Easily denaturing nucleic acids derived from intercalating nucleic acids: thermal stability studies, dual duplex invasion and inhibition of transcription start

The bulged insertions of (R)-1-O-(pyren-1-ylmethyl)glycerol (monomer P) in two complementary 8mer DNA strands (intercalating nucleic acids) opposite to each other resulted in the formation of an easily denaturing duplex, which had lower thermal stability (21.0°C) than the wild-type double-stranded DNA (dsDNA, 26.0°C), but both modified oligodeoxynucleotides had increased binding affinity toward complementary single-stranded DNA (ssDNA) (41.5 and 39.0°C). Zipping of pyrene moieties in an easily denaturing duplex gave formation of a strong excimer band at 480 nm upon excitation at 343 nm in the steady-state fluorescence spectra. The excimer band disappeared upon addition of a similar short dsDNA, but remained when adding a 128mer dsDNA containing the same sequence. When P was inserted into 2′-OMe-RNA strands, the duplex with zipping P was found to be more stable (42.0°C) than duplexes with the complementary ssDNAs (31.5 and 19.5°C). The excimer band observed in the ds2′-OMe-RNA with zipping P had marginal changes upon addition of both 8 and 128mer dsDNA. Synthesized oligonucleotides were tested in a transcriptional inhibition assay for targeting of the open complex formed by Escherichia coli RNA polymerase with the lac UV-5 promoter using the above mentioned 128mer dsDNA. Inhibition of transcription was observed for 8mer DNAs possessing pyrene intercalators and designed to target both template and non-template DNA strands within the open complex. The observed inhibition was partly a result of unspecific binding of the modified DNAs to the RNA polymerase. Furthermore, the addition of 8mer DNA with three bulged insertions of P designed to be complementary to the template strand at the +36 to +43 position downstream of the transcription start resulted in a specific halt of transcription producing a truncated RNA transcript. This is to our knowledge the first report of an RNA elongation stop mediated by a small DNA sequence possessing intercalators. The insertions of P opposite to each other in ds2′-OMe-RNA showed inhibition efficiency of 96% compared with 25% for unmodified ds2′-OMe-RNA

Enzymatic incorporation of LNA nucleotides

The present invention relates to oligonucleotides comprising LNA units and enzymatic methods of synthesizing such oligonucleotides. Oligonucleotide comprising LNA units have various characteristics, e.g. improved biostability and increased > affinity for complementary oligonucleotides. The methods may be part of detection reactions, polymerase chain reaction, RNA transcription or in vitro evolution processes such as SELEX

Enzymatic incorporation of LNA nucleotides

The present invention relates to oligonucleotides comprising LNA units and enzymatic methods of synthesizing such oligonucleotides. Oligonucleotide comprising LNA units have various characteristics, e.g. improved biostability and increased > affinity for complementary oligonucleotides. The methods may be part of detection reactions, polymerase chain reaction, RNA transcription or in vitro evolution processes such as SELEX

Locked nucleoside analogues expand the potential of DNAzymes to cleave structured RNA targets

BACKGROUND: DNAzymes cleave at predetermined sequences within RNA. A prerequisite for cleavage is that the DNAzyme can gain access to its target, and thus the DNAzyme must be capable of unfolding higher-order structures that are present in the RNA substrate. However, in many cases the RNA target sequence is hidden in a region that is too tightly structured to be accessed under physiological conditions by DNAzymes. RESULTS: We investigated how incorporation of LNA (locked nucleic acid) monomers into DNAzymes improves their ability to gain access and cleave at highly-structured RNA targets. The binding arms of DNAzymes were varied in length and were substituted with up to three LNA and α-L-LNA monomers (forming LNAzymes). For one DNAzyme, the overall cleavage reaction proceeded fifty times faster after incorporation of two α-L-LNA monomers per binding arm (k(obs )increased from 0.014 min(-1 )to 0.78 min(-1)). CONCLUSION: The data demonstrate how hydrolytic performance can be enhanced by design of LNAzymes, and indicate that there are optimal lengths for the binding arms and for the number of modified LNA monomers

Ultrafast Structural Dynamics of Photo-Reactions Revealed by Model-Independent X-ray Cross-Correlation Analysis

We applied angular X-ray Cross-Correlation analysis (XCCA) to scattering images from a femtosecond resolution LCLS X-ray free-electron laser (XFEL) pump-probe experiment with solvated PtPOP ([Pt$_2$(P$_2$O$_5$H$_2$)$_4$]$^{4-}$) metal complex molecules. The molecules were pumped with linear polarized laser pulses creating an excited state population with a preferred orientational (alignment) direction. Two time scales of $1.9\pm1.5$ ps and $46\pm10$ ps were revealed by model-independent XCCA, associated with an internal structural changes and rotational dephasing, respectively. Our studies illustrate the potential of XCCA to reveal hidden structural information in a model independent analysis of time evolution of solvated metal complex molecules.Comment: 8 pages, 5 figures, 50 reference

Site-specific O-glycosylation on the MUC_{2} mucin protein inhibits cleavage by the porphyromonas gingivalis secreted cysteine protease (RgpB)

The colonic epithelial surface is protected by an inner mucus layer that the commensal microflora cannot penetrate. We previously demonstrated that Entamoeba histolytica secretes a protease capable of dissolving this layer that is required for parasite penetration. Here, we asked whether there are bacteria that can secrete similar proteases. We screened bacterial culture supernatants for such activity using recombinant fragments of the MUC2 mucin, the major structural component, and the only gel-forming mucin in the colonic mucus. MUC2 has two central heavily O-glycosylated mucin domains that are protease-resistant and has cysteine-rich N and C termini responsible for polymerization. Culture supernatants of Porphyromonas gingivalis, a bacterium that secretes proteases responsible for periodontitis, cleaved the MUC2 C-terminal region, whereas the N-terminal region was unaffected. The active enzyme was isolated and identified as Arg-gingipain B (RgpB). Two cleavage sites were localized to IR↓TT and NR↓QA. IR↓TT cleavage will disrupt the MUC2 polymers. Because this site has two potential O-glycosylation sites, we tested whether recombinant GalNAc-transferases (GalNAc-Ts) could glycosylate a synthetic peptide covering the IRTT sequence. Only GalNAc-T3 was able to glycosylate the second Thr in IRTT, rendering the sequence resistant to cleavage by RgpB. Furthermore, when GalNAc-T3 was expressed in CHO cells expressing the MUC2 C terminus, the second threonine was glycosylated, and the protein became resistant to RgpB cleavage. These findings suggest that bacteria can produce proteases capable of dissolving the inner protective mucus layer by specific cleavages in the MUC2 mucin and that this cleavage can be modulated by site-specific O-glycosylation

Anisotropy enhanced X-ray scattering from solvated transition metal complexes

Time-resolved X-ray scattering patterns from photoexcited molecules in solution are in many cases anisotropic at the ultrafast time scales accessible at X-ray Free Electron Lasers (XFELs). This anisotropy arises from the interaction of a linearly polarized UV-vis pump laser pulse with the sample, which induces anisotropic structural changes that can be captured by femtosecond X-ray pulses. In this work we describe a method for quantitative analysis of the anisotropic scattering signal arising from an ensemble of molecules and we demonstrate how its use can enhance the structural sensitivity of the time-resolved X-ray scattering experiment. We apply this method on time-resolved X-ray scattering patterns measured upon photoexcitation of a solvated di-platinum complex at an XFEL and explore the key parameters involved. We show that a combined analysis of the anisotropic and isotropic difference scattering signals in this experiment allows a more precise determination of the main photoinduced structural change in the solute, i.e. the change in Pt-Pt bond length, and yields more information on the excitation channels than the analysis of the isotropic scattering only. Finally, we discuss how the anisotropic transient response of the solvent can enable the determination of key experimental parameters such as the Instrument Response Function.Comment: Accepted for publication in Journal of Synchrotron Radiatio

On the complexity of resource-bounded logics

We revisit decidability results for resource-bounded logics and use decision problems for vector addition systems with states (VASS) to characterise the complexity of (decidable) model-checking problems. We show that the model-checking problem for the logic RB+-ATL is 2EXPTIME-complete by using recent results on alternating VASS. In addition, we establish that the model-checking problem for RBTL is decidable and has the same complexity as for RBTL* (the extension of RBTL with arbitrary path formulae), namely EXPSPACE-complete, proving a new decidability result as a by-product of the approach. Finally, we establish that the model-checking problem for RB+-ATL* is decidable by a reduction to parity games, and show how to synthesise values for resource parameters

Beta decay and the origin of biological chirality: New experimental results

The proposed connection between the parity-violating handedness of beta particles in radioactive decay and the sign (L) of biological chirality (the Vester-Ulbricht [V-U] hypothesis) is being investigated by measuring the theoretically predicted asymmetry in the formation of triplet positronium in amino acid enantiomers by low energy positrons under reversal of the helicity of the positrons. We find the asymmetry in leucine to be (0.8±1.0)×10 −4 , i.e. consistent with the theoretical, prediction of 10 −6 to 10 −7 . The apparatus is now sensitive enough to test the predicted asymmetry in optically active molecules which have heavy atoms at their chiral centers. The connection between these results and asymmetry in radiolysis by beta-decay electrons is made, and the implications of our limits for the V-U hypothesis discussed. Although the above limits are 10 6 times lower than direct measurements of radiolysis, they are still not small enough to allow us to rule out the V-U hypothesis.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/43347/1/11084_2004_Article_BF00933685.pd

Locked Nucleic Acid Pentamers as Universal PCR Primers for Genomic DNA Amplification

Background: Multiplexing technologies, which allow for simultaneous detection of multiple nucleic acid sequences in a single reaction, can save a lot of time, cost and labor compared to traditional single reaction detection methods. However, the multiplexing method currently used requires precise handiwork and many complicated steps, making a new, simpler technique desirable. Oligonucleotides containing locked nucleic acid residues are an attractive tool because they have strong affinities for their complementary targets, they have been used to avoid dimer formation and mismatch hybridization and to enhance efficient priming. In this study, we aimed to investigate the use of locked nucleic acid pentamers for genomic DNA amplification and multiplex genotyping. Results: We designed locked nucleic acid pentamers as universal PCR primers for genomic DNA amplification. The locked nucleic acid pentamers were able to prime amplification of the selected sequences within the investigated genomes, and the resulting products were similar in length to those obtained by restriction digest. In Real Time PCR of genomic DNA from three bacterial species, locked nucleic acid pentamers showed high priming efficiencies. Data from bias tests demonstrated that locked nucleic acid pentamers have equal affinities for each of the six genes tested from the Klebsiella pneumoniae genome. Combined with suspension array genotyping, locked nucleic acid pentamer-based PCR amplification was able to identify a total of 15 strains, including 3 species of bacteria, by gene- and species-specific probes. Among the 32 specie