Design of allele-specific primers and detection of the human ABO genotyping to avoid the pseudopositive problem

PCR experiments using DNA primers forming mismatch pairing with template lambda DNA at the 3' end were carried out in order to develop allele-specific primers capable of detecting SNP in genomes without generating pseudopositive amplification products, and thus avoiding the so-called pseudopositive problem. Detectable amounts of PCR products were obtained when primers forming a single or two mismatch pairings at the 3' end were used. In particular, 3' terminal A/C or T/C (primer/template) mismatches tended to allow PCR amplification to proceed, resulting in pseudopositive results in many cases. While less PCR product was observed for primers forming three terminal mismatch pairings, target DNA sequences were efficiently amplified by primers forming two mismatch pairings next to the terminal G/C base pairing. These results indicate that selecting a primer having a 3' terminal nucleotide that recognizes the SNP nucleotide and the next two nucleotides that form mismatch pairings with the template sequence can be used as an allele-specific primer that eliminates the pseudopositive problem. Trials with the human ABO genes demonstrated that this primer design is also useful for detecting a single base pair difference in gene sequences with a signal-to-noise ratio of at least 45.     

Encapsulation and Release Characteristics of Carbon Dioxide in α-Cyclodextrin

Encapsulation and release of carbon dioxide (CO₂) into and from α-cyclodextrin (α-CD) was studied. Initial moisture content of α-CD and CO₂ pressure were found to have affected the encapsulation behavior. The increase of CO₂ pressure has constantly accelerated the encapsulation rates and increased the maximum inclusion ratio, whereas the increase of initial moisture content showed no consistent effect. The saturated α-CD solution produced the inclusion complex crystal of similar inclusion ratio to solid α-CD. The release characteristics of inclusion complexes were also monitored at various relative humidities at 25 °C. Predominantly, increase in storage humidity accelerated the release of CO₂. The inclusion complex crystal prepared from saturated α-CD solution showed the most stable release characteristic at all storage humidities investigated. The encapsulation and the release characteristics were analyzed using the first-order reaction equation and the Avrami’s equation respectively, in order to estimate the rate processes of encapsulation and release. The FT-IR spectra of inclusion complexes presented an absorption band at wavenumber around 2338 cm⁻¹, indicating CO₂ molecules resided inside the α-CD cavities in gaseous state rather than being bound to the hydroxyl groups of α-CD. Powder X-ray diffractometry was carried out to investigate the crystal lattice structure of α-CD and inclusion complexes. Scanning electron microscopy was also performed for morphological examination.     

Theoretical Study of Fluorescence Spectra Utilizing the pKa Values of Acids in Their Excited States

Assignment of the fluorescence spectrum of firefly luciferin in aqueous solutions was achieved by utilizing not only emission energies but also theoretical absorption spectra and relative concentrations as estimated by pK_a values. Calculated Gibbs free energies were utilized to estimate pK_a values. These pK_a values were then corrected by employing the experimental results. It was previously thought that the main peak near 550 nm observed in the experimental fluorescence spectra at all pH values corresponds to emission from the first excited state of the luciferin dianion [Ando et al. (2010) Jpn. J. Appl. Phys. 49, 117002–117008]. However, we found that the peak near 550 nm at low pH corresponds to emission from the first excited state of the phenolate monoanion of luciferin. Furthermore, we found that the causes of the red fluorescence at pH 1–2 are not only the emission from phenol monoanion but also the emission from the protonated species at nitrogen atom in the thiazoline ring of dianion.     

Chemical transformations of 4:7,10:13-diepoxy[15]annulenone by carbonyl transposition reactions

The titled annulenone 1 could be converted into new annulenones 3 and 8 by carbonyl transposition reactions. Compound 8 can be regarded as the first 14π hydroxy-enone as a higher homolog of tropolone (6π) and hydroxy[11]annulenones (10π), and was proved to be aromatic.     

Direct Observation of Fluorescently Labeled Single-stranded λDNA Molecules in a Micro-Flow Channel

We developed two labeling methods for the direct observation of single-stranded DNA (ssDNA), using a ssDNA binding protein and a ssDNA recognition peptide. The first approach involved protein fusion between the 70-kDa ssDNA-binding domain of replication protein A and enhanced yellow fluorescent protein (RPA-YFP). The second method used the ssDNA binding peptide of Escherichia coli RecA labeled with Atto488 (ssBP-488; Atto488-IRMKIGVMFGNPETTTGGNALKFY). The labeled ssλDNA molecules were visualized over time in micro-flow channels. We report substantially different dynamics between these two labeling methods. When ssλDNA molecules were labeled with RPA-YFP, terminally bound fusion proteins were sheared from the free ends of the ssλDNA molecules unless 25-mer oligonucleotides were annealed to the free ends. RPA-YFP-ssλDNA complexes were dissociated by the addition of 0.2 M NaCl, although complex reassembly was possible with injection of additional RPA-YFP. In contrast to the flexible dynamics of RPA-YFP-ssλDNA complexes, the ssBP-488-ssλDNA complexes behaved as rigid rods and were not dissociated even in 2 M NaCl.     

Where does the metal cation stay in Gd@C2v(9)-C82? A single-crystal X-ray diffraction study

Metal positions in endohedral metallofullerenes (EMFs) are of special importance because their molecular symmetry and intrinsic properties are strongly influenced by the location and motion of the encapsulated metals. X-ray analyses of the cocrystals of Gd@C(2v)(9)-C(82) with nickel(II) octaethylporphyrin [Ni(II)(OEP)] reveal that the Gd(3+) cation is off-center, being located under a hexagonal ring along the 2-fold axis of the C(2v)(9)-C(82) cage. This result is in sharp contrast to that of a previous study, showing that Gd@C(2v)(9)-C(82) has an anomalous endohedral structure, with the metal being positioned over a [6,6] bond, which is opposite to the hexagonal ring along the C(2) axis (Phys. Rev. B 2004, 69, 113412). In agreement with theoretical calculations and related studies, it is conclusive that the single rare-earth metal in M@C(2v)(9)-C(82) always tends to coordinate with the hexagonal ring along the 2-fold axis, instead of interacting with the [6,6] bond on the other end, regardless of the type of metal atom.     

Roots of Ehrhart polynomials arising from graphs

Several polytopes arise from finite graphs. For edge and symmetric edge polytopes, in particular, exhaustive computation of the Ehrhart polynomials not merely supports the conjecture of Beck et al. that all roots α of Ehrhart polynomials of polytopes of dimension D satisfy −D≤Re(α)≤D−1, but also reveals some interesting phenomena for each type of polytope. Here we present two new conjectures: (1) the roots of the Ehrhart polynomial of an edge polytope for a complete multipartite graph of order d lie in the circle |z+\fracd4| ￡ \fracd4|z+\frac{d}{4}| \le \frac{d}{4} or are negative integers, and (2) a Gorenstein Fano polytope of dimension D has the roots of its Ehrhart polynomial in the narrower strip -\fracD2 ￡ Re(a) ￡ \fracD2-1-\frac{D}{2} \leq \mathrm{Re}(\alpha) \leq \frac{D}{2}-1. Some rigorous results to support them are obtained as well as for the original conjecture. The root distribution of Ehrhart polynomials of each type of polytope is plotted in figures.     

Polymerization of coordinated monomers. XII. Alternating copolymerization of γ-crotonolactone with styrene with the use of stannic chloride

γ-Crotonolactone and styrene copolymerize alternately in the presence of stannic chloride at -10°C under photoirradiation. The intrinsic viscosity of the resulting copolymer is in the range of 0.6–0.8 dl/g at 30°C in chloroform. The equilibrium constants for the complex formation between stannic chloride and γ-crotonolactone were determined in 1,2-dichloroethane-toluene solution at 0 and ?20°C by use of absorption band at 350 nm. Continuous variation plots based on the ¹H-chemical shift show a 1:1 interaction between styrene and the γ-crotonolactone coordinated to stannic chloride. The equilibrium constants for the ternary molecular complex formation between the coordinated γ-crotonolactone and styrene were determined in 1,2-dichloroethane in the temperature range from ?20 to 0°C. The equilibrium constants, derived independently from the measurements of the nonequivalent protons in γ-crotonolactone, are equal to each other within the experimental error. The mechanism of the alternating copolymerization of γ-crotonolactone and styrene in the presence of stannic chloride is discussed in terms of the homopolymerization of the ternary molecular complex.     

Quadratic initial ideals of root systems

Let be one of the root systems , , and and write for the set of positive roots of together with the origin of . Let denote the Laurent polynomial ring over a field and write for the affine semigroup ring which is generated by those monomials with , where if . Let denote the polynomial ring over and write for the toric ideal of . Thus is the kernel of the surjective homomorphism defined by setting for all . In their combinatorial study of hypergeometric functions associated with root systems, Gelfand, Graev and Postnikov discovered a quadratic initial ideal of the toric ideal of . The purpose of the present paper is to show the existence of a reverse lexicographic (squarefree) quadratic initial ideal of the toric ideal of each of , and . It then follows that the convex polytope of the convex hull of each of , and possesses a regular unimodular triangulation arising from a flag complex, and that each of the affine semigroup rings , and is Koszul.