Liquid Crystal Phases of DNA and Implications for The Origin of Life
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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
Liquid crystal condensation of short DNA duplexes provides a means to form long DNA, which is an essential process in origin of life.
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 changed, due to the anisotropy of molecules.
o Lyotropic: exhibit phase transition into the LC phase as a function of concentration of the mesogen, formed by amphiphilic molecules in solution.
o Mesogen is the fundamental unit of a liquid crystal that induces structural order in the crystals.
http://dept.kent.edu/spie/liquidcrystals
Birefringence (Double Refraction)
o Two different refraction indexo no is the refractive indices for o-ray (polarization direction is
perpendicular to the optical axis, so called director)o ne is the refractive indices for e-ray (polarization direction is
parallel to the optical axis)o A typical behavior due to anisotropy, can be affected by
temperature, electrical field, etco Can twist linear polarization into elliptical polarization if the
polarization direction is not parallel or perpendicular to the optical axis.
http://plc.cwru.edu/tutorial/enhanced/files/lc/biref/graphics/birefringence.JPG
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.
http://bly.colorado.edu/lcphysics/lcintro/tnlc.html
Liquid Crystal Phases: Nematic Phase
oThe mesogens exhibit long-range orientational ordero Have no positional order
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.
http://dept.kent.edu/spie/liquidcrystals/From Nature 430, 413-414(22 July 2004)
Schematic of nematic phase
Liquid Crystal Phases: Chiral Nematic Phaseo 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.
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, chracterized by network-like defect lines.
The structure of chiral nematic liquid crystals
http://plc.cwru.edu/tutorial/enhanced/files/lc/phase/phase.htm http://bly.colorado.edu/lcphysics/textures/
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
http://plc.cwru.edu/tutorial/enhanced/files/lc/phase/phase.htm
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
From Nature 406, 868-871, 2000 http://www.rsc.org/ej/JM/2001/b008904o/b008904o-f2.gif
From Science 318, 1276 (2007)
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.
The liquid crystal on the base changes color with temperature change. From http://demo.physics.uiuc.edu/
LCD display
Origin of Life
o Scientific theoryoOrigin of organic moleculesoFrom organic molecules to protocells
o Other theoriesoReligion theory: humankind and other organisms are
created by God.oSpontaneous Generation: small organisms like bacterium
and frogs are spontaneously generated in the mud.oAliens: organisms were brought to earth by aliens
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 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 ,1953
Watson J.D. and Crick F.H.C. Nature, 1953
Genetic Information Flowo 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 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 precursorHow the relatively simple
organic building blocks polymerize and form more complex structures?
From NASA
Miller S. L., Science ,1953.Miller S. L., and Urey, H. C . Science, 1959
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
Huber, C. and Wächterhäuser, G. , Science, 1998
Wächtershäuser, G. , Science 2000.
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
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 proteino 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
RNA World Hypothesis
"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 catalysiso 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.
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, 1998Wächtershäuser, 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 molecules tend to self-organize themselves to larger molecule
Terminology in the 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 Non self-complementary: Not self-complementary. For example: CCTCAAAACTCC
o sDNA: Short DNA double helix (different than single stranded DNA), with less than 28bps.
o lDNA: Long DNA, refers to DNA with more than 28 bps. o DNA ligation: sDNA join together end-to-end to form
lDNA.
A, B , Z Form of Double strand DNA
Notes form Prof. Cherbas, Dept. of Biology, Indiana University
o B-DNA: Common form in all living creatures. Make a turn every 3.4nm and 10 base pairs.
o A-DNA: Similar to B, but with increase in the number of base pairs per rotation.
o Z-DNA: Left handed form.
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 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 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 = 20°C for 20 > N > 8 and T = 10°C for N = 6.
o 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.
o 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.
LC Ordering from Mixed Solutions of Complementary and Non-complementary Oligomers
o 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.
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 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.
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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