An Ethenoadenine FAD Analog Accelerates UV Dimer Repair by DNA Photolyase

Reduced anionic flavin adenine dinucleotide (FADH^?) is the critical cofactor in DNA photolyase (PL) for the repair of cyclobutane pyrimidine dimers (CPD) in UV‐damaged DNA. The initial step involves photoinduced electron transfer from *FADH^? to the CPD. The adenine (Ade) moiety is nearly stacked with the flavin ring, an unusual conformation compared to other FAD‐dependent proteins. The role of this proximity has not been unequivocally elucidated. Some studies suggest that Ade is a radical intermediate, but others conclude that Ade modulates the electron transfer rate constant (k_ET) through superexchange. No study has succeeded in removing or modifying this Ade to test these hypotheses. Here, FAD analogs containing either an ethano‐ or etheno‐bridged Ade between the AN1 and AN6 atoms (e‐FAD and ε‐FAD, respectively) were used to reconstitute apo‐PL, giving e‐PL and ε‐PL respectively. The reconstitution yield of e‐PL was very poor, suggesting that the hydrophobicity of the ethano group prevented its uptake, while ε‐PL showed 50% reconstitution yield. The substrate binding constants for ε‐PL and rPL were identical. ε‐PL showed a 15% higher steady‐state repair yield compared to FAD‐reconstituted photolyase (rPL). The acceleration of repair in ε‐PL is discussed in terms of an ε‐Ade radical intermediate vs superexchange mechanism.     

Experimental and mechanistic investigation of an iodomalonic acid-based Briggs-Rauscher oscillator and its perturbations by resorcinol

Classic Briggs-Rauscher oscillators use malonic acid (MA) as a substrate. The first organic product is iodomalonic acid. Iodomalonic acid (IMA) can serve as a substrate also; thus, the first product in that case is diiodomalonic acid (I(2)MA). Nonoscillating iodination kinetics can be followed by absorbance at 462 nm in acidic KIO(3) so long as IMA is in substantial excess over [I(2)]. At 25 °C, simulations lead to the two most important rate laws, and related rate constant estimates are reported. I(2)MA eventually decomposes by unknown processes, but I(2), O(2), H(2)O(2), and Mn(2+) speed up that decomposition, liberating most of the iodine back to the solution. Resorcinol is an effective inhibitor of oscillations both in MA oscillators and in IMA oscillators. Response of an IMA oscillator to varying amounts of resorcinol is shown herein and is similar to that for MA-based oscillators. The inhibitory effect of resorcinol is diminished by addition of IMA to a MA-based oscillator. The iodination reaction between IMA and resorcinol is too slow (0.043 M(-1) s(-1)) to account for the decreased inhibitory effectiveness of resorcinol. Rather, the decomposition of I(2)MA is responsible for the inhibition decrease.     

An automated instrument for human STR identification: design, characterization, and experimental validation

The microfluidic integration of an entire DNA analysis workflow on a fully integrated miniaturized instrument is reported using lab‐on‐a‐chip automation to perform DNA fingerprinting compatible with CODIS standard relevant to the forensic community. The instrument aims to improve the cost, duration, and ease of use to perform a “sample‐to‐profile” analysis with no need for human intervention. The present publication describes the operation of the three major components of the system: the electronic control components, the microfluidic cartridge and CE microchip, and the optical excitation/detection module. Experimental details are given to characterize the level of performance, stability, reliability, accuracy, and sensitivity of the prototype system. A typical temperature profile from a PCR amplification process and an electropherogram of a commercial size standard (GeneScan 500?, Applied Biosystems) separation are shown to assess the relevance of the instrument to forensic applications. Finally, we present a profile from an automated integrated run where lysed cells from a buccal swab were introduced in the system and no further human intervention was required to complete the analysis.     

The role of the dynamic crossover temperature and the arrest in glass-forming fluids

We discuss the role of the dynamic glass-forming fragile-to-strong crossover (FSC) in supercooled liquids. In the FSC, significant dynamic changes such as the decoupling (the violation of the Stokes-Einstein relation) of homologous transport parameters, e.g., the density relaxation time τ and the viscosity η, occur at a characteristic temperature T _c . We study the FSC using a scaling law approach. In particular, we use both forms of the mode-coupling theory (MCT): the original (ideal) and the extended form, which explicitly describes energy hopping processes. We demonstrate that T _c plays the most important physical role in understanding dynamic arrest processes.     

Isospin splittings of doubly heavy baryons

The SELEX Collaboration has reported a very large isospin splitting of doubly charmed baryons. We show that this effect would imply that the doubly charmed baryons are very compact. One intriguing possibility is that such baryons have a linear geometry Q–q–Q$Q\text{–}q\text{–}Q$ where the light quark q oscillates between the two heavy quarks Q  , analogous to a linear molecule such as carbon dioxide. However, using conventional arguments, the size of a heavy-light hadron is expected to be around 0.5 fm, much larger than the size needed to explain the observed large isospin splitting. Assuming the distance between two heavy quarks is much smaller than that between the light quark and a heavy one, the doubly heavy baryons are related to the heavy mesons via heavy quark–diquark symmetry. Based on this symmetry, we predict the isospin splittings for doubly heavy baryons including Ξ_cc${\Xi }_{cc}$, Ξ_bb${\Xi }_{bb}$ and Ξ_bc${\Xi }_{bc}$. The prediction for the Ξ_cc${\Xi }_{cc}$ is much smaller than the SELEX value. On the other hand, the Ξ_bb${\Xi }_{bb}$ baryons are predicted to have an isospin splitting as large as (6.3±1.7) MeV$(6.3\pm 1.7)\text{MeV}$. An experimental study of doubly bottomed baryons is therefore very important to better understand the structure of baryons with heavy quarks.     

How the Upper Bound Conjecture Was Proved

We give a short history of how the Upper Bound Conjecture for Spheres was proved.     

Double k-sets in symplectic generalized quadrangles

In classical projective geometry, a double six of lines consists of 12 lines ? ₁, ? ₂, . . . , ? ₆, m ₁, m ₂, . . . , m ₆ such that the ? _i are pairwise skew, the m _i are pairwise skew, and ? _i meets m _j if and only if i ≠ j. In the 1960s Hirschfeld studied this configuration in finite projective spaces PG(3, q) showing they exist for almost all values of q, with a couple of exceptions when q is too small. We will be considering double-k sets in the symplectic geometry W(q), which is constructed from PG(3, q) using an alternating bilinear form. This geometry is an example of a generalized quadrangle, which means it has the nice property that if we take any line ? and any point P not on ?, then there is exactly one line through P meeting ?. We will discuss all of this in detail, including all of the basic definitions needed to understand the problem, and give a result classifying which values of k and q allow us to construct a double k-set of lines in W(q).     

13-Acetoxy-13-desmethylretinal-14-3H: Synthesis and Interaction with Bacterioopsin

The title compound (4) was synthesized in three steps from 1,1-dimethoxy-7-methyl-9-(2′,6′,6′-trimethyl-1-cy-clohexen-1-yl)-4E,6E,8E-nonatrien-3-one (1). Interaction of 4 with bacterioopsin produced a pigment absorbing at 573 nm, which, on long standing in the dark, moves to 406 nm, mirroring the behavior of nonradioactive 4 with bacterioopsin (S. Seltzer, J. Org. Chem. 60, 1189–1194, 1993). Compound 4 was designed to test for the involvement of a nucleophilic side chain, presumably asp-212, in catalyzing the dark cis-trans isomerization of bound retinal, through its attack at C-13. Such a mechanism is anticipated to lead to a cross-linked product where the nucleophile replaces the 13-acetoxy group when 4 is substituted for the natural chromophore. The protein, reconstituted with 4, after extensive washing, solubilization in dimethylsulfoxide and extensive dialysis retains its radioactivity suggesting the establishment of a cross-link. Solution in 6 M urea, however, results in substantial loss of radioactivity, suggesting that the unfolded labeled protein suffers hydrolysis of the very labile 13-enolester group followed by proton exchange.     

Nanoscale Hydroxyl Radical Generation from Multiphoton Ionization of Tryptophan

Exposure of solutions containing both tryptophan and hydrogen peroxide to a pulsed (∼180 fs) laser beam at 750 nm induces luminescence characteristic of 5-hydroxytryptophan. The results indicate that 3-photon excitation of tryptophan results in photoionization within the focal volume of the laser beam. The resulting hydrated electron is scavenged by hydrogen peroxide to produce the hydroxyl radical. The latter subsequently reacts with tryptophan to form 5-hydroxytryptophan. The involvement of hydroxyl radicals is confirmed by the use of ethanol and nitrous oxide as scavengers and their effects on the fluorescence yield in this system. It is postulated that such multiphoton ionization of tryptophanyl residues in cellular proteins may contribute to the photodamage observed during imaging of cells and tissues using multiphoton microscopy.