Liquid Crystal Phases of DNA and Implications for The Origin of Life

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Liquid 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


<ul><li><p>Yang Yang, Xianfeng Song Advisor: Sima SetayeshgarJournal Club April 11th, 2008Liquid Crystal Phases of DNA and Implications for The Origin of Life</p></li><li><p>OutlinePart I: Introduction to liquid crystals</p><p>Part II: Background on theories of origin of life</p><p>Part III: Liquid crystal condensation of 6-to-20-base pair DNA duplexes </p></li><li><p>Part I: Introduction to liquid crystals</p></li><li><p>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. </p><p></p></li><li><p>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.</p></li><li><p>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.</p><p>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.</p></li><li><p>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.</p><p>The Schlieren texture, is characteristic of the nematic phase. The dark regions that represent alignment parallel or perpendicular to the director are called brushes. Nature 430, 413-414(22 July 2004)</p></li><li><p>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.</p><p> 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</p></li><li><p>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</p></li><li><p>Liquid Crystal Phases: Columnar Phases100 of texture exhibited by the hexagonal columnar mesophase</p><p>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, 2000 Science 318, 1276 (2007) </p></li><li><p>Part II: Introduction to Theories of Origin of Life</p></li><li><p>Origin of LifeReligion theoryCreation of humankind and other higher organisms by God</p><p>Spontaneous GenerationNon-living objects giving rise to living organisms</p><p>Scientific theoryOrigin of organic moleculesFrom organic molecules to protocells</p></li><li><p>Origin of Organic Molecules</p><p>Miller's experiments (The Primordial Soup Theory)</p><p>The Deep Sea Vent Theory</p><p>Wchtershusers hypothesis</p></li><li><p>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</p><p>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</p></li><li><p>Deep Sea Vent TheoryThe hot environs of undersea hydrothermal vents were the birthplace for life (Balter, M. Science, 1998 ).</p><p>Dr. Gold ,Thomas clammed 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).</p><p>In 1999, Japanese researchers synthesized peptides around an artificial deep-sea vent. (Ei-ichi Imai, et al. ,Science,1999).</p></li><li><p>Wchtershuser's hypothesisEarly 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 peptide could be formed by mixing carbon, monoxide, hydrogen sulfide, nickel sulfide and iron sulfide by Wchtershuser and Claudia Huber, in 1997 and 1998</p><p> Huber, C. and Wchterhuser, G. , Science, 1998Wchtershuser, G. , Science 2000. </p><p> </p></li><li><p>From Organic Molecules to Protocells"Genes first" models-the RNA world</p><p>"Metabolism first" models-iron-sulfur world </p><p>Other theory: Bubble Theory</p></li><li><p> Carl R. Woese first presented this independent RNA idea in late 1960s (Woese, C. The Genetic Code, Harper &amp; 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</p></li><li><p> First X-ray diffraction image of DNA, photo 51 Taken by Rosalind Franklin in 1952 Critical evidence in identifying the structure of DNA</p><p>DNA Structure</p><p> 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</p></li><li><p>"Metabolism first" Models: Iron-Sulfur World </p><p>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. </p><p>Huber, C. and Wchterhuser, G. , Science, 1998Wchtershuser, G. , Science, 2000.</p></li><li><p>Other theory: Bubble Theory</p><p>It could solve the problem where the cell membrane comes fromBubble on the shore acted as a hypothetical precursor to the modern cell membrane It spread the protein inside the bubble when the bubble burst like cell divisionProtocell started to form when accumulating enough material"The Cell: Evolution of the First Organism" by Joseph Panno </p></li><li><p>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 </p></li><li><p>A, B , Z Form of Double strand DNANotes form Prof. Cherbas, Dept. of Biology, Indiana University</p><p>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</p></li><li><p>Part III: Liquid Crystal Condensation of sDNA Duplexes </p></li><li>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 &gt;&gt; </li><li><p>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)</p><p>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&gt;4.7 (N&gt;28bp). If L/D</p></li><li><p>Experiments on sDNASubject: The solutions which contains a series of self-complementary sDNA duplex-forming palindromic oligomers, along with a variety of noncomplementary and partially complementary oligomers</p><p>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</p></li><li><p>DNA Phase DiagramThe 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 &lt; 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 = 20C for 20 &gt; N &gt; 8 and T = 10C 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. </p></li><li><p>LC Ordering from Mixed Solutions of Complementary and Non-complementary OligomersThe 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. Experiment show if there is a large excess of noncomplementary oligomers, the LC phase appears as isolated drops. </p><p>Experiment procedure</p></li><li><p>Discussion &amp; ConclusionThe observation of nematic and columnar LC phase provides clear evidence for end-to-end stacking of sDNA into rod-shaped aggregates.</p><p>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. 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. </p><p>The observation of nematic and columnar LC phase provides clear evidence for end-to-end stacking of sDNA into rod-shaped aggregates.</p></li><li><p>Thanks!</p><p>I am thinking to put Part II and Part II together. </p><p>**</p><p>LCs exhibit birefringence (double refraction): the refraction index is different for different polarizationno: the refractive indices for polarizations parallel(ordinary) to the optical axisNe: the refractive indices for polarization perpendicular(extraordinary) to the optical axis.Application to polarzied light studies of LCConsider the case where a liquid crystal sample is placed between crossed polarizers whose transmission axes are aligned at some angle between the fast and slow direction of the material. Because of the birefringent nature of the sample, the incoming linearly polarized light becomes elliptically polarized, as you have already found in the simulation. When this ray reaches the second polarizer, there is now a component that can pass through, and the region appears bright.If the transmission axis of the first polarizer is parallel to either the ordinary or extraordinary directions, the light is not broken up into components, and no change in the polarization state occurs. In this case, there is not a transmitted component and the region appears dark.</p><p>In a typical liquid crystal, the birefringence and length are not constant over the entire sample. This means that some areas appear light and others appear dark, as shown in the following microscope picture of a nematic liquid crystal, taken between crossed polarizers. The light and dark areas that denote regions of differing director orientation, birefringence, and length. </p><p>*dd*;imgrefurl=;h=338&amp;w=450&amp;sz=52&amp;hl=en&amp;start=2&amp;sig2=-pZ-PWpdkVdwZFsQt-A9hQ&amp;um=1&amp;tbnid=esi7-DsqUsCp2M:&amp;tbnh=95&amp;tbnw=127&amp;ei=T3v_R9vJA5juiwH29pi8Cg&amp;prev=/images%3Fq%3DSchlieren%2Btexture%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26rls%3Dorg.mozilla:en-US:official%26sa%3DN*;imgrefurl=;h=272&amp;w=392&amp;sz=117&amp;hl=en&amp;start=11&amp;sig2=jWKL3xIphkjwMqXjnNVugg&amp;um=1&amp;tbnid=CMc1l_GaokFviM:&amp;tbnh=85&amp;tbnw=123&amp;ei=poD_R-uDCobcigGA3aTXCg&amp;prev=/images%3Fq%3Dcolumnar%2Btexture%26um%3D1%26hl%3Den%26client%3Dfirefox-a%26rls%3Dorg.mozilla:en-US:official%26sa%3DN</p><p>*Some of the fundamental ideas of the iron-sulfur theory can be summarized in the following brief recipe for life: Boil water. Stir in iron sulfide and nickel sulfide. Bubble in carbon monoxide and hydrogen sulfide gas. Wait for peptides to form.More technically, Wchtershuser hypothesized the following steps for producing proteins:Produce acetic acid through metallic ion catalysis. Add carbon to the acetic acid molecule to produce three-carbon pyruvic acid. Add ammonia to form amino acids. Produce peptides and then proteins. </p><p>*lDNA: long DNA, sDNA: short DNA</p><p>Monodisperse: when a polymer has only one molecular mass. They are typically generated by natural processes.*</p></li></ul>


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