DNA polymerase template interactions probed by degenerate isosteric nucleobase analogs

The development of novel artificial nucleobases and detailed X-ray crystal structures for primer/template/DNA polymerase complexes provide opportunities to assess DNA-protein interactions that dictate specificity. Recent results have shown that base pair shape recognition in the context of DNA polymerase must be considered a significant component. The isosteric azole carboxamide nucleobases (compounds 1-5; ) differ only in the number and placement of nitrogen atoms within a common shape and therefore present unique electronic distributions that are shown to dictate the selectivity of template-directed nucleotide incorporation by DNA polymerases. The results demonstrate how nucleoside triphosphate substrate selection by DNA polymerase is a complex phenomenon involving electrostatic interactions in addition to hydrogen bonding and shape recognition. These azole nucleobase analogs offer unique molecular tools for probing nonbonded interactions dictating substrate selection and fidelity of DNA polymerases.     

Hybrid modeling and simulation of stochastic effects on progression through the eukaryotic cell cycle

The eukaryotic cell cycle is regulated by a complicated chemical reaction network. Although many deterministic models have been proposed, stochastic models are desired to capture noise in the cell resulting from low numbers of critical species. However, converting a deterministic model into one that accurately captures stochastic effects can result in a complex model that is hard to build and expensive to simulate. In this paper, we first apply a hybrid (mixed deterministic and stochastic) simulation method to such a stochastic model. With proper partitioning of reactions between deterministic and stochastic simulation methods, the hybrid method generates the same primary characteristics and the same level of noise as Gillespie's stochastic simulation algorithm, but with better efficiency. By studying the results generated by various partitionings of reactions, we developed a new strategy for hybrid stochastic modeling of the cell cycle. The new approach is not limited to using mass-action rate laws. Numerical experiments demonstrate that our approach is consistent with characteristics of noisy cell cycle progression, and yields cell cycle statistics in accord with experimental observations.     

Tunable infrared generation in KTA and applications

Noncollinear difference frequency mixing of dye laser and Nd:YAG second harmonic (fundamental) radiation from a commercial laser system is employed for the generation of 2.7–5.3 μm (1.6–1.7 μm) radiations in a flux-grown KTiOAsO₁ crystal. The generated radiation is used to scan the methane absorption in the fundamental (v ₃) and its first overtone (2v ₃) band at pressure 90 torr in a laboratory made single pass gas cell of length 33 cm.     

Photodissociation spectroscopy and dynamics of the CH2CFO radical

The photodissociation spectroscopy and dynamics resulting from excitation of the B (2)A(")<--X (2)A(") transition of CH(2)CFO have been examined using fast beam photofragment translational spectroscopy. The photofragment yield spectrum reveals vibrationally resolved structure between 29 870 and 38 800 cm(-1), extending approximately 6000 cm(-1) higher in energy than previously reported in a laser-induced fluorescence excitation spectrum. At all photon energies investigated, only the CH(2)F+CO and HCCO+HF fragment channels are observed. Both product channels yield photofragment translational energy distributions that are characteristic of a decay mechanism with a barrier to dissociation. Using the barrier impulsive model, it is shown that fragmentation to CH(2)F+CO products occurs on the ground state potential energy surface with the isomerization barrier between CH(2)CFO and CH(2)FCO governing the observed translational energy distributions.     

Matrix isolation investigation of the photochemical reaction of benzene with CrCl2O2 and OVCl3

The matrix isolation technique, combined with infrared spectroscopy, has been used to characterize the products of the photochemical reactions of benzene with CrCl(2)O(2) and OVCl(3). While initial twin jet deposition of the reagents led to no visible changes in the recorded spectra, strong product bands were noted following irradiation with light of lambda > 300 nm. Wavelength dependence studies determined that light of lambda < 590 nm led to reaction and oxygen atom transfer, forming an eta(1)-complex between 2,4-cyclohexadienone and CrCl(2)O. The identification of the complex was further supported by isotopic labeling ((13)C and (2)H) and by density functional calculations at the B3LYP/6-311G++(d,2p) level. Merged-jet experiments in which thermal reactions are examined were also conducted, at temperatures as high as 150 degrees C. No products were observed.     

Matrix isolation studies of photochemical and thermal reactions of 3- and 5-membered cyclic hydrocarbons with CrCl2O2

The matrix isolation technique has been combined with infrared spectroscopy and theoretical calculations to characterize the products of the photochemical and thermal reactions of cyclopentadiene, cyclopentene, cyclopentane, and cyclopropane with CrCl 2O 2. While initial twin jet deposition of the reagents led to no visible changes in the recorded spectra, product bands were observed following irradiation with light of lambda > 300 nm. The irradiation was shown to lead to oxygen atom transfer to the five-membered rings, forming complexes between cyclic alcohol derivatives and CrCl 2O. For the cyclopentadiene and cyclopentene systems, complexes between cyclic ketone derivatives and CrCl 2O were also observed. For cyclopropane, a ring-opening oxidation reaction followed by fragmentation was observed for the first time, forming the H 2COCrCl 2O complex and C 2H 4. In the room temperature thermal (merged jet) reactions between CrCl 2O 2 and cyclopentadiene, cyclopent-3-enone was observed. At the higher temperatures, 150 and 200 degrees C, 1,3-cyclopentanedione was also observed as well. No product bands were detected in the merged jet experiments for the other three systems. These conclusions were supported by isotopic labeling ((2)H) and by B3LYP/6-311G++(d,2p) density functional calculations.     

The synthesis and determination of acidic ionization constants of certain 5-substituted 2-aminopyrrolo[2,3-d]pyrimidin-4-ones and methylated analogs

The acidic ionization constants were determined for a series of 5-substituted 2-aminopyrrolo[2,3-d]-pyrimidin-4-ones and N -3- and N -7-methylated analogs thereof. The syntheses of the methylated analogs are also described.     

Two- and three-body photodissociation of gas phase I(3) (-)

The photodissociation dynamics of I3- from 390 to 290 nm (3.18 to 4.28 eV) have been investigated using fast beam photofragment translational spectroscopy in which the products are detected and analyzed with coincidence imaging. At photon energies < or = 3.87 eV, two-body dissociation that generates I- + I2(A 3Pi1) and vibrationally excited I2- (X 2Sigmau+) + I(2P(3/2)) is observed, while at energies > or = 3.87 eV, I*(2P(1/2)) + I2- (X 2Sigmau+) is the primary two-body dissociation channel. In addition, three-body dissociation yielding I- +2I(2P(3/2)) photofragments is seen throughout the energy range probed; this is the dominant channel at all but the lowest photon energy. Analysis of the three-body dissociation events indicates that this channel results primarily from a synchronous concerted decay mechanism.