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
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 is changedLyotropic: exhibit phase transition into the LC phase as a function of concentration of the mesogenMesogen is the fundamental unit of a liquid crystal that induces structural order in the crystals.
Birefringence (Double Refraction)A typical behavior due to anisotropyTwo different refraction indexno is the refractive indices for o-ray (polarization direction is perpendicular to the optical axis, called director)ne is the refractive indices for e-ray (polarization direction is parallel to the optical axis)Utilized to view the texture of different phases of LC. 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 PhaseNematic phaseThe mesogens have no positional order, but exhibits long-range orientational order. 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. http://dept.kent.edu/spie/liquidcrystals/From Nature 430, 413-414(22 July 2004)
Liquid Crystal Phases: Chiral Nematic PhaseThe 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. 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 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)
Part II: Introduction to Theories of Origin of Life
Origin of LifeReligion theoryCreation of humankind and other higher organisms by God
Spontaneous GenerationNon-living objects giving rise to living organisms
Scientific theoryOrigin of organic moleculesFrom organic molecules to protocells
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 professor, 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 being the birthplace for life (Balter, M. Science, 1998 ).
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 (Gold, Thomas. The Deep, Hot Biosphere. New York: Springer-Verlag ,1999).
Synthesizing peptides around an artificial deep-sea vent by Japanese researchers in 1999 (Ei-ichi Imai, et al. ,Science,1999).
Wchtershuser's hypothesisEarly chemistry of life starting on mineral surfaces (e.g. iron pyrites) near deep hydrothermal ventsBubbles on the mineral surfaces acting as the first cellDemonstrating amino acids and peptide could be formed by mixing carbon, monoxide, hydrogen sulfide, nickel sulfide and iron sulfide by Wchtershuser and Claudia Huber, in 1997 and 1998
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
Other theory: Bubble Theory
Carl R. Woese first presented this independent RNA idea in late 1960s (Woese, C. The Genetic Code, Harper & Row, New York, 1967). Walter Gilbert first used the phrase "RNA World" in 1986 (Gilbert, Walter, Nature, 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 (Johnston W. K. ,et al. Science, 2001) New enzymes replicate DNA and make RNA copies DNA took the role as the genetic information storageRNA Word Hypothesis
First X-ray diffraction image of DNA, photo 51 Taken by Rosalind Franklin in 1952 Critical evidence in identifying the structure of DNA
First and still-using 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
"Metabolism first" Models: Iron-Sulfur World
Early form of metabolism predated geneticsSteps 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.
Huber, C. and Wchterhuser, G. , Science, 1998Wchtershuser, G. , Science, 2000.
Other theory: Bubble Theory
Solving the problem where the cell membrane comes fromBubble on the shore acting as a hypothetical precursor to the modern cell membrane Spreading the protein inside the bubble when the bubble burst as cell divisionProtocell starting to form when accumulating enough material"The Cell: Evolution of the First Organism" by Joseph Panno
Pending ProblemThe 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 DNANotes form Prof. Cherbas, Dept. of Biology, Indiana University
ABZHelix senseRight handedRight-handedLeft handedRepeating unit1 bp1bp2 bpRotation/bp33.635.960/2Mean bp/turn10.710.012Inclination of bp to axis+19-1.2-9Rise/bp along axis2.33.323.8Pitch/turn of helix24.633.245.6Mean propeller twist+18+160Glycosyl angleantiantiC: anti, G: synSugar puckerC3'-endoC2'-endoC: C2'-endo, G: C2'-exoDiameter262018
Part III: Liquid Crystal Condensation of sDNA Duplexes
- Terminology in LiteratureOligomer: A molecule formed from a small number of monomers.Self-complementary: Each single strand of the duplex-DNA can form double helix with itself. For example: CCTCAATTGAGG >>
Background on lDNA Liquid CrystalDuplex lDNA can form liquid crystal phases when hydrated:Four phases: isotropic phase (I), chiral nematic (N), uniaxial columnar (CU), crystal phase (X)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)
Onsager-Bolhuis-Frenkel(OBF) criterion[*]Model: Monodisperse repulsive hard rods (length L, diameter D)Conclusions: If the rods are sufficiently anisotropic in shape, the appearance of nematic phase require: L/D>4.7 (N>28bp). If L/D
Experiments on sDNASubject: The solutions which contains a series of