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 × 10-11 T-.32 e177/T cm3/molecule/s

Assessing Effects of Rate Parameter Changes on Ozone Models Using Sensitivity Analysis^†

Effects of recommended rate parameter changes in the NASA JPL-2000 evaluation from JPL-94 values on local ozone concentrations in a 2-D model are predicted using local sensitivity analysis results from the LLNL 2-D diurnally averaged model. Ozone decreases of 5% in the middle stratosphere and 10% increases near the tropopause and upper troposphere are indicated. Altered NOx kinetics are largely responsible for these changes, and increased model NOx levels and ozone depletion from stratospheric aircraft are also expected according to sensitivity analysis. Effects of specific changes, such as the nitric acid formation rate, are examined. New error bars on rate parameters in the evaluation are propagated by the sensitivity coefficients to derive revised kinetics uncertainties for the model ozone calculations at several altitudes, latitudes, and seasons. Middle-upper stratospheric ozone uncertainties of 12% from the catalytic photochemistry are indicated, increasing in the lower stratosphere

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

The exothermic H + O₃ reaction produces OH­(<i>v</i>) 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(¹D) 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 (<i>v</i> = 9) product time evolution with excitation of the B²Σ⁺–X²Π (0,9) band at 237 nm and emission in the blue B²Σ⁺–A²Σ⁺ (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

Comprehensive Description of the theoretical model.

Partition Function; Melting Curve Approximations for rsDNA solution; Energetic Parametrization based on α; Pairing Statistics with αi = 0; Effects of the Ionic Strength on the Pairing Statistics.Fig A: Melting Curves of rsDNA, according to the Low T Approximation, High T Approximation and Unification Ansatz. (PDF)</p

Melting temperatures for rsDNA: Theory vs experiment.

Comparison of measured and predicted Tm for rsDNA solutions. Symbols: experimental Tm obtained from the melting curves of 8N, 12N and 20N (Fig 3), as function of salt, cNaCl. Conditions are specified in the legend. Dashed lines: theoretical predictions of Eq (7).</p

Probability of defectless duplexes in rsDNA: Salt dependence.

Fraction of paired 8A*8B* as a function of ϕ, expressing their dilution in 8N, at T = 15°C for cNaCl = 0.15M (blue dots) and cNaCl = 1.0M (red dots). Dashed lines: theoretical predictions, with the shaded regions obtained from the experimental uncertainty on the pairing energy between A*B*, (see S2 Text).</p

Double strand vs. random sequence DNA melting.

Ensemble melting curve as a function of temperature. Green dots: measured ensemble melting of 12N at crsDNA = 0.04 g/l. Shading marks experimental uncertainty resulting from the average over 8 experimental replicas. Dashed lines: theoretical melting predicted for equimolar solutions of two complementary 12mers at cDNA = 0.02 g/l each (dashed blue line) and cDNA = 0.04/412 ≈ 2.4 10−9 g/l each (dashed red line). 12N θe(T) exhibits a behavior intermediate between the two. Dashed lines are obtained by averaging many melting curves of complementary 12mers. cNaCl = 1M in all curves.</p

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 <i>via</i> 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

Further results.

Evidence of Out-of-Equilibrium Conditions; Perfect pairing probability with different energies and number of nucleobases types. Fig A: Evidence of out-of-equilibrium behavior for 12N. T dependence of the fraction of duplexed strands θe measured while heating and cooling at 1°C/min. Fig B: Evidence of out-of-equilibrium behavior for 20N. Absorbance vs. T measured upon heating after one month equilibration at 4°C. Fig C: θA*B*, fraction of paired 12A* − 12B* in 12N, determined from the model and via CQ experiments with different cooling rates. Fig D: computed with different values of fCG in 8N. Fig E: computed with different values of nb in 12N. (PDF)</p

Materials and methods.

Characterization of rsDNA synthesis; Measurement of rsDNA concentration; UV Absorbance: Experimental Setup; Analysis of UV Absorbance Data; Characterization of A* and B* Fluorescence; Contact-Quenching Data Analysis; Free Energy of A*B* Duplex. Fig A: HPLC traces of 12N compared with two different 12mers. HPLC traces of 8N, 12N and 20N. Fig B: Quartz microfluidic. Quantum Northwest Peltier. Fig C: Temperature calibration of T measured by a thermistor in contact with the microfluidic cell vs. the internal control Tpeltier. Fig D: Steps in the analysis of absorbance data A(T) of 12N used to extract the melting curves θe. Fig E: Fluorescence Emission Spectra of labeled DNA systems: A*, B*, A*B*, A*B and AB*. Fig F: Absorbance Spectra of labeled DNA systems: A*, B*, A*B*, A*B and AB*. Fig G: Simplified representation of the 12A*B* duplex, showing the relative size of DNA duplex, linker and fluorescent moieties FAM and TexasRed. Fig H: fluorescence intensity of TexasRed vs. T in a solution of 12A* + 12B*. Fig I: Normalized fluorescence intensity of TexasRed in a solution of 12A*, 12B* and 12B. Fig J: Average normalized fluorescence of 8A*+8B*. The fit enables determining the linear drift at low temperatures, corresponding to the signal of fully paired A*B*. Fig K: Tm vs A*B* concentration measured by CQ for the following systems. (PDF)</p