Double helix conformation, groove dimensions and ligand binding potential of a G/C stretch in B-DNA

The self-complementary DNA fragment CCGGCGCCGG crystallizes in the rhombohedral space group R3 with unit cell parameters a = 54.07 angstrom and c = 44.59 angstrom. The structure has been determined by X-ray diffraction methods at 2.2 angstrom resolution and refined to an R value of 16.7%. In the crystal, the decamer forms B-DNA double helices with characteristic groove dimensions: compared with B-DNA of random sequence, the minor groove is wide and deep and the major groove is rather shallow. Local base pair geometries and stacking patterns are within the range commonly observed in B-DNA crystal structures. The duplex bears no resemblance to A-form DNA as might have been expected for a sequence with only GC base pairs. The shallow major groove permits an unusual crystal packing pattern with several direct intermolecular hydrogen bonds between phosphate oxygens and cytosine amino groups. In addition, decameric duplexes form quasi-infinite double helices in the crystal by end-to-end stacking. The groove geometries and accessibilities of this molecule as observed in the crystal may be important for the mode of binding of both proteins and drug molecules to G/C stretches in DNA.

Conformational polymorphism in G-tetraplex structures: strand reversal by base flipover or sugar flipover

Guanlne rich sequences adopt a variety of four stranded structures, which differ in strand orientation and conformation about the glycosldic bond even though they are all stabilised by Hoogsteen hydrogen bonded guanlne tetrads. Detailed model building and molecular mechanics calculations have been carried out to investigate various possible conformations of guanlnes along a strand and different possible orientations of guanlne strands In a G-tetraplex structure. It is found that for an ollgo G stretch per se, a parallel four stranded structure with all guanines In anti conformation is favoured over other possible tetraplex structures. Hence an alternating syn-anti arrangement of guanlnes along a strand is likely to occur only in folded back tetraplex structures with antiparallel G strands. Our study provides a theoretical rationale for the observed alternation of glycosldic conformation and the inverted stacking arrangement arising from base filpover, In antlparallel G-tetraplex structures and also highlights the various structural features arising due to different types of strand orientations. The molecular mechanics calculations help in elucidating the various interactions which stabilize different G-tetraplex structures and indicate that screening of phosphate charge by counterions could have a dramatic effect on groove width in these four stranded structures.

Formation of a G-quadruplex at the BCL2 major breakpoint region of the t(14;18) translocation in follicular lymphoma

The t(14;18) translocation in follicular lymphoma is one of the most common chromosomal translocations. Most breaks on chromosome 18 are located at the 3'-UTR of the BCL2 gene and are mainly clustered in the major breakpoint region (MBR). Recently, we found that the BCL2 MBR has a non-B DNA character in genomic DNA. Here, we show that single-stranded DNA modeled from the template strand of the BCL2 MBR, forms secondary structures that migrate faster on native PAGE in the presence of potassium, due to the formation of intramolecular G-quadruplexes. Circular dichroism shows evidence for a parallel orientation for G-quadruplex structures in the template strand of the BCL2 MBR. Mutagenesis and the DMS modification assay confirm the presence of three guanine tetrads in the structure. 1H nuclear magnetic resonance studies further confirm the formation of an intramolecular G-quadruplex and a representative model has been built based on all of the experimental evidence. We also provide data consistent with the possible formation of a G-quadruplex structure at the BCL2 MBR within mammalian cells. In summary, these important features could contribute to the single-stranded character at the BCL2 MBR, thereby contributing to chromosomal fragility.

Formation of a G-quadruplex at the BCL2 major breakpoint region of the t(14;18) translocation in follicular lymphoma

The t(14;18) translocation in follicular lymphoma is one of the most common chromosomal translocations. Most breaks on chromosome 18 are located at the 3'-UTR of the BCL2 gene and are mainly clustered in the major breakpoint region (MBR). Recently, we found that the BCL2 MBR has a non-B DNA character in genomic DNA. Here, we show that single-stranded DNA modeled from the template strand of the BCL2 MBR, forms secondary structures that migrate faster on native PAGE in the presence of potassium, due to the formation of intramolecular G-quadruplexes. Circular dichroism shows evidence for a parallel orientation for G-quadruplex structures in the template strand of the BCL2 MBR. Mutagenesis and the DMS modification assay confirm the presence of three guanine tetrads in the structure. 1H nuclear magnetic resonance studies further confirm the formation of an intramolecular G-quadruplex and a representative model has been built based on all of the experimental evidence. We also provide data consistent with the possible formation of a G-quadruplex structure at the BCL2 MBR within mammalian cells. In summary, these important features could contribute to the single-stranded character at the BCL2 MBR, thereby contributing to chromosomal fragility.

E. C. G. Sudarshan and Symmetry in Classical Dynamics, Optics and Quantum Mechanics

We review work initiated and inspired by Sudarshan in relativistic dynamics, beam optics, partial coherence theory, Wigner distribution methods, multimode quantum optical squeezing, and geometric phases. The 1963 No Interaction Theorem using Dirac's instant form and particle World Line Conditions is recalled. Later attempts to overcome this result exploiting constrained Hamiltonian theory, reformulation of the World Line Conditions and extending Dirac's formalism, are reviewed. Dirac's front form leads to a formulation of Fourier Optics for the Maxwell field, determining the actions of First Order Systems (corresponding to matrices of Sp(2,R) and Sp(4,R)) on polarization in a consistent manner. These groups also help characterize properties and propagation of partially coherent Gaussian Schell Model beams, leading to invariant quality parameters and the new Twist phase. The higher dimensional groups Sp(2n,R) appear in the theory of Wigner distributions and in quantum optics. Elegant criteria for a Gaussian phase space function to be a Wigner distribution, expressions for multimode uncertainty principles and squeezing are described. In geometric phase theory we highlight the use of invariance properties that lead to a kinematical formulation and the important role of Bargmann invariants. Special features of these phases arising from unitary Lie group representations, and a new formulation based on the idea of Null Phase Curves, are presented.

8-(3-methylphenoxy)-16H-dinaphtho[2,1-d;1',2'-g][1,3,2]dioxaphosphocine 8-oxide

In the title compound, C28H21O4P, the eight-membered heterocyclic dioxaphosphocine ring has a distorted boat conformation, with the phosphoryl O atom axial and the phenoxy group equatorial. The P=O distance is 1.451 (1) Angstrom and the average length of the three P-O bonds is 1.573 (1) Angstrom. The phenyl ring is nearly perpendicular to both naphthalene planes, making dihedral angles of 91.30 (3) and 97.65 (5)degrees with them. The angle between the two naphthalene planes is 67.73 (3)degrees. The crystal structure is stabilized by van der Waals interactions.

Intraloop and Interloop Interactions in the Folded-G Quartet Structure of Oxytricha Telomeric Sesquence

The antiparallel intramolecular G quartet structure for the 3.5 copy Oxytricha telomeric sequence d(G(4)T(4))(3)G4 has been established using a combination of spectroscopic and chemical probing methods. In the presence of Naf ions, this sequence exhibits a circular dichroism spectrum with a positive band at 295 nm and a negative band around 265 nm, characteristic of an antiparallel G quartet structure. Further, we show that d(G(4)T(4))(3)G(4) adopts an antiparallel intramolecular G quartet structure even in K+ unlike d(G(4)T(4)G(4)). KMnO4 probing experiments indicated the existence of intra and interloop interactions in the Na+ induced structure. We have found that K+ not only increases the thermal stability of,G quartet structure but also binds to the loop region and disrupts stacking and interloop interactions. Biological consequences of such cation-dependent conformational micro-heterogeneity in the loop region of G quartet structures is also discussed.

Popular mixed matchings

We study the problem of matching applicants to jobs under one-sided preferences; that is, each applicant ranks a non-empty subset of jobs under an order of preference, possibly involving ties. A matching M is said to be more popular than T if the applicants that prefer M to T outnumber those that prefer T to M. A matching is said to be popular if there is no matching more popular than it. Equivalently, a matching M is popular if phi(M, T) >= phi(T, M) for all matchings T, where phi(X, Y) is the number of applicants that prefer X to Y. Previously studied solution concepts based on the popularity criterion are either not guaranteed to exist for every instance (e.g., popular matchings) or are NP-hard to compute (e.g., least unpopular matchings). This paper addresses this issue by considering mixed matchings. A mixed matching is simply a probability distribution over matchings in the input graph. The function phi that compares two matchings generalizes in a natural manner to mixed matchings by taking expectation. A mixed matching P is popular if phi(P, Q) >= phi(Q, P) for all mixed matchings Q. We show that popular mixed matchings always exist and we design polynomial time algorithms for finding them. Then we study their efficiency and give tight bounds on the price of anarchy and price of stability of the popular matching problem. (C) 2010 Elsevier B.V. All rights reserved.

Resonance de-enhancement in the 2(1)A(g) state of trans-azobenzene

We analyze the origin of de-enhancement for a number of vibrational modes in the 2(1)A(g) excited state of trans-azobenzene. We have used the time-dependent wave packet analysis of the RR intensities by including the multimode damping effects in the calculation. This avoids the use of unrealistically large values for the damping parameter. It is concluded that the de-enhancement is caused by the interference between the two uncoupled electronic states, and that the intensities observed under the so-called symmetry forbidden 2(1)A(g) <-- 1(1)A(g) transition are purely due to resonance excitation. It is also observed that the use of the time-dependent approach to study the de-enhancement effects caused by multiple electronic states on the RR intensities is not necessarily useful if one is interested in the structural dynamics.

Effect of Zr4+-ion substitution in CeO2 on H2O2-assisted degradation of orange G

A series of Pd ion-substituted CeO2-ZrO2 solid solutions were synthesized using the solution combustion technique. H2O2-assisted degradation of orange G was carried out in the presence of the catalysts. The activity of the catalysts was found to increase with the introduction of the second component in the solid solution, as signified by an increase in the rate constants and lowering of activation energy. The study showed the involvement of lattice oxygen and the importance of reducibility of the compound for the reaction. (C) 2011 Elsevier B.V. All rights reserved.

Analysing Message Sequence Graph Specifications

We give a detailed construction of a finite-state transition system for a com-connected Message Sequence Graph. Though this result is well-known in the literature and forms the basis for the solution to several analysis and verification problems concerning MSG specifications, the constructions given in the literature are either not amenable to implementation, or imprecise, or simply incorrect. In contrast we give a detailed construction along with a proof of its correctness. Our transition system is amenable to implementation, and can also be used for a bounded analysis of general (not necessarily com-connected) MSG specifications.

Bounded Unpopularity Matchings

We investigate the following problem: given a set of jobs and a set of people with preferences over the jobs, what is the optimal way of matching people to jobs? Here we consider the notion of popularity. A matching M is popular if there is no matching M' such that more people prefer M' to M than the other way around. Determining whether a given instance admits a popular matching and, if so, finding one, was studied by Abraham et al. (SIAM J. Comput. 37(4):1030-1045, 2007). If there is no popular matching, a reasonable substitute is a matching whose unpopularity is bounded. We consider two measures of unpopularity-unpopularity factor denoted by u(M) and unpopularity margin denoted by g(M). McCutchen recently showed that computing a matching M with the minimum value of u(M) or g(M) is NP-hard, and that if G does not admit a popular matching, then we have u(M) >= 2 for all matchings M in G. Here we show that a matching M that achieves u(M) = 2 can be computed in O(m root n) time (where m is the number of edges in G and n is the number of nodes) provided a certain graph H admits a matching that matches all people. We also describe a sequence of graphs: H = H(2), H(3), ... , H(k) such that if H(k) admits a matching that matches all people, then we can compute in O(km root n) time a matching M such that u(M) <= k - 1 and g(M) <= n(1 - 2/k). Simulation results suggest that our algorithm finds a matching with low unpopularity in random instances.