liquid crystal phases of dna and implications for the origin of life
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DESCRIPTIONLiquid Crystal Phases of DNA and Implications for The Origin of Life. Yang Yang, Xianfeng Song Advisor: Sima Setayeshgar Journal Club April 11 th , 2008. Outline. Part I: Introduction to liquid crystals Part II: Background on theories of origin of life - PowerPoint PPT Presentation
Yang Yang, Xianfeng Song Advisor: Sima SetayeshgarJournal Club April 11th, 2008Liquid Crystal Phases of DNA and Implications for The Origin of Life
OutlinePart I: Introduction to liquid crystals
Part II: Background on theories of origin of life
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.
Part I: Introduction to liquid crystals
Introduction to Liquid CrystalPhases between liquid and solidCan be divided into two types:Thermotropic: exhibit phase transition into the LC phase as temperature changed, due to the anisotropy of molecules.Lyotropic: exhibit phase transition into the LC phase as a function of concentration of the mesogen, formed by amphiphilic molecules in solution. Mesogen is the fundamental unit of a liquid crystal that induces structural order in the crystals.
Birefringence (Double Refraction)Two different refraction indexno is the refractive indices for o-ray (polarization direction is perpendicular to the optical axis, so called director)ne is the refractive indices for e-ray (polarization direction is parallel to the optical axis)A typical behavior due to anisotropy, can be affected by temperature, electrical field, etcCan 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 PolarizersWhen 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 directors direction, LCs thickness, rays frequency. http://bly.colorado.edu/lcphysics/lcintro/tnlc.html
Liquid Crystal Phases: Nematic PhaseThe mesogens exhibit long-range orientational order Have no positional orderThe 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 PhaseThe 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. 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 crystalshttp://plc.cwru.edu/tutorial/enhanced/files/lc/phase/phase.htmhttp://bly.colorado.edu/lcphysics/textures/
Liquid Crystal Phases: Smectic PhaseForm well-defined layers that can slide over one anotherSmectic A phase: the mesogen are oriented along the layer normalSmectic C phase: the mesogen are tilted away from the layer normalPicture of the smectic A phasePicture of the smectic C phaseTexture of the smectic A phase http://plc.cwru.edu/tutorial/enhanced/files/lc/phase/phase.htm
Liquid Crystal Phases: Columnar Phases100 of texture exhibited by the hexagonal columnar mesophase
Columnar phase formed by discotic moleculesColumnar phase formed by rod-like moleculesA class of liquid crystal phases in which molecules assemble into cylindrical structuresFrom Nature 406, 868-871, 2000http://www.rsc.org/ej/JM/2001/b008904o/b008904o-f2.gifFrom Science 318, 1276 (2007)
Application of liquid crystalsLiquid 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
Part II: Introduction to Theories of Origin of Life
Origin of LifeScientific theoryOrigin of organic moleculesFrom organic molecules to protocells
Other theoriesReligion theory: humankind and other organisms are created by God.Spontaneous Generation: small organisms like bacterium and frogs are spontaneously generated in the mud.Aliens: organisms were brought to earth by aliens
First X-ray diffraction image of DNA, photo 51 Taken by Rosalind Franklin in 1952 Critical evidence in identifying the structure of DNA
Structure model of DNA Presented by James D. Watson and Francis Crick in 1953 Double helix with sugar and phosphate parts of the nucleotides forming the two strand Using hydrogen bonds to pair specifically with A opposing to T, and C opposing to G Opposite directions of the two strands of double helixFranklin R, Gosling RG , Nature ,1953Watson J.D. and Crick F.H.C. Nature, 1953
Genetic Information FlowA 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).In transcription, the codons of a gene are copied into messenger RNA by RNA polymerase(protein).
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
Miller's experiments (The Primordial Soup Theory)
The Deep Sea Vent Theory
Miller-Urey Experiments Performed by Stanley Miller, and his advisor, Harold Urey in 1953 Recreating the chemical conditions of the primitive earth in the laboratoryUsing a highly reduced mixture of gases methane, ammonia and hydrogen to form basic organic monomers, such as amino acids. Proving the spontaneously forming of organic molecule on early earth from inorganic precursor
How the relatively simple organic building blocks polymerize and form more complex structures?From NASAMiller S. L., Science ,1953.Miller S. L., and Urey, H. C . Science, 1959
Deep Sea Vent TheoryThe hot environs of undersea hydrothermal vents were the birthplace for life.
In 1999, Japanese researchers synthesized peptides around an artificial deep-sea vent.
Balter, M. Science, 1998 Imai E., et al. ,Science,1999
Wchtershuser's experimentEarly chemistry of life started on mineral surfaces (e.g. iron pyrites) near deep hydrothermal ventsBubbles on the mineral surfaces acted as the first cellAmino acids and peptides could be formed by mixing simple chemical compounds (carbonmonoxide, hydrogen sulfide, nickel sulfide and iron sulfide)h
Huber, C. and Wchterhuser, G. , Science, 1998Wchtershuser, G. , Science 2000.
From Organic Molecules to Protocells"Genes first" models-the RNA world
"Metabolism first" models-iron-sulfur world
Carl R. Woese first presented this independent RNA idea in late 1960s . Walter Gilbert first used the phrase "RNA World" in 1986 DNA replication need proteins and enzymes while at the origin of life there is no present of any protein RNA catalyzed all the reactions necessary for a precursor to survive and replicateRelatively short RNA molecules which can duplicate others have been artificially produced in the lab New enzymes replicate DNA and make mRNA copies 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, 2001RNA World Hypothesis
"Metabolism first" Models: Iron-Sulfur World
Early form of metabolism predated geneticsMetabolism here means a cycle of chemical reactions that produce energy in a form that can be harnessed by other processesSteps for producing proteins:Produce acetic acid through metallic ion catalysisAdd carbon to the acetic acid molecule to produce three-carbon pyruvic acid(CH3COCO2H) Add ammonia to form amino acidsProduce peptides and then proteins. Once protein had been formed, DNA can be replicated and make RNA copies, and followed by translation to proteins
Huber, C. and Wchterhuser, G. , Science, 1998Wchtershuser, G. , Science, 2000.
Pending ProblemOnce 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.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.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
Part III: Liquid Crystal Condens