Binary decision rules for multistage adaptive mixed-integer optimization

Mathematical Programming - Decision rules provide a flexible toolbox for solving computationally demanding, multistage adaptive optimization problems. There is a plethora of real-valued decision...     

ROOM-TEMPERATURE FLUORESCENCE PROPERTIES OF THE POLYNUCLEOTIDE POLYdA POLYdT

The room-temperature fluorescence spectrum of the non-alternating polynucleotide polydA.polydT is found to have its maximum at about 325 nm and, when exciting in the spectral region where both adenine (A) and thymine (T) absorb, to coincide with that obtained for excitation at 293 nm where thymine is selectively excited. The fluorescence anisotropy is found to be equal to 0.18 and independent of the excitation and emission wavelengths. These observations are consistent with: (i) emission stemming from T; and (ii) transfer of electronic energy from A to T being not efficient. These inferences are also supported by the observed dependence of the fluorescence quantum yield on the excitation wavelength.     

Synthesis and properties of a new member of the calixnaphthalene family: a C(2)-symmetrical endo-calix[4]naphthalene

The synthesis of a new endo-calix[4]naphthalene is described. The reaction sequence involves the cyclocondensation of a key bisnaphthylmethane intermediate (8) with formaldehyde. This key intermediate (8) is formed using a modified Suzuki-Miyaura Pd-catalyzed cross-coupling reaction between bromomethylnaphthyl (6) and naphthylboronic acid (7), both of which can be derived from 2-hydroxynaphthoic acid.     

Synthesis of Calix

The formation of p-tert-butylcalix[4]arene mono-, bis-, tris-, and tetrakistriflates 3, 2, 4, and 5, respectively, and their respective reactions, under typical Pd-catalyzed carbonylative, Suzuki-Miyaura coupling, or deoxygenation conditions are described. A novel, nonsolvent-derived 1:1 clathrate (6) of benzophenone and 3 was formed from the palladium-catalyzed carbonylative reaction of phenylboronic acid and 2. The X-ray crystal structure of this first nonsolvent-derived clathrate of a calix[4]arene derivative is reported. Another 1:1 clathrate of triethylamine and 3 was formed during the attempted Pd-catalyzed deoxygenation of 2.     

COMPLEX FORMATION BETWEEN ETHIDIUM BROMIDE AND THE NUCLEOTIDES AMP AND GMP

Abstract— The antimicrobial drug ethidium bromide (EB) has been found to form molecular complexes with nucleotides, the strongest being those with the purines AMP and GMP. For the EB-AMP and EB-GMP complexes (which we characterized) the values of the ground-state association constant have been found to be 100 and 103 M ^-1, respectively. The fluorescence of the drug is enhanced when complexed to AMP, GMP, and TMP by about 60, 30 and 10%, respectively, whereas it is quenched by about 20% when complexed to CMP. Fluorescence enhancement analysis has yielded the values of 1.1 × 10¹⁰ and 0.7 × 10¹⁰ M ^-1 s^-1 for the excited-state rate constant of complex formation with the former two nucleotides, respectively. About one out of two collisions between an excited EB molecule and an AMP or GMP molecule results in complex formation. The potential implications of these findings for the EB-DNA interaction are discussed.     

Numerical simulation of DNA sample preconcentration in microdevice electrophoresis

A numerical model is presented for the accurate and efficient prediction of preconcentration and transport of DNA during sample introduction and injection in microcapillary electrophoresis. The model incorporates conservation laws for the different buffer ions, salt ions, and DNA sample, coupled through a Gaussian electric field to account for the field modifications that cause electromigration. The accuracy and efficiency required to capture the physics associated with such a complex transient problem are realized by the use of the finite element-flux corrected transport (FE-FCT) algorithm in two dimensions. The model has been employed for the prediction of DNA sample preconcentration and transport during electrophoresis in a double-T injector microdevice. To test its validity, the numerical results have been compared with the corresponding experimental data under similar conditions, and excellent agreement has been found. Finally, detailed results from a simulation of DNA sample preconcentration in electrophoretic microdevices are presented using as parameters the electric field strength and the other species concentrations. The effect of the Tris concentration on sample stacking is also investigated. These results demonstrate the great potential offered by the model for future optimization of such microchip devices with respect to significantly enhanced speed and resolution of sample separation.     

Ester derivatives of hexahomotrioxacalix[3]naphthalenes: conformational and binding properties with alkali metal cations

The syntheses of the triesters formed between ethyl bromoacetate and hexahomotrioxacalix[3]naphthalene 8, and its tert-butyl analogue 11, are described. Depending on the conditions employed, cone or partial cone conformers are produced. The conformations appear to have some influence on their complexation in neutral medium, with alkali metal cations. The X-ray structure of the partial cone triester 10 is presented.     

Excited-State Properties of Thymidine and Their Relevance to Its Heterogeneous Emission in Double-Stranded DNA

Published results on synthetic polynucleotides point to T as the major emitting fluorophore in DNA. We have reported also that the bases of the nonalternating polynucleotide poly(dA).poly(dT), in which T was selectively excited, undergo large-amplitude motions on the picosecond-nanosecond time scales (S. Georghiou et al., Biophys. J. 70, 1909-1922, 1996). In that study, the fluorescence decay profile of the T bases of this polynucleotide was found to contain a number of components; these may be considered to be the result of the motions of the bases that give rise to a distribution of stacked geometries of varying rigidity as well as dispersion and polar interactions. Here, we report the results of a study that we have undertaken in order to test this hypothesis. To this effect, we have studied the photophysical properties of thymidine (1) in aqueous buffer and in a number of organic solvents and (2) in aqueous sucrose solutions of viscosity extending to 149 cP. The results suggest that the fluorescence quantum yield decreases with an increase in the polarizability of the solvent, whereas it increases with an increase in the solvent polarity (on the basis of the empirical parameter of solvent polarity ETN) or viscosity. These findings suggest the following for the photophysical properties of the T bases in DNA: (1) Base stacking results in two antagonistic effects, namely it causes a reduction in fluorescence as a result of dispersion interactions and an enhancement as a result of a reduction in the motions of the bases and (2) exposure of the bases to the aqueous environment results in fluorescence enhancement.