Pairing statistics and melting of random DNA oligomers: Finding your partner in superdiverse environments.

Understanding of the pairing statistics in solutions populated by a large number of distinct solute species with mutual interactions is a challenging topic, relevant in modeling the complexity of real biological systems. Here we describe, both experimentally and theoretically, the formation of duplexes in a solution of random-sequence DNA (rsDNA) oligomers of length L = 8, 12, 20 nucleotides. rsDNA solutions are formed by 4L distinct molecular species, leading to a variety of pairing motifs that depend on sequence complementarity and range from strongly bound, fully paired defectless helices to weakly interacting mismatched duplexes. Experiments and theory coherently combine revealing a hybridization statistics characterized by a prevalence of partially defected duplexes, with a distribution of type and number of pairing errors that depends on temperature. We find that despite the enormous multitude of inter-strand interactions, defectless duplexes are formed, involving a fraction up to 15% of the rsDNA chains at the lowest temperatures. Experiments and theory are limited here to equilibrium conditions.

Mechanism and kinetics for the reaction of methyl peroxy radical with O2.

Quantum chemical calculations and dynamics simulations were performed to study the reaction between methyl peroxy radical (CH3O2) and O2. The reaction proceeds through three different pathways (1) H-atom abstraction, (2) O2 addition and (3) concerted H-atom shift and O2 addition reactions. The concerted H-atom shift and O2 addition pathway is the most favourable reaction both kinetically and thermodynamically. The major product channel formed from these reactions is H2CO + OH + O2. Trajectory calculations also confirm that H2CO + OH + O2 is the main product channel. An estimated rate constant expression for this reaction from master equation calculations is 4.20 × 1013 e-8676/T cm3 mole-1 s-1.

Mono- and bilayer smectic liquid crystal ordering in dense solutions of "gapped" DNA duplexes.

Although its mesomorphic properties have been studied for many years, only recently has the molecule of life begun to reveal the true range of its rich liquid crystalline behavior. End-to-end interactions between concentrated, ultrashort DNA duplexes-driving the self-assembly of aggregates that organize into liquid crystal phases-and the incorporation of flexible single-stranded "gaps" in otherwise fully paired duplexes-producing clear evidence of an elementary lamellar (smectic-A) phase in DNA solutions-are two exciting developments that have opened avenues for discovery. Here, we report on a wider investigation of the nature and temperature dependence of smectic ordering in concentrated solutions of various "gapped" DNA (GDNA) constructs. We examine symmetric GDNA constructs consisting of two 48-base pair duplex segments bridged by a single-stranded sequence of 2 to 20 thymine bases. Two distinct smectic layer structures are observed for DNA concentration in the range [Formula: see text] mg/mL. One exhibits an interlayer periodicity comparable with two-duplex lengths ("bilayer" structure), and the other has a period similar to a single-duplex length ("monolayer" structure). The bilayer structure is observed for gap length ≳10 bases and melts into the cholesteric phase at a temperature between 30 °C and 35 °C. The monolayer structure predominates for gap length ≲10 bases and persists to [Formula: see text]C. We discuss models for the two layer structures and mechanisms for their stability. We also report results for asymmetric gapped constructs and for constructs with terminal overhangs, which further support the model layer structures.

Backbone-free duplex-stacked monomer nucleic acids exhibiting Watson-Crick selectivity.

We demonstrate that nucleic acid (NA) mononucleotide triphosphates (dNTPs and rNTPs), at sufficiently high concentration and low temperature in aqueous solution, can exhibit a phase transition in which chromonic columnar liquid crystal ordering spontaneously appears. Remarkably, this polymer-free state exhibits, in a self-assembly of NA monomers, the key structural elements of biological nucleic acids, including: long-ranged duplex stacking of base pairs, complementarity-dependent partitioning of molecules, and Watson-Crick selectivity, such that, among all solutions of adenosine, cytosine, guanine, and thymine NTPs and their binary mixtures, duplex columnar ordering is most stable in the A-T and C-G combinations.

Liquid Crystal Ordering and Isotropic Gelation in Solutions of Four-Base-Long DNA Oligomers.

Liquid crystal ordering is reported in aqueous solutions of the oligomer 5'-ATTAp-3' and of the oligomer 5'-GCCGp-3'. In both systems, we quantitatively interpret ordering as stemming from the chaining of molecules via a "running-bond" type of pairing, a self-assembly process distinct from the duplex aggregation previously reported for longer oligonucleotides. While concentrated solutions of 5'-ATTAp-3' show only a columnar liquid crystal phase, solutions of 5'-GCCGp-3' display a rich phase diagram, featuring a chiral nematic phase analogous to those observed in solutions of longer oligonucleotides and two unconventional phases, a columnar crystal and, at high concentration, an isotropic amorphous gel. The appearance of these phases, which can be interpreted on the basis of features of 5'-GCCGp-3'molecular structure, suggests distinctive assembly motifs specific to ultrashort oligonucleotides.

Laser Measurements of the H Atom + Ozone Rate Constant at Mesospheric Temperatures.

The exothermic H + O3 reaction produces OH(v) Meinel band emissions, used to derive mesospheric H concentrations and chemical heating rates. We remeasured its rate constant to reduce its uncertainty and extended the measurements to lower mesospheric temperatures using modern laser-induced fluorescence (LIF) techniques. H atoms were produced by pulsed ultraviolet laser trace photolysis of O3, followed by reaction of O((1)D) with added H2. A second, delayed, frequency-mixed dye laser measured the reaction decay rate with the remaining ozone using LIF. We monitored either the H atom decay by two photon excitation at 205 nm and detection of red fluorescence, or the OH (v = 9) product time evolution with excitation of the B(2)Σ(+)-X(2)Π (0,9) band at 237 nm and emission in the blue B(2)Σ(+)-A(2)Σ(+) (0,7) band. By cooling the enclosed low pressure flow cell we obtained measurements from 140 to 305 K at 20 to 200 Torr in Ar. Small kinetic modeling corrections were made for secondary regeneration of H atoms. The results are consistent with the current NASA JPL recommendation for this rate constant and establish its extrapolation down to the lower temperatures of the mesosphere.

Phases and structures of sunset yellow and disodium cromoglycate mixtures in water.

We study phases and structures of mixtures of two representative chromonic liquid crystal materials, sunset yellow FCF (SSY) and disodium cromoglycate (DSCG), in water. A variety of combinations of isotropic, nematic (N), and columnar (also called M) phases are observed depending on their concentrations, and a phase diagram is made. We find a tendency for DSCG-rich regions to show higher-order phases while SSY-rich regions show lower-order ones. We observe uniform mesophases only when one of the materials is sparse in the N phases. Their miscibility in M phases is so low that essentially complete phase separation occurs. X-ray scattering and spectroscopy studies confirm that SSY and DSCG molecules do not mix when they form chromonic aggregates and neither do their aggregates when they form M phases.

Abiotic ligation of DNA oligomers templated by their liquid crystal ordering.

It has been observed that concentrated solutions of short DNA oligomers develop liquid crystal ordering as the result of a hierarchically structured supramolecular self-assembly. In mixtures of oligomers with various degree of complementarity, liquid crystal microdomains are formed via the selective aggregation of those oligomers that have a sufficient degree of duplexing and propensity for physical polymerization. Here we show that such domains act as fluid and permeable microreactors in which the order-stabilized molecular contacts between duplex terminals serve as physical templates for their chemical ligation. In the presence of abiotic condensing agents, liquid crystal ordering markedly enhances ligation efficacy, thereby enhancing its own phase stability. The coupling between order-templated ligation and selectivity provided by supramolecular ordering enables an autocatalytic cycle favouring the growth of DNA chains, up to biologically relevant lengths, from few-base long oligomers. This finding suggests a novel scenario for the abiotic origin of nucleic acids.

Liquid crystal self-assembly of random-sequence DNA oligomers.

In biological systems and nanoscale assemblies, the self-association of DNA is typically studied and applied in the context of the evolved or directed design of base sequences that give complementary pairing, duplex formation, and specific structural motifs. Here we consider the collective behavior of DNA solutions in the distinctly different regime where DNA base sequences are chosen at random or with varying degrees of randomness. We show that in solutions of completely random sequences, corresponding to a remarkably large number of different molecules, e.g., approximately 10(12) for random 20-mers, complementary still emerges and, for a narrow range of oligomer lengths, produces a subtle hierarchical sequence of structured self-assembly and organization into liquid crystal (LC) phases. This ordering follows from the kinetic arrest of oligomer association into long-lived partially paired double helices, followed by reversible association of these pairs into linear aggregates that in turn condense into LC domains.

Composite mantle cell and diffuse large B-cell lymphoma: report of two cases.

Composite lymphomas are rare and involve the concurrent evolution of 2 distinct lymphoma types within a single organ or tissue. This study describes 2 cases of composite mantle cell lymphoma (MCL) and diffuse large B-cell lymphoma (DLBCL), which has not previously been reported. Each case demonstrated distinct populations of CD20 positive small and large atypical B cells. In both cases, only the small lymphocytes were positive for CD5 and cyclin D1, and fluorescence in situ hybridization (FISH) showed a t(11;14) translocation in the small lymphocytes but not in the large cells. Molecular studies for B-cell clonality showed a possible clonal relationship between the 2 components in one case but not the other. This study describes in detail the morphology, immunophenotype, FISH, and molecular analysis of both components in each case. To the authors' knowledge, this represents the first report of juxtaposition of MCL with DLBCL that does not represent transformation of the mantle cell component.

Temperature dependence of O + OH at 136-377 K using ozone photolysis.

Ozone was photolyzed at 248 nm in 40 Torr nitrogen with small amounts of water or hydrogen added in a cooled or heated flow cell, to measure the O + OH rate constant at 136-377 K. Rate constant values were determined by kinetic modeling of the OH decays in excess O as monitored by laser-induced fluorescence and are in reasonable agreement with current recommendations. Results may be summarized by the expression k = 11.2 x 10(-11) T(-.32) e(177/T) cm3/molecule/s.