In vitro selection, characterization, and application of deoxyribozymes that cleave RNA

Over the last decade, many catalytically active DNA molecules (deoxyribozymes; DNA enzymes) have been identified by in vitro selection from random-sequence DNA pools. This article focuses on deoxyribozymes that cleave RNA substrates. The first DNA enzyme was reported in 1994 and cleaves an RNA linkage. Since that time, many other RNA-cleaving deoxyribozymes have been identified. Most but not all of these deoxyribozymes require a divalent metal ion cofactor such as Mg(2+) to catalyze attack by a specific RNA 2′-hydroxyl group on the adjacent phosphodiester linkage, forming a 2′,3′-cyclic phosphate and a 5′-hydroxyl group. Several deoxyribozymes that cleave RNA have utility for in vitro RNA biochemistry. Some DNA enzymes have been applied in vivo to degrade mRNAs, and others have been engineered into sensors. The practical impact of RNA-cleaving deoxyribozymes should continue to increase as additional applications are developed

Subunit Stoichiometry of a Heteromultimeric G protein-coupled Inward-rectifier K^+ Channel

We investigated the stoichiometry of the heteromultimeric G protein-coupled inward-recitfier K^+ channel (GIRK) formed from GIRK1 and GIRK4 subunits. Multimeric GIRK constructs with several concatenated channel subunits were expressed in Xenopus oocytes. Coexpression of various trimeric constructs with different monomers clearly showed that the functional channel has stoichiometry (GIRK1)_2(GIRK4)_2. Efforts to establish a preferred arrangement of subunits around the channel pore suggest that more than one arrangement may be viable

Site‐Specific Fluorescent Labeling of Large RNAs with Pyrene

Pyrene is a useful chromophore for monitoring the tertiary structure and folding of large RNAs. This unit describes the general preparation of a large RNA (>80 nucleotides in length) that has been site‐specifically modified with pyrene at the 2′‐position of an individual internal nucleotide. A protocol is provided for derivatizing a 2′‐amino‐RNA oligonucleotide with a suitably activated pyrene reagent. This pyrene‐labeled oligonucleotide is then assembled with other RNA(s) either by covalent ligation or by noncovalent hybridization to form a full‐length structured RNA, which may then be studied by equilibrium and stopped‐flow fluorescence spectroscopy.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143792/1/cpnc1111.pd

Fluorescence of covalently attached pyrene as a general RNA folding probe

Fluorescence techniques are commonly and powerfully applied to monitor biomolecular folding. In a limited fashion, the fluorescence emission intensity of covalently attached pyrene has been used as a reporter of RNA conformational changes. Here, we pursue two goals: we examine the relationship between tether identity and fluorescence response, and we determine the general utility of pyrene fluorescence to monitor RNA folding. The P4–P6 domain of the Tetrahymena group I intron RNA was systematically modified at multiple nucleotide positions with pyrene derivatives that provide a range of tether lengths and compositions between the RNA and chromophore. Certain tethers typically lead to a superior fluorescence signal upon RNA folding, as demonstrated by equilibrium titrations with Mg(2+). In addition, useful fluorescence responses were obtained with pyrene placed at several nucleotide positions dispersed throughout P4–P6. This suggests that monitoring of tertiary folding by fluorescence of covalently attached pyrene will be generally applicable to structured RNA molecules

Conformational effects on high-spin organic molecules

The ability of m-phenylene to ferromagnetically couple spin-containing substituents that are substantially twisted out of conjugation is investigated. The "bis(TMM)" strategy is employed, in which two triplet TMM biradicals are linked through m-phenylene to produce relatively stable, organic tetraradicals that are characterized by EPR spectroscopy. Under conditions of moderate twisting (4), ferromagnetic coupling is seen, and the tetraradical has a quintet ground state. Severely twisting both TMMs as in 13 disrupts spin communication, and two noninteracting triplets are produced. This is in contrast to other highly twisted m-phenylene derivatives, in which antiferromagnetic coupling has been observed. Surprisingly, severely twisting only one TMM (14) still produces ferromagnetic coupling and a quintet ground state through a spin polarization mechanism analogous to that proposed for 90° twisted ethylene. Several ring-constrained TMMs (17-19) are investigated as models for more nearly planar systems

A deoxyribozyme that synthesizes 2′,5′-branched RNA with any branch-site nucleotide

RNA molecules with internal 2′,5′-branches are intermediates in RNA splicing, and branched RNAs have recently been proposed as retrotransposition intermediates. A broadly applicable in vitro synthetic route to branched RNA that does not require self-splicing introns or spliceosomes would substantially improve our ability to study biochemical processes that involve branched RNA. We recently described 7S11, a deoxyribozyme that was identified by in vitro selection and has general RNA branch-forming ability. However, an important restriction for 7S11 is that the branch-site RNA nucleotide must be a purine (A or G), because a pyrimidine (U or C) is not tolerated. Here, we describe the compact 6CE8 deoxyribozyme (selected using a 20 nt random region) that synthesizes 2′,5′-branched RNA with any nucleotide at the branch site. The Mn(2+)-dependent branch-forming ligation reaction is between an internal branch-site 2′-hydroxyl nucleophile on one RNA substrate with a 5′-triphosphate on another RNA substrate. The preference for the branch-site nucleotide is U > C ≅ A > G, although all four nucleotides are tolerated with useful ligation rates. Nearly all other nucleotides elsewhere in both RNA substrates allow ligation activity, except that the sequence requirement for the RNA strand with the 5′-triphosphate is 5′-pppGA, with 5′-pppGAR (R = purine) preferred. These characteristics permit 6CE8 to prepare branched RNAs of immediate practical interest, such as the proposed branched intermediate of Ty1 retrotransposition. Because this branched RNA has two strands with identical sequence that emerge from the branch site, we developed strategies to control which of the two strands bind with the deoxyribozyme during the branch-forming reaction. The ability to synthesize the proposed branched RNA of Ty1 retrotransposition will allow us to explore this important biochemical pathway in greater detail

Conformational effects on high-spin organic molecules

The ability of m-phenylene to ferromagnetically couple spin-containing substituents that are substantially twisted out of conjugation is investigated. The "bis(TMM)" strategy is employed, in which two triplet TMM biradicals are linked through m-phenylene to produce relatively stable, organic tetraradicals that are characterized by EPR spectroscopy. Under conditions of moderate twisting (4), ferromagnetic coupling is seen, and the tetraradical has a quintet ground state. Severely twisting both TMMs as in 13 disrupts spin communication, and two noninteracting triplets are produced. This is in contrast to other highly twisted m-phenylene derivatives, in which antiferromagnetic coupling has been observed. Surprisingly, severely twisting only one TMM (14) still produces ferromagnetic coupling and a quintet ground state through a spin polarization mechanism analogous to that proposed for 90° twisted ethylene. Several ring-constrained TMMs (17-19) are investigated as models for more nearly planar systems

Serving within the British army: research into mental health benefits

This document is the Accepted Manuscript version of a Published Work that appeared in final form in British Journal of Nursing, copyright © MA Education, after peer review and technical editing by the publisher. To access the final edited and published work see http://www.magonlinelibrary.com/doi/abs/10.12968/bjon.2011.20.19.1256The mental health (MH) of soldiers remains extremely newsworthy and is regularly featured in high profile media forums that focus on post-traumatic stress disorder. However, the authors feel that there are distinct benefits to serving within the Army, and that it provides effective occupational medical, MH and welfare support. This research study explores potential benefits and stressors of being in the Army and provides an overview of Army mental health services (AMHS) through the perspectives of AMHS personnel, 84% of which were nurses. The study indicated that the Army can provide a protective community, sharing a bond based on common values and experiences. The Army can provide soldiers with career opportunities that are not available in civilian life, and there are opportunities to develop an employment profile, enhanced by internal and external educational training, and encapsulated within a progressive career pathway. The Army can also be seen to offer an escape route, preventing soldiers entering a life of crime, and supplying the stable family these soldiers had never experienced. The provision of leadership, within an environment where soldiers are valued and stigma is not tolerated can potentially shield against MH problems

Mutual inhibition through hybrid oligomer formation of daptomycin and the semisynthetic lipopeptide antibiotic CB-182,462

The final publication is available at Elsevier via http://doi.org/10.1016/j.bbamem.2012.10.008 © 2013. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/Daptomycin is a clinically important lipopeptide antibiotic that kills Gram-positive bacteria through membrane depolarization. Its activity requires calcium and the presence of phosphatidylglycerol in the target membrane. Calcium and phosphatidylglycerol also promote the formation of daptomycin oligomers, which have been assumed but not proven to be required for the bactericidal effect. Daptomycin shares substantial structural similarity with another lipopeptide antibiotic, A54145; the two have identical amino acid residues in 5 out of 13 positions and similar ones in 4 more positions. We here examined whether these conserved residues are sufficient for oligomer formation. To this end, we used fluorescence energy transfer and excimer fluorescence to detect hybrid oligomers of daptomycin and CB-182,462, a semisynthetic derivative of A54145. Mixtures of the two compounds indeed produced hybrid oligomers, but at the same time displayed a significantly less than additive antibacterial activity against Bacillus subtilis. The existence of functionally impaired oligomers indicates that oligomer formation is indeed important for antibacterial function. However, it also shows that oligomerization is not sufficient; once formed, the oligomers must take another step in order to acquire antibacterial activity. Thus, the amino acid residues shared between daptomycin and CB-182,462 suffice for formation of the oligomer, but not for its subsequent activation.This work was supported by a CHRP grant from NSERC and CIHR (M. Palmer and S. Taylor), by Yeshiva University (Evan Mintzer) and by a Henry Kressel scholarship (Nasim Tishbi)

Testing limits to airflow perturbation device (APD) measurements

This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens