End-to-End Stacking and Liquid Crystal Condensation of 6– to 20–Base Pair DNA Duplexes

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. Structural study shows that these phases are produced by the end-to-end adhesion and consequent stacking of the duplex oligomers into polydisperse anisotropic rod-shaped aggregates, which can order into liquid crystals. Upon cooling mixed solutions of short DNA oligomers, in which only a small fraction of the DNA present is complementary, the duplex-forming oligomers phase-separate into liquid crystal droplets, leaving the unpaired single strands in isotropic solution. In a chemical environment where oligomer ligation is possible, such ordering and condensation would provide an autocatalytic link whereby complementarity promotes the extended polymerization of complementary oligomers.

[1]  Jean Sturm,et al.  Persistence Length of Single-Stranded DNA , 1997 .

[2]  A. Leforestier,et al.  Condensed phases of DNA: Structures and phase transitions , 1996 .

[3]  F. Livolant,et al.  The highly concentrated liquid-crystalline phase of DNA is columnar hexagonal , 1989, Nature.

[4]  R. Brandes,et al.  Magnetic ordering of DNA liquid crystals. , 1986, Biochemistry.

[5]  Polydispersity and ordered phases in solutions of rodlike macromolecules. , 1995, Physical review letters.

[6]  V. R. Horowitz,et al.  Aggregation behavior and chromonic liquid crystal properties of an anionic monoazo dye. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[7]  J. Herzfeld,et al.  A model for nematic and columnar ordering in a self-assembling system , 1990 .

[8]  T. Richmond,et al.  Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution. , 2002, Journal of molecular biology.

[9]  Jonathan V Selinger,et al.  Hexagonal and nematic phases of chains. II. Phase transitions. , 1991, Physical review. A, Atomic, molecular, and optical physics.

[10]  Jeffery T. Davis.  G-quartets 40 years later: from 5'-GMP to molecular biology and supramolecular chemistry. , 2004, Angewandte Chemie.

[11]  P. Flory.  Statistical Thermodynamics of Mixtures of Rodlike Particles. 5. Mixtures with Random Coils , 1978 .

[12]  Peter G. Bolhuis,et al.  Tracing the phase boundaries of hard spherocylinders , 1997 .

[13]  J. Ferris,et al.  Oligomerization of ribonucleotides on montmorillonite: reaction of the 5'-phosphorimidazolide of adenosine. , 1992, Science.

[14]  T. Alam,et al.  Magnetic ordering in synthetic oligonucleotides. A deuterium nuclear magnetic resonance investigation , 1990 .

[15]  Fumio Oosawa,et al.  On Interaction between Two Bodies Immersed in a Solution of Macromolecules , 1954 .

[16]  R. Rill,et al.  DNA length and concentration dependencies of anisotropic phase transitions of DNA solutions. , 1997, Biophysical journal.

[17]  P. Hagerman.  Flexibility of DNA. , 1988, Annual review of biophysics and biophysical chemistry.

[18]  Herzfeld,et al.  Isotropic, nematic, and columnar ordering in systems of persistent flexible hard rods. , 1991, Physical review. A, Atomic, molecular, and optical physics.

[19]  P. Teixeira,et al.  REVIEW ARTICLE: The effect of dipolar forces on the structure and thermodynamics of classical fluids , 2000 .

[20]  M. Cates,et al.  Growth, Static Light Scattering, and Spontaneous Ordering of Rodlike Micelles , 1994 .

[21]  Conmar Robinson.  LIQUID-CRYSTALLINE STRUCTURES IN POLYPEPTIDE SOLUTIONS , 1961 .

[22]  J. Champoux,et al.  Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA. , 1998, Science.

[23]  J. G. Elias,et al.  The dimensions of DNA in solution. , 1981, Journal of molecular biology.

[24]  Richard E. Dickerson,et al.  Crystal structure analysis of a complete turn of B-DNA , 1980, Nature.

[25]  J. Kindt,et al.  Monte Carlo simulation of the self-assembly and phase behavior of semiflexible equilibrium polymers. , 2004, The Journal of chemical physics.

[26]  H. R. Wilson,et al.  Molecular Structure of Nucleic Acids: Molecular Structure of Deoxypentose Nucleic Acids , 1953, Nature.

[27]  R. Franklin,et al.  Molecular Configuration in Sodium Thymonucleate , 1953, Nature.

[28]  M. Davidson,et al.  Ordered phases in concentrated DNA solutions , 1991 .

[29]  D. Frenkel,et al.  Influence of polydispersity on the phase behavior of colloidal liquid crystals: A Monte Carlo simulation study , 1998 .

[30]  V. Luzzati,et al.  Etude par diffusion des rayons X aux petits angles des gels d’acide désoxyribonucléique et de nucléoprotéines : (note préliminaire) , 1959 .

[31]  L. Onsager.  THE EFFECTS OF SHAPE ON THE INTERACTION OF COLLOIDAL PARTICLES , 1949 .

[32]  H. Hinz,et al.  Thermodynamic Data for Biochemistry and Biotechnology , 1986 .