Method for detection of single-base mismatches using bimolecular beacons

This paper describes a method for the detection of single-base mismatches using DNA microarrays in a format that does not require labeling of the sample ("target") DNA. The method is based on disrupting fluorescence energy transfer (FRET) between a fluorophore attached to an immobilized DNA strand ("probe") and a quencher-containing sequence that is complementary except for an artificial mismatch (e.g. 5-nitroindole, 3-nitropyrole, or abasic site) at the site of interrogation. As the displacement of the FRET acceptor and hybridization of the unlabeled probe are bimolecular, the term "bimolecular beacons" is used to describe this approach. The analysis of a mismatch was based on differences in the amount of disruption in FRET upon hybridization of perfectly matched DNA targets and those containing single-base mismatches. Using this method and an oligonucleotide model system, A/C single-base mismatches were successfully discriminated at levels greater than that observed using surface-immobilized molecular beacons. The amount of discrimination was dependent on the identity of the artificial mismatch; greater discrimination was observed with 5-nitroindole (a "universal" base) than with an abasic site. G/T mismatches, considered to be particularly difficult to detect, were also successfully discriminated when quencher sequences containing 5-nitroindole were used.     

A variational coupled cluster theory for closed shells using a propagator modification procedure

A general partial summation method for including arbitrary classes of diagrams to all orders in the coupled cluster based size consistent energy functional for closed shell states is developed. Since the various reduced density matrices which appear in the energy functional are essentially the time-independent analogues of the corresponding many body Green functions, it is possible to derive Dyson-like equations for these quantities. By expanding the associated proper self energy parts in terms of the T-amplitudes, one can carry out partial summations in the reduced density matrices and thus in energy. At a higher level, higher order terms in a proper self energy can also be generated by renormalizing the internal propagators in it, and considering only the irreducible self-energy terms.     

Comparison of low-order multireference many-body perturbation theories

Tests have been made to benchmark and assess the relative accuracies of low-order multireference perturbation theories as compared to coupled cluster (CC) and full configuration interaction (FCI) methods. Test calculations include the ground and some excited states of the Be, H(2), BeH(2), CH(2), and SiH(2) systems. Comparisons with FCI and CC calculations show that in most cases the effective valence shell Hamiltonian (H(v)) method is more accurate than other low-order multireference perturbation theories, although none of the perturbative methods is as accurate as the CC approximations. We also briefly discuss some of the basic differences among the multireference perturbation theories considered in this work.     

Eigenvalues of large even annulenes in terms ofK 3,S 4 andS 5

Squares of the adjacency matrices of bipartite cycles (C_v) can be block-factored into matrices which correspond to vertex-weighted complete graphs forv = 6, vertex-weighted strongly regular graphs forv = 8 and 10, and vertex-weighted metrically regular graphs forv > 10. Using this fact and some properties of strongly and metrically regular graphs, it is shown that eigenvalues of large bipartite C _v graphs (i.e. large even annulenes) can be expressed by the general formula ± (2 ± (2 ± (... ± (2 +r _p)) ...), wherev = 2 ⁿ ×p,n is the number of surd () signs required andp = 3, 4 and 5. Here,r ₃,r ₄, andr ₅, are the eigenvalues of the complete graphK ₃ and the strongly regular graphsS ₄ andS ₅ respectively. The procedure does not require construction of characteristic polynomials for the determination of eigenvalues, and brings out a common topological origin for the two-fold degeneracies observed in the eigenvalue spectra of all even cycles and many odd cycles.     

Redox reactions of disulfiram: a pulse-radiolysis study

Redox reactions of disulfiram (DSF) were studied in aqueous solutions using the pulse-radiolysis technique. Reactions of DSF with one-electron oxidants Br₂ ^- and N₃, generated pulse radiolytically in aqueous solution at pH 7, yielded a transient (_max = 480 nm) which exhibited the characteristics of a disulphide cation radical and decayed by second-order kinetics. Reactions of DSF with halogenated peroxyl radicals CCl₃O₂, CHCl₂O₂, CH₂ClO₂ and CBr₃O₂ led to the formation of an adduct absorbing at 580 nm. The reduction potential was estimated to be 1.24 ± 0.06 V vs. NHE.     

Convenient and efficient stereoselective synthesis of (2Z)-2-(chloromethyl)alk-2-enoates using iron(III) or indium(III) chloride

The stereoselective synthesis of (2Z)-2-(chloromethyl)alk-2-enoates has been achieved efficiently and in high yields and in short reaction times from Baylis-Hillman adducts, 3-hydroxy-2-methylene-alkanoates, by treatment with FeCl₃ or InCl₃ at room temperature.     

Two (E)‐2‐arylidene‐1,4‐di‐p‐tosyl‐1,2,3,4‐tetrahydroquinoxaline compounds: supramolecular frameworks built with C—H...O and C—H...π(arene) hydrogen bonds and π–π stacking interactions

The pyrazine ring in two N‐substituted quinoxaline derivatives, namely (E)‐2‐(2‐methoxybenzylidene)‐1,4‐di‐p‐tosyl‐1,2,3,4‐tetrahydroquinoxaline, C₃₀H₂₈N₂S₂O₅, (II), and (E)‐methyl 2‐[(1,4‐di‐p‐tosyl‐1,2,3,4‐tetrahydroquinoxalin‐2‐ylidene)methyl]benzoate, C₃₁H₂₈N₂S₂O₆, (III), assumes a half‐chair conformation and is shielded by the terminal tosyl groups. In the molecular packing of the compounds, intermolecular C—H...O hydrogen bonds between centrosymmetrically related molecules generate dimeric rings, viz. R₂²(22) in (II) and R₂²(26) in (III), which are further connected through C—H...π(arene) hydrogen bonds and π–π stacking interactions into novel supramolecular frameworks.     

A simple and effective technique to locate quasi-degeneracy in a symmetric double well potential

Perturbation theory based model can be used to locate the quasi-degeneracy in an arbitrary double well potential. This method, extensively explain the effect of the coupling term on pair of states called quasi-degenerate. This model helps us to calculate the energy of the pair of quasi-degenerate states using appreciably small basis. Dispersion equation corresponding to the split energy levels are presented in a very explicit form. Numerical calculation shows that the proposed method can give extremely accurate results for symmetric double-well potentials.     

MYMIV-AC2, a Geminiviral RNAi Suppressor Protein, Has Potential to Increase the Transgene Expression

Gene silencing is one of the limiting factors for transgene expression in plants. But the plant viruses have learnt to suppress gene silencing by encoding the protein(s), called RNA silencing suppressor(s) (RSS). Hence, these proteins could be used to overcome the limitation for transgene expression. The RNAi suppressors, namely HC-Pro and P19, have been shown to enhance the transgene expression but other RSS proteins have not been screened for similar role. Moreover, none of RSSs from the DNA viruses are known for enhancing the expression of transgenes. The Mungbean Yellow Mosaic India Virus (MYMIV) belonging to the genus Begomovirus within the family of Geminiviridae encodes an RSS called the AC2 protein. Here, we used AC2 to elevate the expression of the transgenes. Upon introduction of MYMIV-AC2 in the silenced GFP transgenic tobacco lines, by either genetic hybridisation or transgenesis, the GFP expression was enhanced several fold in F1 and T0 lines. The GFP-siRNA levels were much reduced in F1 and T0 lines compared with those of the initial parental silenced lines. The enhanced GFP expression was also observed at the cellular level. This approach was also successful in enhancing the expression of another transgene, namely topoisomeraseII.