Chemical cleavage reactions of DNA on solid support: application in mutation detection

Background  

The conventional solution-phase Chemical Cleavage of Mismatch (CCM) method is time-consuming, as the protocol requires purification of DNA after each reaction step. This paper describes a new version of CCM to overcome this problem by immobilizing DNA on silica solid supports.     

Energy-conformation studies of HCN,HNC and CN−: A comparison of results from EH-SCC and SCF molecular orbital calculations

We have made an Extended Hückel Self Consistent Charge (EH-SCC) molecular orbital calculation for hydrogen cyanide, hydrogen isocyanide and cyanide ion. The main purpose of this calculation was to compare the EH-SCC and the more accurate SCF MO calculations for HCN in order to evaluate the method we used here for future use. Specifically, we have calculated and compared the following properties of HCN: total energy, binding energy, variation of ground state energy with geometric conformation, ionization potential and dipole moment. In addition, we have extended previous calculations of HCN by also considering its energy variation with bond angle for two excited state configurations and deducing some of the characteristics of its electronic spectra. Finally we have also made an MO calculation of the isocyanide isomer HNC and CN^– ion to compare with and add to the known characterization of the H, C, N, system.

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Zusammenfassung Rechnungen nach der erweiterten Hückeltheorie werden für HCN, HNC und CN^– durchgeführt und mit ab initio Resultaten verglichen. Im einzelnen wurden Gesamtenergie, Bindungsenergie in Abhängigkeit von der geometrischen Struktur, Ionisierungspotential und Dipolmoment von HCN berechnet und außerdem die Energie für zwei doppelt angeregte Konfigurationen in Abhängigkeit vom Bindungswinkel bestimmt. Darüber hinaus sind MO-Rechnungen für HNC und CN^– gemacht worden.

     

Mechanistic studies of oxene reactions with organic substrates: Reaction paths on MNDO enthalpy surfaces—models for cytochrome P450 oxidations

In a systematic study, the characteristics of triplet oxene models for alkane, alkene, chloroalkane, and aryl oxidations by the cytochrome P450s have been examined using the semiempirical molecular orbital method MNDO and the formalism of statistical mechanics. Specific model substrates chosen were: methane, ethylene, propene, carbon tetrachloride, chloroform, and toluene. It was found that transition state geometries and activation entropies were reliably predicted, but that an empirical factor was necessary to correct overestimation of activation enthalpies. It was determined that both hydroxylations and epoxidation initiated by a O(³P) atom are nonconcerted; and that oxidations of C? Cl bonds (halosylations) occur by a two-step mechanism similar to hydroxylation. It is shown that the radical mechanisms derived from these studies are consistent with a range of observed properties of cytochrome P450 reactions and provide reasonable explanations for secondary deuterium isotope effects and substituent effects in cytochrome P450 epoxidation of styrenes, suicide inactivation of a P450 enzyme by ethylene, and the characteristics of aerobic CCl₄ and CHCl₃ metabolism. A triplet oxene mechanism for the initial steps of aromatic epoxidation and hydroxylation is also discussed.     

Differentiation of δ, μ, and κ opioid receptor agonists based on pharmacophore development and computed physicochemical properties

Compounds that bind with significant affinity to the opioid receptor types, , , and , with different combinations of activation and inhibition at these three receptors could be promising behaviorally selective agents. Working on this hypothesis, the chemical moieties common to three different sets of opioid receptor agonists with significant affinity for each of the three receptor types , , or were identified. Using a distance analysis approach, common geometric arrangements of these chemical moieties were found for selected , , or opioid agonists. The chemical and geometric commonalities among agonists at each opioid receptor type were then compared with a non-specific opioid recognition pharmacophore recently developed. The comparison provided identification of the additional requirements for activation of , , and opioid receptors. The distance analysis approach was able to clearly discriminate -agonists, while global molecular properties for all compounds were calculated to identify additional requirements for activation of and receptors. Comparisons of the combined geometric and physicochemical properties calculated for each of the three sets of agonists allowed the determination of unique requirements for activation of each of the three opioid receptors. These results can be used to improve the activation selectivity of known opioid agonists and as a guide for the identification of novel selective opioid ligands with potential therapeutic usefulness.     

Aminobis(Diorganylamino)Phosphanes: Versatile Reagents in Hydridophosphazene Chemistry

Abstract

The synthesis, crystal structure, polymerisation and metal complexation of aminobis(diorganylamino)phosphanes are discussed.     

The effect of nonlinearity on unstable zones of Mathieu equation

Mathieu equation is a well-known ordinary differential equation in which the excitation term appears as the non-constant coefficient. The mathematical modelling of many dynamic systems leads to Mathieu equation. The determination of the locus of unstable zone is important for the control of dynamic systems. In this paper, the stable and unstable regions of Mathieu equation are determined for three cases of linear and nonlinear equations using the homotopy perturbation method. The effect of nonlinearity is examined in the unstable zone. The results show that the transition curves of linear Mathieu equation depend on the frequency of the excitation term. However, for nonlinear equations, the curves depend also on initial conditions. In addition, increasing the amplitude of response leads to an increase in the unstable zone.     

Direct measurement of the voltage sensitivity of second-harmonic generation from a membrane dye in patch-clamped cells

We report what is to our knowledge the first optical imaging of voltage-clamped cells by second-harmonic generation. For the membrane-staining styryl dye di-4-ANEPPS, we determined the sensitivity of second-harmonic generation to be 18%/100 mV at an excitation wavelength of 850 ns. This sensitivity is significantly better than the optimal 10%/100 mV under fluorescence and further establishes the importance of second-harmonic generation for the functional imaging of membrane potential in living cells.     

Structural and electronic requirements for binding at the Mu–opioid receptor

A pharmacophore for μ-opioid receptor recognition based on a study of the fentanyl class of opioids has recently been characterized in our laboratories. To validate this pharmacophore, we have extended our theoretical studies to include four opiate analogs from structurally different classes and with high affinity but varying selectivity for the μ-opiate receptor. An extensive conformational search of the flexible regions of these compounds has been carried out at two levels of approximations, using the CHARMm force field and the semiempirical molecular orbital method AM 1. In a subsequent step, we have determined a series of structural, environmental, and electronic properties for each low-energy conformer of the analogs studied. All four analogs studied can assume a low-energy conformation in which at least three of the four stereoelectronic properties identified as modulators of recognition in the fentanyls are present in the same spatial arrangement. These results provide additional evidence for the plausibility of the proposed pharmacophore for μ–opioid receptor recognition. © 1992 John Wiley & Sons, Inc.     

A theoretical examination of substituent effects on the detoxification reaction between glutathione and halogenated methanes

An important metabolic pathway for halogenated methanes is the detoxification reaction with glutathione in the cell cytosol fraction. Experimental studies have shown that the rate of this S_N2 displacement reaction is directly related to the leaving group ability of the dissociating halide; the rate increases in order of the ions F^?, Cl^?, Br^?, and I^? leaving. In this study, we examine the role of the other halomethane substituents on the rate of this reaction for compounds with a common leaving anion. To this end, reaction Cl^? + CY₃Cl → ClCY₃ + Cl^? (Y = H,F,Cl) is examined using ab initio methods. The barrier for this exchange process may arise from requiring an inversion of the CY₃ group in the transition structure, the energy required to homolytically cleave the C? Cl bond, or from unfavorable steric and electronic interactions in the five-coordinated transition structure. Of these three factors, only the third explains the calculated ordering of barrier heights. This suggests that successive halogenation of methane not only increases its activity as a substrate for anaerobic reduction, as was shown earlier, but also decreases its ability to take part in the detoxification reaction with glutathione.