Novel,Monomeric Cyanine Dyes as Reporters for DNA Helicase Activity

The dimeric cyanine dyes, YOYO-1 and TOTO-1, are widely used as DNA probes because of their excellent fluorescent properties. They have a higher fluorescence quantum yield than ethidium homodimer, DAPI and Hoechst dyes and bind to double-stranded DNA with high affinity. However, these dyes are limited by heterogeneous staining at high dye loading, photocleavage of DNA under extended illumination, nicking of DNA, and inhibition of the activity of DNA binding enzymes. To overcome these limitations, seven novel cyanine dyes (Cyan-2, DC-21, DM, DM-1, DMB-2OH, SH-0367, SH1015-OH) were synthesized and tested for fluorescence emission, resistance to displacement by Mg²⁺, and the ability to function as reporters for DNA unwinding. Results show that Cyan-2, DM-1, SH-0367 and SH1015-OH formed highly fluorescent complexes with dsDNA. Of these, only Cyan-2 and DM-1 exhibited a large fluorescence enhancement in buffers, and were resistant to displacement by Mg²⁺. The potential of these two dyes to function as reporter molecules was evaluated using continuous fluorescence, DNA helicase assays. The rate of DNA unwinding was not significantly affected by either of these two dyes. Therefore, Cyan-2 and DM-1 form the basis for the synthesis of novel cyanine dyes with the potential to overcome the limitations of YOYO-1 and TOTO-1.     

Angular momentum polarization in molecular collisions : Classical and quantum theory for measurements using resonance fluorescence

Inelastic or reactive collisions typically produce an anisotropic distribution of rotational angular momentum. An explicit and general treatment is given for the intensity and polarization of resonance fluorescence from molecules produced in such processes. Both classical and quantum results are expressed in terms of bipolar harmonics and state multipoles formed from linear combinations of density matrix elements. The treatment provides an inversion procedure for determining moments of the rotational angular momentum distribution ; twelve independent moments can be obtained. The combinations of angular momentum operators involved are even in eight of these moments and odd in four, with respect to reflection in a plane containing the initial and final relative velocity vectors. Measurements of the even moments require linearly polarized excitation and fluorescence, whereas measurements of the odd moments require circularly polarized excitation. The requisite experimental geometry and other practical aspects are discussed. In the three appendices are discussed the classical limits of transition intensities, a density matrix treatment of atom-rigid-rotor collisions, including analysis of state multipole symmetries ; and the coupling coefficients for parallel angular momenta.     

Laser cooling without repumping: a magneto-optical trap for erbium atoms

We report on a novel mechanism that allows for strong laser cooling of atoms that do not have a closed cycling transition. This mechanism is observed in a magneto-optical trap (MOT) for erbium, an atom with a very complex energy level structure with multiple pathways for optical-pumping losses. We observe surprisingly high trap populations of over 10(6) atoms and densities of over 10(11) atoms cm(-3), despite the many potential loss channels. A model based on recycling of metastable and ground state atoms held in the quadrupole magnetic field of the trap explains the high trap population, and agrees well with time-dependent measurements of MOT fluorescence. The demonstration of trapping of a rare-earth atom such as erbium opens a wide range of new possibilities for practical applications and fundamental studies with cold atoms.     

A Reinvestigation of the Structure and Torsional Potential of N2O5 by Gas‐Phase Electron Diffraction Augmented by Ab Initio Theoretical Calculations

Gaseous N₂O₅ consists of two NO₂ groups bonded to a bridging O‐atom to form a nonlinear N−O−N moiety. The NO₂ groups undergo slightly hindered internal rotation around the bonds to the bridge so that instantaneous composition of the gaseous system is characterized by molecules with all combinations of torsion angles. In an earlier investigation, an attempt was made to determine the coefficients for an empirical form of the double‐rotor torsional potential, and the bond lengths and bond angles measured subject to assumptions that the structure of the O−NO₂ groups was invariant to torsion angle and that these groups had C_2v symmetry. The system has now been reinvestigated in terms of a more realistic model in which this symmetry restriction was relaxed, account was taken of structural changes in the NO₂ groups with torsion angle as predicted by ab initio theory at the B3LYP/6‐311+G* level, and a more convenient form of the torsional potential was assumed. The most stable conformation has C₂ symmetry with torsion angles τ₁ (defined as ∢(N−O−N=O₄)) equal to τ₂ (defined as ∢(N−O−N=O₆)) equal to 33.7°; because of the broad potential minimum in this region, the uncertainty in these angles is difficult to estimate, but is probably 3 – 4°. The results for the bond lengths and bond angles for the most stable conformation are r_g(N−O)=1.505(4) Å, r_g(N=O)=1.188(2) Å, ∢_α(N−O−N)=112.3(17)°, ∢_α(O=N=O)=134.2(4)°, 〈∢_α(O−N=O)〉=112.8(2)°. The difference between the symmetry‐nonequivalent O−N=O angles is estimated to be ca. 6.7° with the larger angle positioning the two N=O bonds on different NO₂ groups nearest each other. These average values are similar to those obtained in the original study. The main difference is found in the shape of the torsional potential, which at τ₁/τ₂=0/0 has a saddle point in the present work and a substantial peak in the earlier. The implication of the torsion‐angle findings for electron‐diffraction investigations of this type is discussed.     

Detection of tethered biocide moiety segregation to silicone surface using sum frequency generation vibrational spectroscopy

Polymer surface properties are controlled by the molecular surface structures. Sum frequency generation (SFG) vibrational spectroscopy has been demonstrated to be a powerful technique to study polymer surface structures at the molecular level in different chemical environments. In this research, SFG has been used to study the surface segregation of biocide moieties derived from triclosan (TCS) and tetradecyldimethyl (3-trimethoxysilylpropyl) ammonium chloride (C-14 QAS) that have been covalently bound to a poly(dimethylsiloxane) (PDMS) matrix. PDMS materials are being developed as coatings to control biofouling. This SFG study indicated that TCS-moieties segregate to the surface when the bulk concentration of TCS-moieties exceeds 8.75% by weight. Surface segregation of C-14 QAS moieties was detected after 5% by weight incorporation into a PDMS matrix. SFG results were found to correlate well with antifouling activity, providing a molecular interpretation of such results. This research showed that SFG can aid in the development of coatings for controlling biofouling by elucidating the chemical structure of the coating surface.     

Subfrequency noise signal extraction in fiber-optic strain sensors using postprocessing

Laser frequency fluctuations typically limit the performance of high-resolution interferometric fiber strain sensors. Using time delay interferometry, we demonstrate a frequency noise immune fiber sensing system, where strain signals were extracted well below the noise floor normally imposed by the frequency fluctuations of the laser. Initial measurements show a reduction in the noise floor by a factor of 30, with strain sensitivities of a nanostrain/Hz at 100 mHz and reaching 100 ps/Hz at 1 Hz. Further characterization of the system indicates the potential for at least 4.5 orders of magnitude frequency fluctuation rejection.     

High-resolution time-of-flight mass spectrometry fingerprinting of metabolites from cecum and distal colon contents of rats fed resistant starch

Time-of-flight mass spectrometry along with statistical analysis was utilized to study metabolic profiles among rats fed resistant starch (RS) diets. Fischer 344 rats were fed four starch diets consisting of 55 % (w/w, dbs) starch. A control starch diet consisting of corn starch was compared against three RS diets. The RS diets were high-amylose corn starch (HA7), HA7 chemically modified with octenyl succinic anhydride, and stearic-acid-complexed HA7 starch. A subgroup received antibiotic treatment to determine if perturbations in the gut microbiome were long lasting. A second subgroup was treated with azoxymethane (AOM), a carcinogen. At the end of the 8-week study, cecal and distal colon content samples were collected from the sacrificed rats. Metabolites were extracted from cecal and distal colon samples into acetonitrile. The extracts were then analyzed on an accurate-mass time-of-flight mass spectrometer to obtain their metabolic profile. The data were analyzed using partial least-squares discriminant analysis (PLS-DA). The PLS-DA analysis utilized a training set and verification set to classify samples within diet and treatment groups. PLS-DA could reliably differentiate the diet treatments for both cecal and distal colon samples. The PLS-DA analyses of the antibiotic and no antibiotic-treated subgroups were well classified for cecal samples and modestly separated for distal colon samples. PLS-DA analysis had limited success separating distal colon samples for rats given AOM from those not treated; the cecal samples from AOM had very poor classification. Mass spectrometry profiling coupled with PLS-DA can readily classify metabolite differences among rats given RS diets.     

Backscatter tolerant squeezed light source for advanced gravitational-wave detectors

We report on the performance of a dual-wavelength resonant, traveling-wave optical parametric oscillator to generate squeezed light for application in advanced gravitational-wave interferometers. Shot noise suppression of 8.6±0.8 dB was measured across the detection band of interest to Advanced LIGO, and controlled squeezing measured over 5900 s. Our results also demonstrate that the traveling-wave design has excellent intracavity backscattered light suppression of 47 dB and incident backscattered light suppression of 41 dB, which is a crucial design issue for application in advanced interferometers.