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: Introduction to DNA Part III: Background on theories of origin of life - PowerPoint PPT Presentation

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<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: Introduction to DNA</p><p>Part III: Background on theories of origin of life</p><p>Part IV: 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></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. </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 structures</p></li><li><p>Part II: Introduction to DNA</p></li><li><p>DNAIn 1952, Rosalind Franklin took the first X-ray diffraction image of DNA , photo 51, which was critical evidence in identifying the structure of DNA.In 1953, James D. Watson and Francis Crick described the double helix structure of DNA .DNA is a double helix, with the sugar and phosphate parts of nucleotides forming the two strands of the helix, and the nucleotide bases pointing into the helix and stacking on top of each other.The nucleotide bases use hydrogen bonds to pair specifically, with an A always opposing a T, and a C always opposing a G.The two strands of the double helix run in opposite directions.</p></li><li><p>DNA and RNA Structure</p></li><li><p>A, B , Z form of DNA</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>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. </p><p>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.</p></li><li><p>Part III: Theories of origin of life</p></li><li><p>Origin of LifeBefore the mid-17th century, most people believed that God had created humankind and other higher organisms and that insects, frogs and other small creatures could arise spontaneously in mud or decaying matter.</p><p>Scientific theoryOrigin of organic moleculesFrom organic molecules to protocells</p></li><li><p>Origin of organic moleculesMiller's experiments (The Primordial Soup Theory): using a highly reduced mixture of gases methane, ammonia and hydrogen to form basic organic monomers, such as amino acids.</p><p>The Deep Sea Vent Theory: hydrogen-sulfide and hydrogen coming out from the vent in contact with a suitable oxidant, such as carbon dioxide can release chemical energy.</p><p>Wchtershuser's hypothesis: In 1997, Wchtershuser and Claudia Huber mixed carbon monoxide, hydrogen sulfide, nickel sulfide, and iron sulfide particles at 100C and demonstrated that amino acids could form.</p><p>Radioactive beach theory: stronger tidal processes from a much closer moon may have concentrated radioactive grains of uranium and other radioactive elements at the high water mark on primordial beaches where they may have been responsible for generating life's building blocks.</p></li><li><p>Origin of Organic Molecules: Miller's experiments In 1953 a graduate student, Stanley Miller, and his professor, Harold Urey, performed an experiment that proved organic molecules could have spontaneously formed on early Earth from inorganic precursors. The now-famous Miller-Urey experiment used a highly reduced mixture of gases methane, ammonia and hydrogen to form basic organic monomers, such as amino acids.The Miller-Urey experiment attempted to recreate the chemical conditions of the primitive Earth in the laboratory, and synthesized some of the building blocks of life.How the relatively simple organic building blocks polymerase and form more complex structures?</p></li><li><p>From Organic Molecules to Protocells"Genes first" models-the RNA world: the nucleic acids comes first. </p><p>"Metabolism first" models-iron-sulfur world : the evolution of biochemical reactions and pathways comes first </p><p>Bubble Theory: Bubble on the shore is a hypothetical precursor to the modern cell membrane. If protein appears in the bubble, it will spread when bubble burst. When the material accumulate enough, protocell may be occur.</p></li><li><p>From Organic Molecules to Protocells: RNA world hypothesisIn the late 1960s Carl R. Woese present this independent RNA idea. The phrase "RNA World" was first used by Nobel laureate Walter Gilbert in 1986, in a commentary on recent observations of the catalytic properties of various forms of RNA. This is a world in which RNA catalyzed all the reactions necessary for a precursor of life's last common ancestor to survive and replicate. </p></li><li><p>DifficultiesThe 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>Part IV: Liquid crystal condensation of 6-to-20-base pair DNA duplexes </p></li><li><p>BackgroundDuplex lDNA can form liquid crystal phases when hydrated:Four phases: isotropic phase (I), chiral nematic (N), uniaxial columnar (CU)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) criterionModel: 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>ExperimentsSubject: 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>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.</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></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>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. 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. </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*http://images.google.com/imgres?imgurl=http://dept.kent.edu/spie/liquidcrystals/schlieren1.jpg&amp;imgrefurl=http://dept.kent.edu/spie/liquidcrystals/textures1.html&amp;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*http://images.google.com/imgres?imgurl=http://www.rsc.org/ej/JM/2001/b008904o/b008904o-f2.gif&amp;imgrefurl=http://www.rsc.org/ej/jm/2001/b008904o/&amp;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>*</p></li></ul>

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