Probing the structure and function of U2 snRNP with antisense oligonucleotides made of 2'-OMe RNA

We have used oligonucleotides made of 2'-OMe RNA to analyze the role of separate domains of U2 snRNA in the splicing process. We show that antisense 2'-OMe RNA oligonucleotides bind efficiently and specifically to U2 snRNP and demonstrate that masking of two separate regions of U2 snRNA can inhibit splicing by affecting different steps in the spliceosome assembly pathway. Masking the 5' terminus of U2 snRNA does not prevent U2 snRNP binding to pre-mRNA but blocks subsequent assembly of a functional spliceosome. By contrast, masking of U2 sequences complementary to the pre-mRNA branch site completely inhibits binding of pre-mRNA. Hybrid formation at the branch site complementary region also triggers a specific change which affects the 5' terminus of U2 snRNA.     

Zwitterionic oligonucleotides: a study on binding properties of 2'-O-aminohexyl modifications

2'-O-Aminohexyl side chains provide excellent conditions for zwitterionic interstrand and intrastrand interactions of oligonucleotides. 2'-O-Aminoalkylated phosphoramidites of adenosine and uridine were synthesized and incorporated in increasing number into homo adenosine and homo uridine/thymidine dodecamers, respectively. CD spectra of these dodecamers with complementary sense DNA exhibited a B-DNA type structure. While duplex stability values of all tested oligonucleotides were lower than those of the native oligonucleotides, they were significantly higher than those of 2'-O-heptyl modified oligonucleotides. The destabilization amounted to 0.9, 1.5, and 2.7 degrees C per modification for 2'-O-aminohexyl adenosine, 2'-O-aminohexyl uridine, and 2'-O-heptyl adenosine substitutions. These findings are pointing to a duplex stabilizing effect of the interaction of side chain amino groups with backbone phosphoric acid.     

Insights from crystal structures into the opposite effects on RNA affinity caused by the S- and R-6'-methyl backbone modifications of 3'-fluoro hexitol nucleic acid

Locked nucleic acid (LNA) analogues with 2',4'-bridged sugars show promise in antisense applications. S-5'-Me-LNA has high RNA affinity, and modified oligonucleotides show weakened immune stimulation in vivo. Conversely, an R-5'-methyl group dramatically lowers RNA affinity. To test the effects of S- and R-6'-methyl groups on 3'-fluoro hexitol nucleic acid (FHNA) stability, we synthesized S- and R-6'-Me-FHNA thymidine and incorporated them into oligo-2'-deoxynucleotides. As with LNA, S-6'-Me is stabilizing whereas R-6'-Me is destabilizing. Crystal structures of 6'-Me-FHNA-modified DNAs explain the divergent consequences for stability and suggest convergent origins of these effects by S- and R-6'-Me (FHNA) [-5'-Me (LNA and RNA)] substituents.     

The influence of jasmonic acid on biophysical properties of potato leaf protoplasts and roots

Summary Jasmonic acid (JA) and its derivatives are a novel group of plant endogenous growth regulators. In our experiments some new data about the physiological effects of JA were obtained using electron paramagnetic resonance spectroscopy. Experiments were performed on potato plants (Solanum tuberosum L. cv. Vesna) grown in vitro. Different quantities of JA (0.1–10 M) were added to the growth medium. Root samples of plants grown on media supplemented with JA showed a more rapid spin probe N-oxyl-2,2,6,6-tetramethyl piperidine reduction than the control plants, which is a possible indicator of altered root permeability. Samples of leaf protoplasts were probed with methyl ester of 5-doxyl-haxadecanoic acid. We observed a membrane fluidity decrease in protoplasts isolated from plants grown on higher concentrations of JA (1 and 10 M).Abbreviations JA jasmonic acid - Me-JA methyl jasmonate - EPR electron paramagnetic resonance - RubisCO ribulose-1,5-biphosphate carboxylase/oxigenase - MeFASL(10,3) methyl ester of 5-doxyl-hexadecanoic acid - MES (2(N-morpholino)ethanesulfonic acid) - TEMPO N-oxyl-2,2,6,6-tetramethyl piperidine     

The crystal structure and physicochemical properties of L-ascorbic acid 2-glucoside.

The stable L-ascorbic acid glucoside produced by the action of the cyclomaltodextrin glucanotransferase (CGTase, EC 2.4.1.19) from Bacillus stearothermophilus was crystallized from an aqueous solution. Determination of the molecular structure by single crystal X-ray analysis showed the compound to be 2-O-alpha-D-glucopyranosyl-L-ascorbic acid (AA-2G). The crystals are orthorhombic, space group P2(1)2(1)2(1), with unit-cell dimensions a = 11.929 A, b = 24.351 A, and c = 4.864 A. The D-glucopyranose residue has the 4C1 conformation. These conclusions are in good agreement with those based on the 13C-NMR spectrum. The general physicochemical properties of crystalline AA-2G are reported.     

Intrinsic electrostatic properties and base sequence effects in the structure of oligonucleotides

Molecular electrostatic potentials and steric accessibilities are calculated for Dickerson's dodecanucleotide CGCGAAT- TCGCG and compared with those for the ‘inverted’ sequence TATAGGCCTATA. The results are used to distinguish between properties due to base sequence (the location of the deepest potential minimum in the minor groove of A-T sequences and in the major groove of G-C sequences) and those due to the finite length of the oligonucleotide (location of the deepest potential in the central part of the oligonucleotide).     

The influence of locked nucleic acid residues on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexes

The influence of locked nucleic acid (LNA) residues on the thermodynamic properties of 2′-O-methyl RNA/RNA heteroduplexes is reported. Optical melting studies indicate that LNA incorporated into an otherwise 2′-O-methyl RNA oligonucleotide usually, but not always, enhances the stabilities of complementary duplexes formed with RNA. Several trends are apparent, including: (i) a 3′ terminal U LNA and 5′ terminal LNAs are less stabilizing than interior and other 3′ terminal LNAs; (ii) most of the stability enhancement is achieved when LNA nucleotides are separated by at least one 2′-O-methyl nucleotide; and (iii) the effects of LNA substitutions are approximately additive when the LNA nucleotides are separated by at least one 2′-O-methyl nucleotide. An equation is proposed to approximate the stabilities of complementary duplexes formed with RNA when at least one 2′-O-methyl nucleotide separates LNA nucleotides. The sequence dependence of 2′-O-methyl RNA/RNA duplexes appears to be similar to that of RNA/RNA duplexes, and preliminary nearest-neighbor free energy increments at 37°C are presented for 2′-O-methyl RNA/RNA duplexes. Internal mismatches with LNA nucleotides significantly destabilize duplexes with RNA.     

Theoretical analysis on the structure and properties of thiourea dioxide crystal

The equilibrium geometry, electronic structure and optical properties of thiourea S, S-dioxide crystal have been studied using DFT within generalized gradient approximation (GGA) and the local density approximation (LDA), implemented using ultrasoft pseudo-potentials. The optimum bulk geometry is in good agreement with crystallographic data. An analysis of electronic structure, charge and bond order is presented. The energy gap of thiourea dioxide with GGA and LDA calculation is 3.217 or 3.210 eV, respectively, indicating that the compound is an insulator. The calculated absorption spectrum shows a number of absorption peaks, which are believed to be associated with different exciton states, in the fundamental absorption region.     

Differential effects of conjugated linoleic acid isomers on the biophysical and biochemical properties of model membranes

Conjugated linoleic acids (CLA) are known to exert several isomer-specific biological effects, but their mechanisms of action are unclear. In order to determine whether the physicochemical effects of CLA on membranes play a role in their isomer-specific effects, we synthesized phosphatidylcholines (PCs) with 16:0 at sn-1 position and one of four CLA isomers (trans 10 cis 12 (A), trans 9 trans 11 (B), cis 9 trans 11 (C), and cis 9 cis 11 (D)) at sn-2, and determined their biophysical properties in monolayers and bilayers. The surface areas of the PCs with the two natural CLA (A and C) were similar at all pressures, but they differed significantly in the presence of cholesterol, with PC-A condensing more than PC-C. Liposomes of PC-A similarly showed increased binding of cholesterol compared to PC-C liposomes. PC-A liposomes were less permeable to carboxyfluorescein compared to PC-C liposomes. The PC with two trans double bonds (B) showed the highest affinity to cholesterol and lowest permeability. The two natural CLA-PCs (A and C) stimulated lecithin-cholesterol acyltransferase activity by 2-fold, whereas the unnatural CLA-PCs (B and D) were inhibitory. These results suggest that the differences in the biophysical properties of CLA isomers A and C may partly contribute to the known differences in their biological effects.     

Effects of N2,N2-dimethylguanosine on RNA structure and stability: crystal structure of an RNA duplex with tandem m2 2G:A pairs

Methylation of the exocyclic amino group of guanine is a relatively common modification in rRNA and tRNA. Single methylation (N²-methylguanosine, m²G) is the second most frequently encountered nucleoside analog in Escherichia coli rRNAs. The most prominent case of dual methylation (N²,N²-dimethylguanosine, m²₂G) is found in the majority of eukaryotic tRNAs at base pair m²₂G26:A44. The latter modification eliminates the ability of the N² function to donate in hydrogen bonds and alters its pairing behavior, notably vis-à-vis C. Perhaps a less obvious consequence of the N²,N²-dimethyl modification is its role in controlling the pairing modes between G and A. We have determined the crystal structure of a 13-mer RNA duplex with central tandem m²₂G:A pairs. In the structure both pairs adopt an imino-hydrogen bonded, pseudo-Watson–Crick conformation. Thus, the sheared conformation frequently seen in tandem G:A pairs is avoided due to a potential steric clash between an N²-methyl group and the major groove edge of A. Additionally, for a series of G:A containing self-complementary RNAs we investigated how methylation affects competitive hairpin versus duplex formation based on UV melting profile analysis.     

HER2-mediated effects on EGFR endosomal sorting: analysis of biophysical mechanisms

Overexpression of HER2, a receptor-like tyrosine kinase and signaling partner for the epidermal growth factor receptor (EGFR), has been implicated in numerous experimental and clinical studies as promoting the progression of many types of cancer. One avenue by which HER2 overexpression may dysregulate EGFR-mediated cell responses, such as proliferation and migration, downstream of EGF family ligand binding, is by its modulation on EGFR endocytic trafficking dynamics. EGFR signaling is regulated by downregulation and compartmental relocalization arising from endocytic internalization and endosomal sorting to degradation versus recycling fates. HER2 overexpression influences both of these processes. At the endosomal sorting stage, increased HER2 levels elicit enhanced EGFR recycling outcomes, but the mechanism by which this transpires is poorly understood. Here, we determine whether alternative mechanisms for HER2-mediated enhancement of EGFR recycling can be distinguished by comparison of corresponding mathematical models to experimental literature data. Indeed, we find that the experimental data are clearly most consistent with a mechanism in which HER2 directly competes with EGFR for a stoichiometrically-limited quantity of endosomal retention components (ERCs), thereby reducing degradation of ERC-coupled EGFR. Model predictions based on this mechanism exhibited qualitative trends highly similar to data on the fraction of EGF/EGFR complexes sorted to recycling fate as a function of the amount of internalized EGF/EGFR complexes. In contrast, model predictions for alternative mechanisms-blocking of EGFR/ERC coupling, or altering EGF/EGFR dissociation-were inconsistent with the qualitative trends of the experimental data.     

Nuclease resistance of oligonucleotides containing the tricyclic cytosine analogues phenoxazine and 9-(2-aminoethoxy)-phenoxazine ("G-clamp") and origins of their nuclease resistance properties.

The tricyclic cytosine analogues phenoxazine and 9-(2-aminoethoxy)-phenoxazine ("G-clamp") are known to significantly enhance the binding affinity of oligonucleotides to their complementary target DNA or RNA strands. To investigate their effect on the nuclease resistance, they were incorporated into model oligomers with a natural phosphodiester backbone, and enzymatic degradation was monitored in an in vitro assay with snake venom phosphodiesterase as the hydrolytic enzyme. In both cases, a single incorporation at the 3'-terminus completely protected the oligonucleotides against 3'-exonuclease attack. Further investigations indicate that the observed high nuclease resistance is not due to the lack of binding affinity to the enzyme's active site, since these modified oligonucleotides were able to inhibit degradation of a natural DNA fragment by bovine intestinal mucosal phosphodiesterase in a dose-dependent manner.     

One pot synthesis of Cu(II) 2,2'-bipyridyl complexes of 5-hydroxy-hydurilic acid and alloxanic acid: synthesis, crystal structure, chemical nuclease activity and cytotoxicity

A barbiturate derivative [1,5-dihydro-5-[5-pyrimidine-2,4(1H,3H)-dionyl]-2H-chromeno[2,3-d] pyrimidine-2,4(3H)-dione] (LH₄) was allowed to react with 2,2′-bipyridyl-dinitrato-Copper(II)-dihydrate which provides two complexes, characterized as [Cu(bpy)(L1)]·3H₂O () and [Cu(bpy)(L2)]·H₂O (), where bpy = 2,2′-bipyridine, L1 = 5-hydroxy-hydurilic acid and L2 = alloxanic acid. In a separate reaction of LH₄ with Cu(NO₃)₂·H₂O another type of complex [Cu(LH₃)₂·(H₂O)₂]·4H₂O () is formed. The complexes were characterized by single crystal X-ray crystallography, physicochemical and electrochemical studies. The interaction of complexes 1 and 3 with DNA was monitored using absorption and emission titrations as well as circular dichroism spectroscopy. The complexes were found to cleave supercoiled plasmid DNA to nicked circular and linear DNA. Complexes 1 and 3 were also tested against T-cell lymphoma (Dalton lymphoma DL) and showed significant cytotoxic activity with IC₅₀ values of ~ 9.0 nM and 0.6 nM.     

Collapsin response mediator protein 2: high-resolution crystal structure sheds light on small-molecule binding,post-translational modifications,and conformational flexibility

Amino Acids - Collapsin response mediator protein 2 (CRMP-2) is a neuronal protein involved in axonal pathfinding. Intense research is focusing on its role in various neurological diseases. Despite...     

The crystal structure of a high affinity RNA stem-loop complexed with the bacteriophage MS2 capsid: further challenges in the modeling of ligand-RNA interactions

We have determined the structure to 2.8 A of an RNA aptamer (F5), containing 2'-deoxy-2-aminopurine (2AP) at the -10 position, complexed with MS2 coat protein by soaking the RNA into precrystallised MS2 capsids. The -10 position of the RNA is an important determinant of binding affinity for coat protein. Adenine at this position in other RNA stem-loops makes three hydrogen bonds to protein functional groups. Substituting 2AP for the -10 adenine in the F5 aptamer yields an RNA with the highest yet reported affinity for coat protein. The refined X-ray structure shows that the 2AP base makes an additional hydrogen bond to the protein compared to adenine that is presumably the principal origin of the increased affinity. There are also slight changes in phosphate backbone positions compared to unmodified F5 that probably also contribute to affinity. Such phosphate movements are common in structures of RNAs bound to the MS2 T = 3 protein shell and highlight problems for de novo design of RNA binding ligands.     

Conformation and packing properties of phosphatidic acid: The crystal structure of monosodium dimyristoylphosphatidate

The conformation and molecular packing of monosodium 1,2-dimyristoyl-sn-glycerophosphate (DMPA) has been determined by single crystal analysis (R = 0.107). The lipid crystallizes in the space group P2₁ with unit cell dimensions: $\text{a = 5.44, b = 7.95, c = 43.98}\text{A}\text{?}$ and β = 114.2°. The two molecules of the unit cell are related by a two-fold screw axis and pack tail-to-tail in a bilayer structure. The monosodium phosphate group packs with rather a small cross-section (24 Ų) relative to the two hydrocarbon chains. This unbalance in packing cross-section is overcome by an interdigitation of the phosphate head groups of adjacent bilayers and the formation of a single, common phosphate group layer at the bilayer interfaces. The phosphate groups are linked by hydrogen bonds to linear strands which laterally are separated by strands of sodium ions. The conformation of the molecules differs from that of other phospholipids. The glycerol chain is oriented parallel (instead of perpendicular) to the layer surface and the parallel stacking of the hydrocarbon chains is achieved by a bend of the γ-chain (instead of the β-chain). Otherwise the conformation of the glycerol dicarboxyl ester group displays the same preferred features as generally found in glycerophospholipids. The hydrocarbon chains pack according to the triclinic (T_∥) packing mode. The interaction and packing principles of the phosphate head group are discussed in relation to the structural behaviour of phosphatidic acid.