Crucial role of linker portion in acridine-bearing oligonucleotides for highly efficient site-selective RNA scission

Through a series of linkers, 9-amino-2-methoxy-6-nitroacridine and 9-amino-6-chloro-2-methoxyacridine were tethered to the middle of oligonucleotide, and the abilities of these conjugates for site-selective activation of RNA (inducing site-selective scission by Lu(III)) were compared. The RNA-activating ability was strongly dependent on the structures of both acridine and linker. By tethering 9-amino-2-methoxy-6-nitroacridine with a rigid and chiral linker, derived from l-threoninol, quite fast site-selective RNA scission was accomplished.     

Photochemical generation of ribose abasic sites in RNA oligonucleotides

[reaction: see text] A general method for the photochemical generation of ribose abasic sites within RNA oligonucleotides is reported. Photochemically caged nucleoside phosphoramidite analogues were prepared and incorporated into RNA oligonucleotides by automated RNA synthesis. Irradiation of the modified RNA at 350 nm efficiently produced ribose abasic sites at specific sites within RNA sequences. The current approach offers a chemical route to RNA abasic lesions for RNA biochemical studies.     

Metal ion-induced site-selective RNA hydrolysis by use of acridine-bearing oligonucleotide as cofactor

New types of noncovalent ribozyme-mimics for site-selective RNA scission are prepared by combining metal ions with oligonucleotides bearing an acridine. Lanthanide(III) ions and various divalent metal ions (Zn(II), Mn(II), Cu(II), Ni(II), Co(II), Mg(II), and Ca(II)) are employed without being bound to any sequence-recognizing moiety. The modified oligonucleotide forms a heteroduplex with the substrate RNA, and selectively activates the phosphodiester linkages in front of the acridine. As a result, these linkages are preferentially hydrolyzed over the others, even though the metal ions are not fixed anywhere. The scission is efficient under physiological conditions, irrespective of the sequence at the target site. Site-selective RNA scission is also successful with the combination of an oligonucleotide bearing an acridine at its terminus, another unmodified oligonucleotide, and the metal ion. In a proposed mechanism, the acridine pushes the unpaired ribonucleotide out of the heteroduplex and changes the conformation of RNA at the target site for the sequence-selective activation.     

Site-selective RNA scission at two sites for precise genotyping of SNPs by mass spectrometry

Short RNA fragments containing single nucleotide polymorphism (SNP) sites have been selectively clipped out of substrate RNA by using complementary DNA having two acridine residues and Lu(III), and the genotype of the substrate is accurately and easily determined by mass analysis of these fragments.     

Comparison of glass fragments by neutron activation analysis

A method of comparing glass fragments of potential application to forensic sicence has been developed and evaluated. A representative sample of window glass from England and Wales has been collected and analysed for about 25 elements. An automated radiochemical separation followed by gamma-spectroscopy was used in order to determine the concentration of the maximum number of elements. Frequency distributions of the elemental concentration are shown and used to assess the discrimination of the technique and compare it with the measurement of refractive index. A few simulated cases have been included to demonstrate the possible application to forensic science problems.     

Selective activation of organic molecules by elemental fluorine

Reactions on tertiary hydrogen atoms, attached to unactivated saturated carbons, are very rare and usually inefficient. The electron density however, of a carbon-tertiary hydrogen bond is relatively high and therefore there is a chance it will react with a strong electrophile. One of the strongest electrophiles existing is, of course, the electrophilic fluorine. Two main sources for such an unusual species exist. One source is the various fluoroxy compounds like CF₃OF or CF₃COOF ant the other is the elemental fluorine itself.Indeed, when fluorine is allowed to react, at low temperatures, with various alkylcyclohexanol esters, a highly regio- and an absolutely stereospecific electrophilic substitution on the tertiary unactivated hydrogen takes place as for example:

The radical pathway possibility of these reactions is excluded and it is believed that they are of ionic nature. By dehydrofluorination, a double bond is introduced in sites that no other reagent is known to do, thus activating the molecule towards further chemical transformations. The influence of the electron-withdrawing group on the reaction center will also be discussed.The described reaction is not restricted only to cyclic compounds as aliphatic chains also react as expected, i.e.

The scope of these unusual reactions in both alicyclic and aliphatic fields will be evaluated.     

Preferred RNA binding sites for a threading intercalator revealed by in vitro evolution

In pursuit of small molecules capable of controlling the function of RNA targets, we have explored the RNA binding properties of peptide-acridine conjugates (PACs). In vitro evolution (SELEX) was used to isolate RNAs capable of binding the PAC Ser-Val-Acr-Arg, where Acr is an acridine amino acid. The PAC binds RNA aptamers selectively and with a high degree of discrimination over DNA. PAC binding sites contain the base-paired 5'-CpG-3' sequence, a known acridine intercalation site. However, RNA structure flanking this sequence causes binding affinities to vary over 30-fold. The preferred site (K(D) = 20 nM) contains a base-paired 5'-CpG-3' step flanked on the 5' side by a 4 nt internal loop and the 3' side by a bulged U. Several viral 5'- and 3'-UTR RNA sequences that likely form binding sites for this PAC are identified.     

Gaussian mapping of chemical fragments in ligand binding sites

We present a new approach to automatically define a quasi-optimal minimal set of pharmacophoric points mapping the interaction properties of a user-defined ligand binding site. The method is based on a fitting algorithm where a grid of sampled interaction energies of the target protein with small chemical fragments in the binding site is approximated by a linear expansion of Gaussian functions. A heuristic approximation selects from this expansion the smallest possible set of Gaussians required to describe the interaction properties of the binding site within a prespecified accuracy. We have evaluated the performance of the approach by comparing the computed Gaussians with the positions of aromatic sites found in experimental protein-ligand complexes. For a set of 53 complexes, good correspondence is found in general. At a 95% significance level, approximately 65% of the predicted interaction points have an aromatic binding site within 1.5 A. We then studied the utility of these points in docking using the program DOCK. Short docking times, with an average of approximately 0.18 s per conformer, are obtained, while retaining, both for rigid and flexible docking, the ability to sample native-like binding modes for the ligand. An average 4-5-fold speed-up in docking times and a similar success rate is estimated with respect to the standard DOCK protocol.     

Selective recognition of HIV RNA by dinuclear metallic ligands

We describe the development of dinuclear metallic ligands to target specific HIV RNA structures. Two series of dipyridinyl-N bridged dinuclear metal complexes were synthesized and their binding activities toward TAR and RRE RNA were studied both experimentally and theoretically.     

Preparation of methacrylate-based anion-exchange monolithic microbore column for chromatographic separation of DNA fragments and oligonucleotides

In this paper, we report on the preparation of a microbore-scale (1 mm i.d.) anion-exchange monolithic column suitable not only for analytical purposes but also for potentially preparative applications. In order to meet the conflicting requirements of high permeability and good mechanical strength, the following two-step procedure was applied. First, an epoxy-containing monolith was synthesized by in situ copolymerization of glycidyl methacrylate (GMA) and ethylene dimethacrylate (EDMA) within the confines of a silicosteel tubing of 1.02 mm i.d. and 1/16″ o.d. in the presence of a ternary porogenic mixture of 1-propanol, 1,4-butanediol, and water. The monolithic matrix was subsequently converted into weak anion-exchanger via the ring-opening reaction of epoxy group with diethyl amine. The dynamic binding capacity was 21.4 mg mL⁻¹ for bovine serum albumin (BSA) at 10% breakthrough. The morphology and porous structure of this monolith were assessed by scanning electron microscope (SEM) and inverse size exclusion chromatography (ISEC). To optimize the separation efficiency, the effects of various chromatographic parameters upon the separation of DNA fragments were investigated. The resulting monolithic anion exchanger demonstrated good potential for the separation of both single- and double-stranded DNA molecules using a gradient elution with NaCl in Tris–HCl buffer (20 mM). Oligodeoxythymidylic acids (dT₁₂–dT₁₈) were successfully resolved at pH 8, while the fragments of 20 bp DNA ladder, 100 bp DNA ladder, and pBR322-HaeIII digest were efficiently separated at pH 9.     

Site-specific cleavage of RNA by a metal-free artificial nuclease attached to antisense oligonucleotides

RNA cleaving tris(2-aminobenzimidazoles) have been attached to DNA oligonucleotides via disulfide or amide bonds. The resulting conjugates are effective organocatalytic nucleases showing substrate and site selectivity as well as saturation kinetics. The benzimidazole conjugates also degrade enantiomeric RNA. This observation rules out contamination effects as an alternative explanation of RNA degradation. The pH dependency shows that the catalyst is most active in the deprotonated state. Typical half-lifes of RNA substrates are in the range of 12-17 h. Thus, conjugates of tris(2-aminobenzimidazoles) can compete with the majority of metal-dependent artificial nucleases.     

Selective stabilization of natively folded RNA structure by DNA constraints

Learning how native RNA conformations can be stabilized relative to unfolded states is an important objective, for both understanding natural RNAs and improving the design of artificial functional RNAs. Here we show that covalently attached double-stranded DNA constraints (ca. 14 base pairs in length) can significantly stabilize the native conformation of an RNA molecule. Using the P4-P6 domain of the Tetrahymena group I intron as the test system, we identified pairs of RNA sites where attaching a DNA duplex is predicted to be structurally compatible with only the folded state of the RNA. The DNA-constrained RNAs were synthesized and shown by nondenaturing polyacrylamide gel electrophoresis (native PAGE) to have substantial decreases in their Mg2+ midpoints ([Mg2+]1/2 values). These changes are equivalent to free energy stabilizations as large as DeltaDeltaGdegrees = -2.5 kcal/mol, which is approximately 14% of the total tertiary folding energy. For comparison, the sole modification of P4-P6 previously reported to stabilize this RNA is a single-nucleotide deletion (DeltaC209) that provides only 1.1 kcal/mol of stabilization. Our findings indicate that nature has not completely optimized P4-P6 RNA folding. Furthermore, the DNA constraints are designed not to interact directly and extensively with the RNA, but rather more indirectly to modulate the relative stabilities of folded and unfolded RNA states. The successful implementation of this strategy to further stabilize a natively folded RNA conformation suggests an important element of modularity in stabilization of RNA structure, with implications for how nature might use other molecules such as proteins to stabilize specific RNA conformations.     

Nucleophilic assistance in methane activation by superelectrophiles with halogen-centered cationic sites

Simulation of fragments of potential energy surface for systems CH₄ + CBr ₃ ⁺ , CH₄ + CBr ₃ ⁺ AlBr ₄ ^? , CH₄ + CCl ₃ ⁺ AlCl ₄ ^? , and CH₄ + CCl ₃ ⁺ Al₂Cl ₇ ^? was performed by DFT-B3LYP and DFT-PBE methods. The important role of nucleophilic assistance in methane halogenation by these superelectrophiles was confirmed. These reactions occur with a synchronous hydride transfer from methane to the electrophile within the cyclic transition states in linear C-H-C fragment of the rings and a generation of a C-Hlg bond between the carbon atom of the arising methyl group and the halogen atom of the electrophile. The nucleophilic assistance from the unshared electron pair of this halogen atom provides the lowering of the potential barriers to methane halogenation by complexes CBr ₃ ⁺ AlBr ₄ ^? , CCl ₃ ⁺ AlCl ₄ ^? , and CCl ₃ ⁺ Al₂Cl ₇ ^? to the values of the order of 20 kcal mol^?1. These essential features of the mechanism of methane halogenation are independent of the halogen nature and are retained on going from the model electrophiles to the real ones.     

Cooperative catalytically active sites for methanol activation by single metal ion-doped H-ZSM-5

Catalytic conversion of methanol to aromatics and hydrocarbons is regarded as a key alternative technology to oil processing. Although the inclusion of foreign metal species in H-ZSM-5 containing Brønsted acid site (BAS) is commonly found to enhance product yields, the nature of catalytically active sites and the rationalization for catalytic performance still remain obscure. Herein, by acquiring comparable structural parameters by both X-ray and neutron powder diffractions over a number of metal-modified ZSM-5 zeolites, it is demonstrated for the first time that active pairs of metal site-BAS within molecular distance is created when single and isolated transition metal cation is ion-exchanged with the zeolites. According to our DFT model, this could lead to the initial heterolytic cleavage of small molecules such as water and methanol by the pair with subsequent reactions to form products at high selectivity as that observed experimentally. It may account for their active and selective catalytic routes of small molecule activations.

Diffraction studies and DFT calculations show the formation of frustrated Lewis pair (FLP) over M-ZSM-5 for heterolytic cleavage of CH₃OH.     

Electrospray tandem mass spectrometry of mixed-sequence RNA/DNA oligonucleotides

The fragmentation of electrospray-generated multiply deprotonated RNA and mixed-sequence RNA/DNA pentanucleotides upon low-energy collision-induced dissociation (CID) in a hybrid quadrupole time-of-flight mass spectrometer was investigated. The goal of unambiguous sequence identification of mixed-sequence RNA/DNA oligonucleotides requires detailed understanding of the gas-phase dissociation of this class of compounds. The two major dissociation events, base loss and backbone fragmentation, are discussed and the unique fragmentation behavior of oligoribonucleotides is demonstrated. Backbone fragmentation of the all-RNA pentanucleotides is characterized by abundant c-ions and their complementary y-ions as the major sequence-defining fragment ion series. In contrast to the dissociation of oligodeoxyribonucleotides, where backbone fragmentation is initiated by the loss of a nucleobase which subsequently leads to the formation of the w- and [a-base]-ions, backbone dissociation of oligoribonucleotides is essentially decoupled from base loss. The different behavior of RNA and DNA oligonucleotides is related to the presence of the 2'-hydroxyl substituent, which is the only structural alteration between the DNA and RNA pentanucleotides studied. CID of mixed-sequence RNA/DNA pentanucleotides results in a combination of the nucleotide-typical backbone fragmentation products, with abundant w-fragment ions generated by cleavage of the phosphodiester backbone adjacent to the deoxy building blocks, whereas backbone cleavage adjacent to ribonucleotides induces the formation of c- and y-ions.