MgCl2 Enhances Cluster Formation by Nanoscale Toroidal DNA Condensates

Multivalent cations can cause DNA to condense from its extended state in solution into high-density toroid-shaped particles. Developing methods to control the size and size distribution of DNA toroids is an important goal for the development of artificial gene delivery systems. Here we demonstrate that changes in salt conditions, prior to condensation by multivalent cations, can significantly affect DNA condensation. Specifically, millimolar concentrations of MgCl₂ are shown to cause the formation of toroid clusters, whereas NaCl at the same ionic strength does not.     

Laser-Induced Fluorescence (LIF) Probe for <Emphasis Type="Italic">In-situ</Emphasis> Nitric Oxide Concentration Measurement in a Non-thermal Pulsed Corona Discharge Plasma Reactor

Laser-induced fluorescence (LIF) is an effective in-situ probe for NO concentrations below 300 ppm in a non-thermal plasma reactor. A new method has been developed to measure in-situ NO concentration in the reactor discharge region using a long-time—on the order of seconds—averaged fluorescence detection. This method, for quantifying NO concentration in a nonthermal plasma reactor, is simpler than a short-time—on the order of nanoseconds—fluorescence detection. For accurate measurement based on the new method, the LIF intensity must be close to the corona-induced fluorescence (CIF) intensity; the CIF intensity serves as a guide in selecting the LIF intensity. We find that a kinetic model proposed earlier works for two-tube reactors and represents the NO concentration in the middle of the reactor, which verifies the assumption of gas plug flow.     

Novel solid-phase synthesis of 1,2-dialkoxyindoles

[reaction: see text] A novel solid-phase synthesis of 1,2-dialkoxyindoles on SynPhase lanterns is described. A unique C-C bond formation involving a nucleophilic displacement of a solid-bound aryl fluorine by dimethyl malonate afforded the arylnitro methyl ester, which upon treatment with tin(II) chloride dihydrate gave the N-hydroxyindolone. Alkylation of the N-hydroxyindolones afforded the corresponding N-hydroxy-2-alkoxyindoles, which were further alkylated to give the 1,2-dialkoxyindole. A library of 64 (8R(1) x 8R(2)) discrete 1,2-dialkoxyindoles was prepared using a color encoding technique on SynPhase A-series lanterns.     

Versatile organic (fullerene)-inorganic (CdTe nanoparticle) nanoensembles

Novel organic (positively charged fullerene)-inorganic (negatively charged CdTe nanoparticle) nanoensembles were devised through electrostatic interactions and probed as versatile donor-acceptor hybrids. Photoirradiation of their homogeneous solutions, containing the electrostatically packed components, let to very long-lived (1.3 ms) charge separated states.     

Damage control of DNA in nucleosome core particles: when a histone's loving, protective embrace is just not good enough

Packaging DNA into nucleosome core particles generally offers protection from damage by molecules diffusing in solution. However, on page 403 of this issue, Barton and coworkers report that although noncovalently bound, activated Rh (Rhodium) does not readily bind within nucleosomal DNA, activated Rh that is covalently tethered to the 5' terminus of a histone-associated oligonucleotide oxidizes guanine bases from a distance of up to 24 base pairs, demonstrating that histones do not protect DNA from long-range damage from the transport of charge through stacked bases. This implies that oxidative damage generated on DNA in vivo may spread from an initially damaged site to distal sites. Once created, such sites may persist and be resistant to repair because of the protective packaging by histones; they thus may result in permanent mutations.     

Conformational and photophysical studies on porphyrin-containing donor-bridge-acceptor compounds. Charge separation in micellar nanoreactors

Photophysical studies with semi-rigid, 1, and flexible, 2, donor-bridge-acceptor (D-b-A2+) molecules with D a porphyrin and A2+ a methyl viologen moiety, were performed in neat polar solvents as well as included in surfactant (DTAB) aqueous and in reverse AOT/n-alkane micelles. The micelles acted as nanoreactors for the photoinduced electron transfer reaction upon laser excitation. In spite of the longer lifetime of the charge separated (CS) state in the semi-rigid tetrad 1(ca. 200 ns vs. ca. 100 ns for the flexible dyad 2), the CS formation quantum yield, for example in acetonitrile, was lower for the former (phi(CS) = 0.13) than for the latter (0.58). Comparison of the time-resolved fluorescence data in neat solvent and in the micelles yielded the phi(CS) values in the dilute micellar solutions. Application of laser-induced optoacoustic spectroscopy at various temperatures to 1 dissolved in a polar organic solvent (benzonitrile, BZN) included in aqueous DTAB nanoreactors afforded structural volume changes for the production in hundreds of ps of the CS state upon excitation of a polar molecule. The contraction during CS formation upon excitation of the collapsed conformer in BZN is attributed to the entering of solvent into the open molecular cavity. The opening upon formation of the CS state due to photoinduced electron transfer in the 1 collapsed conformation arises from the repulsion of the two positively charged ends in this state, as previously calculated. Inclusion of 1 in reverse AOT micelles in various n-alkanes also led to a contraction upon excitation, but the data had much more error due to the limited range of variability of the ratio of thermoelastic parameters. The data obtained with the more flexible "supermolecule" 2 showed the predicted large conformation flexibility of these molecules.     

Furan Decorated Nucleoside Analogues as Fluorescent Probes: synthesis, photophysical evaluation and site-specific incorporation

The synthesis and photophysical evaluation of modified nucleoside analogues in which a five-membered heterocycle (furan, thiophene, oxazole, and thiazole) is attached to the 5-position of 2′-deoxyuridine are reported. The furan-containing derivative is identified as the most promising responsive nucleoside of this family due to its emission quantum efficiency and degree of sensitivity to its microenvironment. The furan moiety was then attached to the 5-position of 2′-deoxycytidine as well as the 8-position of adenosine and guanosine. Photophysical evaluation of these four furan-containing nucleoside analogues reveals distinct differences in the absorption, emission, and quantum efficiency depending upon the class of nucleoside (pyrimidine or purine). Comparing the photophysical properties of all furan-containing nucleosides, identifies the furan thymidine analogue, 5-(fur-2-yl)-2′-deoxyuridine, as the best candidate for use as a responsive fluorescent probe in nucleic acids. 5-(Fur-2-yl)-2′-deoxyuridine was then converted to the corresponding phosphoramidite and site specifically incorporated into DNA oligonucleotides with greater than 88% coupling efficiency. Such furan-modified oligonucleotides form stable duplexes upon hybridization to their complementary DNA strands and display favorable fluorescent features.     

Reductive activation of nitrate reductases

Protein film voltammetry of Paracoccus pantotrophus respiratory nitrate reductase (NarGH) and Synechococcus elongatus assimilatory nitrate reductase (NarB) shows that reductive activation of these enzymes may be required before steady state catalysis is observed. For NarGH complementary spectroscopic studies suggest a structural context for the activation. Catalytic protein film voltammetry at a range of temperatures has allowed quantitation of the activation energies for nitrate reduction. For NarGH with an operating potential of ca. 0.05 V the activation energy of ca. 35 kJ mol-1 is over twice that measured for NarB whose operating potential is ca. -0.35 V.     

Quasiclassical trajectory calculations to evaluate a kinematic constraint on internal energy in suprathreshold collision energy abstraction reactions

Experimentally observed product quantum state distributions across a wide range of abstraction reactions at suprathreshold collision energies have shown a strong bias against product internal energy. Only a fraction, sometimes quite a small fraction, of the energetically accessible product quantum states are populated. Picconatto et al. [J. Chem. Phys. 114, 1663 (2001)] noted a simple mathematical relationship between the highest-energy rovibrational states observed and the kinematics of the reaction system. They proposed a reaction model based on reaction kinematics that quantitatively explains this behavior. The model is in excellent agreement with measured quantum state distributions. The assumptions of the model invoke detailed characteristics of reactive trajectories at suprathreshold collision energies. Here we test those assumptions using quasiclassical trajectory calculations for the abstraction reactions H+HCl-->H2+Cl, D+HCl-->HD+Cl, and H+DCl-->HD+Cl. Trajectories were run on a potential-energy surface calculated with a London-Eyring-Polyani-Sato function with a localized 3-center term (LEPS-3C) previously shown to accurately reproduce experimentally observed product state distributions for the H+HCl abstraction reaction. The trajectories sample collision energies near threshold and also substantially above it. Although the trajectories demonstrate some aspects of the model, they show that it is not valid. However, the inadequacy of the proposed model does not invalidate the apparent kinematic basis of the observed energy constraint. The present results show that there must be some other molecular behavior rooted in the reaction kinematics that is the explanation and the source of the constraint.