Yang Yang, Xianfeng Song Advisor: Sima Setayeshgar

Journal Club April 11th, 2008

Liquid Crystal Phases of DNA and Implications for The Origin

of Life

Outline

o Part I: Introduction to liquid crystals

o Part II: Background on theories of origin of life

o Part III: Liquid crystal condensation of 6-to-20-base pair DNA duplexes

Part I: Introduction to liquid crystals

Introduction to Liquid Crystal

o Phases between liquid and solido Can be divided into two types:

o Thermotropic: exhibit phase transition into the LC phase as temperature is changed

o Lyotropic: exhibit phase transition into the LC phase as a function of concentration of the mesogen

o 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)

o A typical behavior due to anisotropyo Two different refraction indexo no is the refractive indices for o-ray (polarization direction

is perpendicular to the optical axis, called director)o ne is the refractive indices for e-ray (polarization direction

is parallel to the optical axis)o 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

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.

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

Liquid Crystal Phases: Nematic Phaseo Nematic phaseoThe mesogens have no

positional order, but exhibits long-range orientational order.

oMost 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 Phaseo 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.

o 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 crystals

http://plc.cwru.edu/tutorial/enhanced/files/lc/phase/phase.htm http://bly.colorado.edu/lcphysics/textures/

Liquid Crystal Phases: Smectic Phase

o Form well-defined layers that can slide over one anothero Smectic A phase: the mesogen are oriented along the layer

normalo Smectic C phase: the mesogen are tilted away from the layer

normal

Picture of the smectic A phase

Picture of the smectic C phase

Texture of the smectic A phase

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

Liquid Crystal Phases: Columnar Phases

100× of texture exhibited by the

hexagonal columnar mesophase

Columnar phase formed

by discotic molecules

Columnar phase formed

by rod-like molecules

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

From Nature 406, 868-871, 2000 http://www.rsc.org/ej/JM/2001/b008904o/b008904o-f2.gif

From Science 318, 1276 (2007)

Part II: Introduction to Theories of Origin of Life

Origin of Life

o Scientific theoryoOrigin of organic moleculesoFrom organic molecules to protocells

o Other theoriesoReligion theory: humankind and other organisms are

created by God.oSpontaneous Generation: small organisms like bacterium

and frogs are spontaneously generated in the mud.oAliens: organisms were brought to earth by aliens

o First X-ray diffraction image of DNA, photo 51o Taken by Rosalind Franklin in 1952o Critical evidence in identifying the structure of

DNA

DNA Structure

o Structure model of DNAo Presented by James D. Watson

and Francis Crick in 1953o Double helix with sugar and

phosphate parts of the nucleotides forming the two strand

o Using hydrogen bonds to pair specifically with A opposing to T, and C opposing to G

o Opposite directions of the two strands of double helix

Franklin R, Gosling RG , Nature ,1953

Watson J.D. and Crick F.H.C. Nature, 1953

Genetic Information Flowo A 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).

o In transcription, the codons of a gene are copied into messenger RNA by RNA polymerase(protein).

o 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

o Miller's experiments (The Primordial Soup Theory)

o The Deep Sea Vent Theory

o Wächtershäuser’s experiment

“Miller-Urey” Experiments

o Performed by Stanley Miller, and his advisor, Harold Urey in 1953

o Recreating the chemical conditions of the primitive earth in the laboratoryoUsing a highly reduced mixture of gases – methane, ammonia and hydrogen – to form basic organic monomers, such as amino acids.o Proving the spontaneously forming of organic molecule on early earth from inorganic precursorHow the relatively simple

organic building blocks polymerize and form more complex structures?

From NASA

Miller S. L., Science ,1953.Miller S. L., and Urey, H. C . Science, 1959

Deep Sea Vent Theory

o The hot environs of undersea hydrothermal vents were the birthplace for life.

o In 1999, Japanese researchers synthesized peptides around an artificial deep-sea vent.

Balter, M. Science, 1998

Imai E., et al. ,Science,1999

Wächtershäuser's experiment

o Early chemistry of life started on mineral surfaces (e.g. iron pyrites) near deep hydrothermal vents

o Bubbles on the mineral surfaces acted as the first ‘cell’

o Amino acids and peptides could be formed by mixing simple chemical compounds (carbonmonoxide, hydrogen sulfide, nickel sulfide and iron sulfide)h

Huber, C. and Wächterhäuser, G. , Science, 1998

Wächtershäuser, G. , Science 2000. 

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

From Organic Molecules to Protocells

o"Genes first" models-the RNA world

o"Metabolism first" models-iron-sulfur world

o Carl R. Woese first presented this independent RNA idea in late 1960s . o Walter Gilbert first used the phrase "RNA World" in 1986 o DNA replication need proteins and enzymes while at the origin of life there is no present of any proteino RNA catalyzed all the reactions necessary for a precursor to survive and replicate

oRelatively short RNA molecules which can duplicate others have been artificially produced in the lab

o New enzymes replicate DNA and make mRNA copies o 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, 2001

RNA World Hypothesis

"Metabolism first" Models:

Iron-Sulfur World o Early form of metabolism predated genetics

o Metabolism here means a cycle of chemical reactions that produce energy in a form that can be harnessed by other processes

o Steps for producing proteins:o Produce acetic acid through metallic ion catalysiso Add carbon to the acetic acid molecule to produce

three-carbon pyruvic acid(CH3COCO2H) o Add ammonia to form amino acidso Produce peptides and then proteins.

o Once protein had been formed, DNA can be replicated and make RNA copies, and followed by translation to proteins

Huber, C. and Wächterhäuser, G. , Science, 1998Wächtershäuser, G. , Science, 2000.

Pending Problem

o Once 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.

o 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.

o 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 molecule s tend to self-organize themselves to larger molecule

Part III: Liquid Crystal Condensation of sDNA Duplexes

Terminology in Papero Oligomer: A molecule formed from a small number of monomers.o Self-complementary: Each single strand of the duplex-DNA can

form double helix with itself. For example:

CCTCAATTGAGG >>

<<GGAGTTAACTCCo sDNA: Short DNA double helix o lDNA: Long DNA double helixo DNA ligation: sDNA join together end-to-end to form lDNA.

o B form of DNA: normal right-handed DNA, every 3.4 nm makes a turn and there are 10 base pairs per turno A form of DNA: right-handed DNA, but every 2.3 nm makes a turn and there are 11 base pairs per turn. o Z form of DNA: left-handed DNA due to zigzag bases, every 4.6 nm makes a turn and there are 12 base pairs per turn.

Notes form Prof. Cherbas, Dept. of Biology, Indiana University

Background on lDNA Liquid Crystal

o Duplex lDNA can form liquid crystal phases when hydrated:o Four phases: isotropic phase (I), chiral nematic (N), uniaxial

columnar (CU), crystal phase (X)o 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)

o Onsager-Bolhuis-Frenkel(OBF) criterion[*]oModel: Monodisperse repulsive hard rods (length L,

diameter D)o 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

o 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

o 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 Diagramo 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

o 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.

o Experiment show if there is a

large excess of noncomplementary oligomers, the LC phase appears as isolated drops.

Experiment procedure

Discussion & Conclusion

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

o 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.

o 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.

Thanks!