment parallel
or perpendicular to the director are called brushes.
http://dept.kent.edu/spie/liquidcrystals/
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.
http://plc.cwru.edu/tutorial/enhanced/files/lc/phase/phase.htm
The structure of chiral
nematic liquid crystals
http://bly.colorado.edu/lcphysics/textures/
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
http://plc.cwru.edu/tutorial/enhanced/files/lc/phase/phase.htm
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
From Nature 406, 868-871, 2000
Columnar phase
formed by discotic
molecules
From Science 318, 1276 (2007)
Columnar phase
formed by rod-like
molecules
http://www.rsc.org/ej/JM/2001/
b008904o/b008904o-f2.gif
100× of texture exhibited by
the hexagonal columnar
mesophase
Part II: Introduction to Theories of
Origin of Life
Origin of Life
o Scientific theory
o Origin of organic molecules
o From organic molecules to protocells
o Other theories
o Religion theory: humankind and other organisms are created by
God.
o Spontaneous Generation: small organisms like bacterium and frogs
are spontaneously generated in the mud.
o Aliens: organisms were brought to earth by aliens
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 ,1953
o 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
Watson J.D. and Crick F.H.C. Nature, 1953
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(protein).
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.
Origin of Organic Molecules
o Miller's experiments (The Primordial Soup Theory)
o The Deep Sea Vent Theory
o Wächtershäuser’s experiment
“Miller-Urey” Experiments
o Performed by Stanley Miller, and his advisor,
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
Miller S. L., Science ,1953.
Miller S. L., and Urey, H. C . Science, 1959
From NASA
How the relatively simple organic building
blocks polymerize and form more
complex structures?
Deep Sea Vent Theory
o The hot environs of undersea hydrothermal vents were the
birthplace for life.
o In 1999, Japanese researchers synthesized peptides around an
artificial deep-sea vent.
Balter, M. Science, 1998
Imai E., et al. ,Science,1999
Wächtershäuser's experiment
o Early chemistry of life started on mineral
surfaces (e.g. iron pyrites) near deep
hydrothermal vents
o Bubbles on the mineral surfaces acted as
the first ‘cell’
o Amino acids and peptides could be
formed by mixing simple chemical
compounds (carbonmonoxide, hydrogen
sulfide, nickel sulfide and iron sulfide)h
ajdubre.tripod.com/.../OriginLifeSci-82500.html
Huber, C. and Wächterhäuser, G. , Science, 1998
Wächtershäuser, G. , Science 2000.
From Organic Molecules to Protocells
o"Genes first" models-the RNA world
o"Metabolism first" models-iron-sulfur world
RNA World Hypothesis
o Carl R. Woese first presented this independent RNA
idea in late 1960s .
oWalter 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 to survive and replicate
oRelatively short RNA molecules which can
duplicate others have been artificially produced in
the lab
o New enzymes replicate DNA and make mRNA copies
o 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
"Metabolism first" Models:
Iron-Sulfur World
o Early form of metabolism predated genetics
o Metabolism here means a cycle of chemical reactions that produce
energy in a form that can be harnessed by other processes
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.
o 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.
Pending Problem
o 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.
o 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.
o 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
molecule s tend to self-organize themselves to
larger molecule
Part III: Liquid Crystal
Condensation of sDNA Duplexes
Terminology in Paper
o Oligomer: A molecule formed from a small number of monomers.
o Self-complementary: Each single strand of the duplex-DNA can form double
helix with itself. For example:
CCTCAATTGAGG >>
<<GGAGTTAACTCC
o sDNA: Short DNA double helix
o lDNA: Long DNA double helix
o DNA ligation: sDNA join together end-to-end to form lDNA.
o B form of DNA: normal right-handed DNA, every 3.4 nm
makes a turn and there are 10 base pairs per turn
o A form of DNA: right-handed DNA, but every 2.3 nm makes a
turn and there are 11 base pairs per turn.
o Z form of DNA: left-handed DNA due to zigzag bases, every
4.6 nm makes a turn and there are 12 base pairs per turn.
Notes form Prof. Cherbas, Dept. of Biology, Indiana University
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), crystal phase (X)
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.
[*]Onsager, Ann. N.Y. Acad. Sci. 51, 627 (1949); Bolhuis etc, J. Chem. Phys. 106, 666 (1997)
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; NCU, circles; CU-C2, 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.
The phase diagram presents clear 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.
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.
Experiment procedure
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 Within the LC drops, 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.
o Additionally, every ligation in the LC phase produces an extended
complementary oligomer. Thus, LC phase 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!