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Association of DNA Quadruplexes through G:C:G:C Tetrads. Solution Structure of d(GCGGTGGAT)
No full textThe structure formed by the DNA sequence d(GCGGTGGAT) in a 100 mM Na+ solution has
been determined using molecular dynamics calculations constrained by distance and dihedral restraints
derived from NMR experiments performed at isotopic natural abundance. The sequence folds into a dimer
of dimers. Each symmetry-related half contains two parallel stranded G:G:G:G tetrads flanked by an A:A
mismatch and by four-stranded G:C:G:C tetrads. Each of the two juxtaposed G:C:G:C tetrads is composed
of alternating antiparallel strands from the two halves of the dimer. For each single strand, a thymine
intersperses a double chain reversal connecting the juxtaposed G:G:G:G tetrads. This architecture has
potential implications in genetic recombination. It suggests a pathway for oligomerization involving
association of quadruplex entities through GpC steps
Experimental Demonstration of T:(G:G:G:G):T Hexad and T:A:A:T Tetrad Alignments within a DNA Quadruplex Stem
No full textA template-based approach was used to design unprecedented architectural motifs into a known
DNA framework. The structure formed by the sequence d(GCGGTTGGAT) in 0.1 M Na+ solution has
been determined using molecular dynamics simulations constrained by distance and dihedral restraints
derived from NMR experiments. The molecular topology has been previously observed for the sequence
d(GCGGTGGAT) (Webba da Silva, M. (2003) Biochemistry 42, 14356−65). Insertion of a single thymine
into the double chain reversal formed by the segment GGTGG results in the unprecedented experimental
demonstration of a T:(G:G:G:G):T hexad. The bi-stranded hexad results from the pairing alignment of
two G(T−G) triads. Each triad results from recognition of the sheared edge of a guanine by the Watson−Crick edge of a thymine of the segment GGTTGG. The alignment is stabilized by base-stacking of the
thymine to the sugar pucker of the preceding thymine. The latter is involved in formation of the T:A:A:T
tetrad alignment by forming a hydrogen bond with the free amino proton of a Watson−Crick aligned
A:A mispair. We have thus established that residues in double chain reversal loops linking juxtaposed
tetrads of a quadruplex stem may facilitate formation of yet unknown hydrogen bond alignments. By
employing a systematic approach analysis of sequence motifs appearing in double chain reversals, bridging
tetrad layers should allow for the prediction of topologies and architectural motifs appearing in biologically
relevant genomic regions
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Unique Structural Features of Interconverting Monomeric and Dimeric G-Quadruplexes Adopted by a Sequence from the Intron of the N-myc Gene
No full textStructural Probes in Quadruplex Nucleic Acid Structure Determination by NMR
No full textTraditionally, isotope-labelled DNA and RNA have been fundamental to nucleic acid structural studies by NMR. Four-stranded nucleic acid architectures studies increasingly benefit from a plethora of nucleotide conjugates for resonance assignments, the identification of hydrogen bond alignments, and improving the population of preferred species within equilibria. In this paper, we review their use for these purposes. Most importantly we identify reasons for the failure of some modifications to result in quadruplex formation
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
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