Dynamical properties of a two-level atom in three variants of the two-photon q-deformed Jaynes-Cummings model

Temporal evolution of atomic properties including the population inversion and quantum fluctuations of atomic dipole variables are discussed in three various variants of two-photon q-deformed Jaynes-Cummings model.With the the field initially being in three different types of q-deformed coherent states,the quantum collapse and revival effects as well as atomic diploe squeezing are studied for both on-and off-resonant atom-field interaction. Particularly, it is shown that for nonzero detuning the atomic inversion exhibits superstructures which are absent in the non-deformed Jaynes-Cummings model and the dipole squeezing may be enhanced.Comment: 39 pages, 20 figure

Unexpected A-form formation of 4′-thioDNA in solution, revealed by NMR, and the implications as to the mechanism of nuclease resistance

Fully modified 4′-thioDNA, an oligonucleotide only comprising 2′-deoxy-4′-thionucleosides, exhibited resistance to an endonuclease, in addition to preferable hybridization with RNA. Therefore, 4′-thioDNA is promising for application as a functional oligonucleotide. Fully modified 4′-thioDNA was found to behave like an RNA molecule, but no details of its structure beyond the results of circular dichroism analysis are available. Here, we have determined the structure of fully modified 4′-thioDNA with the sequence of d(CGCGAATTCGCG) by NMR. Most sugars take on the C3′-endo conformation. The major groove is narrow and deep, while the minor groove is wide and shallow. Thus, fully modified 4′-thioDNA takes on the A-form characteristic of RNA, both locally and globally. The only structure reported for 4′-thioDNA showed that partially modified 4′-thioDNA that contained some 2′-deoxy-4′-thionucleosides took on the B-form in the crystalline form. We have determined the structure of 4′-thioDNA in solution for the first time, and demonstrated unexpected differences between the two structures. The origin of the formation of the A-form is discussed. The remarkable biochemical properties reported for fully modified 4′-thioDNA, including nuclease-resistance, are rationalized in the light of the elucidated structure

GRSDB2 and GRS_UTRdb: databases of quadruplex forming G-rich sequences in pre-mRNAs and mRNAs

G-quadruplex motifs in the RNA play significant roles in key cellular processes and human disease. While sequences capable of forming G-quadruplexes in the pre-mRNA are involved in regulation of polyadenylation and splicing events in mammalian transcripts, the G-quadruplex motifs in the UTRs may help regulate mRNA expression. GRSDB2 is a second-generation database containing information on the composition and distribution of putative Quadruplex-forming G-Rich Sequences (QGRS) mapped in ∼29 000 eukaryotic pre-mRNA sequences, many of which are alternatively processed. The data stored in the GRSDB2 is based on computational analysis of NCBI Entrez Gene entries with the help of an improved version of the QGRS Mapper program. The database allows complex queries with a wide variety of parameters, including Gene Ontology terms. The data is displayed in a variety of formats with several additional computational capabilities. We have also developed a new database, GRS_UTRdb, containing information on the composition and distribution patterns of putative QGRS in the 5′- and 3′-UTRs of eukaryotic mRNA sequences. The goal of these experiments has been to build freely accessible resources for exploring the role of G-quadruplex structure in regulation of gene expression at post-transcriptional level. The databases can be accessed at the G-Quadruplex Resource Site at: http://bioinformatics.ramapo.edu/GQRS/

Teleocidin-producing genotype of Streptomyces clavuligerus ATCC 27064.

Streptomyces clavuligerus is an industrially important producer of clavulanic acid (CA), a β-lactamase inhibitor which is used together with amoxicillin in one of the most widely prescribed antibacterial medicines, the co-amoxiclav. In a mid-eighties ATCC vial of S. clavuligerus ATCC 27064 culture, we have found a new genotype, which was apparently lost from the subsequent ATCC collection stocks, and has remained obscure to the scientific community. Most importantly, this genotype harbors teleocidin (lyngbyatoxin) biosynthetic genes, which are located on an enigmatic 138 kb chromosomal region and support accumulation of significant amounts of these highly toxic, tumor-promoting secondary metabolites in cultures of S. clavuligerus. While this genomic region is completely absent from all published sequences for S. clavuligerus ATCC strain, at least one of the industrial strains for commercial production of CA, originating from ATCC 27064, retained the genetic potential for production of teleocidins. The origin of teleocidin biosynthetic cluster can now be traced back to early S. clavuligerus stocks at the ATCC. Our work provides a genome sequence and a deposited monoisolate of this genotype. Given the scale of industrial use of S. clavuligerus world-wide and toxicity of teleocidins, we also discuss the environmental and safety implications and provide a method of abolishing teleocidin production without affecting productivity of CA. KEY POINTS: • Early stocks of S. clavuligerus ATCC 27064 produce toxic teleocidins • Teleocidin biosynthetic genes were found within a distinct S. clavuligerus genotype • The genotype has been passed on to some industrial clavulanic acid producer strains

Interaction of G-rich GT oligonucleotides with nuclear-associated eEF1A is correlated with their antiproliferative effect in haematopoietic human cancer cell lines.

4noG-rich GT oligonucleotides with a different content of G clusters have beenevaluated for their ability to exert cytotoxicity and to bind to nuclear-associatedproteins in T-lymphoblast CCRF-CEM cells. Only the oligomersthat did not form G-based structures or had a poor structure, under physiologicalconditions, were able to exert significant cellular growth inhibitioneffect. The cytotoxicity of these oligomers was related to their bindingto the nuclear-associated eEF1A protein, but not to the recognition ofnucleolin or other proteins. In particular, GT oligomers adopting a conformationcompatible with G-quadruplex, did not exert cytotoxicity and didnot bind to eEF1A. The overall results suggest that the ability of oligomersto adopt a G-quadruplex-type secondary structure in a physiological buffercontaining 150 mm NaCl is not a prerequisite for antiproliferative effect inhaematopoietic cancer cells. The cytotoxicity of G-rich GT oligomers wasshown to be tightly related to their binding affinity for eEF1A protein.nonemixedScaggiante, Bruna; Dapas, Barbara; Grassi, Gabriele; Manzini, GiorgioScaggiante, Bruna; Dapas, Barbara; Grassi, Gabriele; Manzini, Giorgi