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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

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liquid crystal phases of dna and implications for the origin of life

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

Yang Yang, Xianfeng Song

Advisor: Sima Setayeshgar

Journal Club

April 11th, 2008

outline
Outline
  • Part 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
introduction to liquid crystal
Introduction to Liquid Crystal
  • Phases between liquid and solid
  • Can be divided into two types:
    • Thermotropic: exhibit phase transition into the LC phase as temperature is changed
    • Lyotropic: exhibit phase transition into the LC phase as a function of concentration of the mesogen
  • 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
Birefringence (Double Refraction)
  • A typical behavior due to anisotropy
  • Two different refraction index
    • no 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 polarizers
Optical Devices: Crossed Polarizers

http://bly.colorado.edu/lcphysics/lcintro/tnlc.html

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.

liquid crystal phases nematic phase
Liquid Crystal Phases: Nematic Phase
  • Nematic phase
    • The mesogens have no positional order, but exhibits long-range orientational order.
    • Most nematics are uniaxial, but some liquid crystals are biaxial nematics.

From Nature 430, 413-414(22 July 2004)

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/

liquid crystal phases chiral nematic phase
Liquid Crystal Phases: Chiral Nematic Phase
  • The 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.

http://plc.cwru.edu/tutorial/enhanced/files/lc/phase/phase.htm

http://bly.colorado.edu/lcphysics/textures/

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

liquid crystal phases smectic phase
Liquid Crystal Phases: Smectic Phase
  • Form well-defined layers that can slide over one another
  • Smectic A phase: the mesogen are oriented along the layer normal
  • Smectic C phase: the mesogen are tilted away from the layer normal

http://plc.cwru.edu/tutorial/enhanced/files/lc/phase/phase.htm

Texture of the smectic A phase

Picture of the smectic A phase

Picture of the smectic C phase

liquid crystal phases columnar phases
Liquid Crystal Phases: Columnar Phases

A class of liquid crystal phases in which molecules assemble into cylindrical structures

http://www.rsc.org/ej/JM/2001/b008904o/b008904o-f2.gif

From Nature 406, 868-871, 2000

From Science 318, 1276 (2007)

100× of texture exhibited by the hexagonal columnar mesophase

Columnar phase formed by discotic molecules

Columnar phase formed by rod-like molecules

origin of life
Origin of Life
  • Religion theory
    • Creation of humankind and other higher organisms by God
  • Spontaneous Generation
    • Non-living objects giving rise to living organisms
  • Scientific theory
    • Origin of organic molecules
    • From organic molecules to protocells
origin of organic molecules
Origin of Organic Molecules
  • Miller\'s experiments (The Primordial Soup Theory)
  • The Deep Sea Vent Theory
  • Wächtershäuser’s hypothesis
miller urey experiments
“Miller-Urey” Experiments
  • Performed by Stanley Miller, and his professor, Harold Urey in 1953
    • Recreating the chemical conditions of the primitive earth in the laboratory
    • Using 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 polymerase and form more complex structures?

From NASA

deep sea vent theory
Deep Sea Vent Theory
  • The hot environs of undersea hydrothermal vents being the birthplace for life.
  • 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.
  • Synthesizing peptides around an artificial deep-sea vent by Japanese researchers in 1999 (Ei-ichi Imai, et al. Science,1999).
w chtersh user s hypothesis
Wächtershäuser\'s hypothesis
  • Early chemistry of life starting on mineral surfaces (e.g. iron pyrites) near deep hydrothermal vents
  • Bubbles on the mineral surfaces acting as the first ‘cell’
  • Demonstrating amino acids could form by mixing carbon, monoxide, hydrogen sulfide, nickel sulfide and iron sulfide by Wächtershäuser and Claudia Huber, in 1997

ajdubre.tripod.com/.../OriginLifeSci-82500.html

from organic molecules to protocells
From Organic Molecules to Protocells
  • "Genes first" models-the RNA world
  • "Metabolism first" models-iron-sulfur world
  • Other theory: Bubble Theory
rna word hypothesis
RNA Word Hypothesis
  • 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 of life’s last common ancestor to survive and replicate
  • New enzymes replicate DNA and make RNA copies
  • DNA took the role as the genetic information storage
dna structure
DNA Structure
  • First X-ray diffraction image of DNA, photo 51
    • Taken by Rosalind Franklin in 1952
    • Critical evidencein 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 helix

Franklin R, Gosling RG , Nature 171,1953

metabolism first models iron sulfur world
"Metabolism first" Models: Iron-Sulfur World
  • Early form of metabolism predated genetics
  • steps for producing proteins:
    • Produce acetic acid through metallic ion catalysis
    • Add carbon to the acetic acid molecule to produce three-carbon pyruvic acid(CH3COCO2H)
    • Add ammonia to form amino acids
    • Produce peptides and then proteins.
other theory bubble theory
Other theory: Bubble Theory
  • Solving the problem where the cell membrane comes from
  • Bubble 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 division
  • Protocell starting to form when accumulating enough ‘material’
pending problem
Pending Problem
  • The 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 dna
A, B , Z Form of Double strand DNA

Notes form Prof. Cherbas, Dept. of Biology,

Indiana University

terminology in literature
Terminology in Literature
  • Oligomer: 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 >>

<<GGAGTTAACTCC

  • Non self-complementary: Not self-complementary. For example: CCTCAAAACTCC
  • sDNA: Short DNA double helix (Attention: different than single stranded DNA)
  • DNA ligation: sDNA join together end-to-end to form lDNA.
background on ldna liquid crystal
Background on lDNA Liquid Crystal
  • Duplex 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<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
Experiments on sDNA
  • 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
  • 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 diagram
DNA Phase Diagram
  • 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 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 = 20°C for 20 > N > 8 and T = 10°C 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.

lc ordering from mixed solutions of complementary and non complementary oligomers
LC Ordering from Mixed Solutions of Complementary and Non-complementary Oligomers
  • The 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.

Experiment procedure

discussion conclusion

The observation of nematic and columnar LC phase provides clear evidence for end-to-end stacking of sDNA into rod-shaped aggregates.

Discussion & Conclusion
  • The observation of nematic and columnar LC phase provides clear evidence for end-to-end stacking of sDNA into rod-shaped aggregates.
  • 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.
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