Yang Yang, Xianfeng Song Advisor: Sima Setayeshgar
Journal Club April 11th, 2008
Liquid Crystal Phases of DNA and Implications for The Origin
of Life
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 solido 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 anisotropyo Two different refraction indexo 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 Phaseo Nematic phaseoThe mesogens have no
positional order, but exhibits long-range orientational order.
oMost 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 Phaseo 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.
A typical texture of chiral nematic liquid crystal with long pitch helix. Network-like defect
lines are oily-streak lines.
The structure of chiral nematic liquid crystals
Liquid Crystal Phases: Smectic Phase
o Form well-defined layers that can slide over one anothero Smectic A phase: the mesogen are oriented along the layer
normalo Smectic C phase: the mesogen are tilted away from the layer
normal
Picture of the smectic A phase
Picture of the smectic C phase
Texture of the smectic A phase
Liquid Crystal Phases: Columnar Phases
100× of texture exhibited by the
hexagonal columnar mesophase
Columnar phase formed
by discotic molecules
Columnar phase formed
by rod-like molecules
A class of liquid crystal phases in which molecules assemble into cylindrical structures
Part II: Introduction to Theories of Origin of Life
Origin of Life
o Religion theoryoCreation of humankind and other higher organisms by
God
o Spontaneous Generationonon-living objects giving rise to living organisms
o Scientific theoryoOrigin of organic moleculesoFrom 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 laboratoryoUsing 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
How the relatively simple organic building blocks polymerase and form more complex structures?
From NASA
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 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
ajdubre.tripod.com/.../OriginLifeSci-82500.html
From Organic Molecules to Protocells
o"Genes first" models-the RNA world
o"Metabolism first" models-iron-sulfur world
oOther theory: Bubble Theory
o Carl R. Woese first presented this independent RNA idea in late 1960so Walter Gilbert first used the phrase "RNA World" in 1986o DNA replication need proteins and enzymes while at the origin of life there is no present of any proteino RNA catalyzed all the reactions necessary for a precursor of life’s last common ancestor to survive and replicateo New enzymes replicate DNA and make RNA copies o DNA took the role as the genetic information storage
RNA Word Hypothesis
o First X-ray diffraction image of DNA, photo 51o Taken by Rosalind Franklin in 1952o Critical evidence in identifying the structure of
DNA
DNA Structure
o First and still-using structure model of DNAo Presented by James D. Watson
and Francis Crick in 1953o 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
Franklin R, Gosling RG , Nature 171,1953
"Metabolism first" Models:
Iron-Sulfur World
o Early form of metabolism predated geneticso 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 acidso 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
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 axis
+19° -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
Notes form Prof. Cherbas, Dept. of Biology, Indiana University
Terms Using in The Paper
o DNA ligation: joining linear DNA fragments together with covalent bonds.
o Self-complementary DNA: each of the single strand of the duplex-DNA can form double helix, ex: CCTCAATTGAGG
o Non self-complementary DNA: neither of the single strand of the duplex-DNA can form double helix ex: CCTCAAAACTCC
o Oligomer:o sDNA: short DNA double helix (not single strand
DNA)o 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) criterionoModel: 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 self-complementary sDNA duplex-forming “palindromic” oligomers, along with a variety of noncomplementary and partially complementary oligomers
o 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
DNA Phase Diagramo 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; 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.
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!