Intramolecular Base Research Articles

Monitoring the site-specific incorporation of dual fluorophore-quencher base analogues for target DNA detection by an unnatural base pair system

We developed intramolecular dual fluorophore-quencher base analogues for site-specific incorporation into DNA by an unnatural base pair replication system. An unnatural base pair between 7-(2-thienyl)-imidazo[4,5-b]pyridine (Ds) and 2-nitro-4-propynylpyrrole (Px) exhibits high fidelity in PCR amplification, and the 2-nitropyrrole moiety of Px acts as a quencher. Deoxyribonucleoside triphosphates of Px linked with a fluorophore (Cy3, Cy5 or FAM) were chemically synthesized, and the fluorescent properties and the enzymatic incorporation of the fluorophore-linked dPxTPs into DNA were examined in PCR amplification. The fluorophore-linked dPxTPs were site-specifically incorporated by PCR into DNA, opposite Ds in templates, with high selectivity. Furthermore, we found that the fluorescence of the triphosphates was partially quenched, but increased upon their incorporation into DNA. These dual fluorophore-quencher base analogues would be useful for site-specific DNA labeling and for monitoring the amplification products of target nucleic acid molecules with a specific sequence. We have demonstrated the utility of the fluorophore-linked Px substrates and the Ds-Px pairing in real-time quantitative PCR for target DNA molecule detection.

Direct observation of single flexible polymers using single stranded DNA().

Over the last 15 years, double stranded DNA (dsDNA) has been used as a model polymeric system for nearly all single polymer dynamics studies. However, dsDNA is a semiflexible polymer with markedly different molecular properties compared to flexible chains, including synthetic organic polymers. In this work, we report a new system for single polymer studies of flexible chains based on single stranded DNA (ssDNA). We developed a method to synthesize ssDNA for fluorescence microscopy based on rolling circle replication, which generates long strands (>65 kb) of ssDNA containing "designer" sequences, thereby preventing intramolecular base pair interactions. Polymers are synthesized to contain amine-modified bases randomly distributed along the backbone, which enables uniform labelling of polymer chains with a fluorescent dye to facilitate fluorescence microscopy and imaging. Using this approach, we synthesized ssDNA chains with long contour lengths (>30 μm) and relatively low dye loading ratios (~1 dye per 100 bases). In addition, we used epifluorescence microscopy to image single ssDNA polymer molecules stretching in flow in a microfluidic device. Overall, we anticipate that ssDNA will serve as a useful model system to probe the dynamics of polymeric materials at the molecular level.

PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences

Motivation: Predicting RNA–RNA interactions is essential for determining the function of putative non-coding RNAs. Existing methods for the prediction of interactions are all based on single sequences. Since comparative methods have already been useful in RNA structure determination, we assume that conserved RNA–RNA interactions also imply conserved function. Of these, we further assume that a non-negligible amount of the existing RNA–RNA interactions have also acquired compensating base changes throughout evolution. We implement a method, PETcofold, that can take covariance information in intra-molecular and inter-molecular base pairs into account to predict interactions and secondary structures of two multiple alignments of RNA sequences.Results: PETcofold's ability to predict RNA–RNA interactions was evaluated on a carefully curated dataset of 32 bacterial small RNAs and their targets, which was manually extracted from the literature. For evaluation of both RNA–RNA interaction and structure prediction, we were able to extract only a few high-quality examples: one vertebrate small nucleolar RNA and four bacterial small RNAs. For these we show that the prediction can be improved by our comparative approach. Furthermore, PETcofold was evaluated on controlled data with phylogenetically simulated sequences enriched for covariance patterns at the interaction sites. We observed increased performance with increased amounts of covariance.Availability: The program PETcofold is available as source code and can be downloaded from http://rth.dk/resources/petcofold.Contact: gorodkin@rth.dk; backofen@informatik.uni-freiburg.deSupplementary information: Supplementary data are available at Bioinformatics online.

Importance of Equilibrium Fluctuations between Most Stable Conformers in the Control of the Reaction Mechanism

Hydrolysis of closely related compounds show how subtle structural differences markedly change reaction mechanisms. While in the hydrolysis of 3-acetoxy-2-naphthoic acid (3AC2NA) the reacting groups rotate freely, favoring intramolecular general base catalysis, the 1-acetoxy-2-naphthoic acid (1AC2NA) isomer is caged in an energy wall that freezes a conformation suitable for intramolecular nucleophilic attack, in contrast to the results expected for reactions governed largely by electronic effects. The results highlight the importance of the dynamics of equilibrium fluctuations between most stable conformers in the control of the reaction mechanism, (i) promoting the nucleophilic attack in 1AC2NA by allowing the most stable conformers to equilibrate only via rotation in a direction that intercepts the reaction coordinate and (ii) favoring a general base-catalyzed water attack in 3AC2NA by favoring equilibration via rotation that allows inclusion of a water molecule in a proper position for reaction.

Overview of the Mechanistic Work on the Concerted Metallation–Deprotonation Pathway

Abstract The cleavage of aromatic C–H bonds promoted by a metal and an intramolecular base has been described over 50 years ago. Herein, discussion of selected mechanistic studies of this transformation will be presented. The basic ligand on the metal was proven to play a pivotal role in the C–H bond cleavage step and evidence of a single operative concerted metallation–deprotonation mechanism unifies the different mechanistic studies.

Intramolecular reaction and intramolecular catalysisd̊ II. Mechanism of intramolecular catalysis in hydrolysis of 2-(2'-benzimidazolyl)phenyl acetate by benzimidazolyl group

As a model for acetyl-α-chymotrypsin, 2-(2'-benzimidazolyl)phenyl acetate was synthesized in a good yield and its hydrolytic kinetics has been studied in buffer solutions at 45'C within a wide pH range (0.65–8.80). The measured pseudo-first-order rate constants (kobs) at different pH values conform well with the data derived from the proposed theoretical model. It is shown that in an acidic solution of medium strength (pH = 2.0–3.0), the ester is hydrolyzed via intramolecular general acid catalysis by benzimidazolium cation; while at pH values near neutrality (pH = 5.5–7.0), this ester is hydrolyzed via intramolecular general base catalysis by neutral benzimidazole. These findings are discussed and the activation parameters of the hydrolysis reaction were also determined.

Structural Characterization of Zinc and Iron (II/III) Complexes of a Porphyrin Bearing Two Built-in Nitrogen Bases. An Example of High-Spin Diaqua-Iron(III) Bromo Complex

A bis-strapped porphyrin with two intramolecular nitrogen bases was synthesized, and its zinc(II), iron(II), and iron(III) complexes have been structurally characterized. Whereas the zinc(II) complex is square pyramidal five-coordinate and the iron(II) complex is six-coordinate despite a significant distortion of the macrocycle induced by the rigidity of the straps, the iron(III) complex exhibits a peculiar bis-aqua structure in which no intramolecular axial base is bound to the iron atom in the porphyrin. Furthermore, on one side, the bromide counteranion of the iron is bound inside the cycle formed by a strap and establishes a hydrogen bond with an axially bound water molecule. On the other side, a residual HBr molecule protonates one pyridine base leading to the formation of an intermolecular pyridinium-pyridine hydrogen bond. The large ionic radius of the high-spin iron(III) cation is accommodated in the macrocycle with no displacement of the metal out of the mean porphyrinic plane, with an average Fe-Np bond distance of 2.057 A, and the axial Fe-Ow(aqua) bond distance measured at 2.090 A. As a result, this high-spin iron(III) bis-aqua complex is only lightly distorted.

What is the conformation of physiologically-active dinucleoside polyphosphates in solution? Conformational analysis of free dinucleoside polyphosphates by NMR and molecular dynamics simulations

Dinucleoside polyphosphates, or dinucleotides (Np(n)N'; N, N' = A, U, G, C; n = 2-7), are naturally occurring ubiquitous physiologically active compounds. Despite the interest in dinucleotides, and the relevance of their conformation to their biological function, the conformation of dinucleotides has been insufficiently studied. Therefore, here we performed conformational analysis of a series of Np(n)N' Na(+) salts (N = A, G, U, C; N' = A, G, U, C; n = 2-5) by various NMR techniques. All studied dinucleotides, except for Up(4/5)U, formed intramolecular base stacking interactions in aqueous solutions as indicated by NMR. The conformation around the glycosidic angle in Np(n)N's was found to be anti/high anti and the preferred conformation around the C4'-C5', C5'-O5' bonds was found to be gauche-gauche (gg). The ribose moiety in Np(n)N's showed a small preference for the S conformation, but when attached to cytosine the ribose ring preferred the N conformation. However, no predominant conformation was observed for the ribose moiety in any of the dinucleotides. Molecular dynamics simulations of Ap(2)A and Ap(4)A Na(+) salts supported the experimental results. In addition, three modes of base-stacking were found for Ap(2/4)A: α-α, β-β and α-β, which exist in equilibrium, while none is dominant. We conclude that natural, free Np(n)N's (n = 2-5) at physiological pH exist mostly in a folded (stacked), rather than extended conformation, in several interconverting stacking modes. Intramolecular base stacking of Np(n)N's does not alter the conformation of each of the nucleotide moieties, which remains the same as that of the mononucleotides in solution.

Activating Water: Efficient Intramolecular General Base Catalysis of the Hydrolysis of a Phosphate Triester

We have identified the first highly efficient intramolecular general base catalysis (IGBC) of a hydrolysis reaction, in a system where two general bases are available to assist the attack of the same nucleophilic water molecule. The suggested mechanism, available uniquely to a phosphate triester model, is readily available in enzyme active sites, and the results suggest a possible solution to the long-unsolved question of how enzymes are able to activate a water molecule to be a highly effective nucleophile.

Mechanistic Insights into Cyclooxygenase Irreversible Inactivation by Aspirin

A mechanistic hypothesis for the acetylation of cyclooxygenase (COX) by aspirin is proposed on the basis of a QM/MM study. This mechanism is consistent with previous experimental findings by other investigators. Ser 530 appears to be acetylated under intramolecular general base catalysis provided by the carboxylate moiety of aspirin, while Tyr 385 plays a crucial role in orienting and polarizing the acetyl group.

A partition function algorithm for interacting nucleic acid strands

Recent interests, such as RNA interference and antisense RNA regulation, strongly motivate the problem of predicting whether two nucleic acid strands interact.Motivation: Regulatory non-coding RNAs (ncRNAs) such as microRNAs play an important role in gene regulation. Studies on both prokaryotic and eukaryotic cells show that such ncRNAs usually bind to their target mRNA to regulate the translation of corresponding genes. The specificity of these interactions depends on the stability of intermolecular and intramolecular base pairing. While methods like deep sequencing allow to discover an ever increasing set of ncRNAs, there are no high-throughput methods available to detect their associated targets. Hence, there is an increasing need for precise computational target prediction. In order to predict base-pairing probability of any two bases in interacting nucleic acids, it is necessary to compute the interaction partition function over the whole ensemble. The partition function is a scalar value from which various thermodynamic quantities can be derived. For example, the equilibrium concentration of each complex nucleic acid species and also the melting temperature of interacting nucleic acids can be calculated based on the partition function of the complex.Results: We present a model for analyzing the thermodynamics of two interacting nucleic acid strands considering the most general type of interactions studied in the literature. We also present a corresponding dynamic programming algorithm that computes the partition function over (almost) all physically possible joint secondary structures formed by two interacting nucleic acids in O(n6) time. We verify the predictive power of our algorithm by computing (i) the melting temperature for interacting RNA pairs studied in the literature and (ii) the equilibrium concentration for several variants of the OxyS–fhlA complex. In both experiments, our algorithm shows high accuracy and outperforms competitors.Availability: Software and web server is available at http://compbio.cs.sfu.ca/taverna/pirna/Contact: cenk@cs.sfu.ca; backofen@informatik.uni-freiburg.deSupplementary information: Supplementary data are avaliable at Bioinformatics online.

The importance of inter- and intramolecular base pairing for translation reinitiation on a eukaryotic bicistronic mRNA

Calicivirus structure proteins are expressed from a subgenomic mRNA with two overlapping cistrons. The first ORF of this RNA codes for the viral major capsid protein VP1, and the second for the minor capsid protein VP2. Translation of VP2 is mediated by a termination/reinitiation mechanism, which depends on an upstream sequence element of approximately 70 nucleotides denoted "termination upstream ribosomal binding site" (TURBS). Two short sequence motifs within the TURBS were found to be essential for reinitiation. By a whole set of single site mutations and reciprocal base exchanges we demonstrate here for the first time conclusive evidence for the necessity of mRNA/18S rRNA hybridization for translation reinitiation in an eukaryotic system. Moreover, we show that motif 2 exhibits intramolecular hybridization with a complementary region upstream of motif 1, thus forming a secondary structure that positions post-termination ribosomes in an optimal distance to the VP2 start codon. Analysis of the essential elements of the TURBS led to a better understanding of the requirements for translation termination/reinitiation in eukaryotes.

Efficient non-coding RNA gene searches through classical and evolutionary methods

Successful non-coding RNA gene searching requires examination of long-range intramolecular base pairing possibilities. This results in search algorithms with extremely long run times such that large-scale use of the algorithms often becomes computationally infeasible. Methods for the efficient search of the solution space are examined. A review of the standard dynamic-programming covariance model search algorithm is given. An analysis of the statistically probable regions of the search space is undertaken and a method of limiting the traditional dynamic-programming algorithm to this region is shown. An alternative search method using a Genetic Algorithm (GA) which favours the probable region of the search space is also given.

Mild and efficient palladium-catalyzed intramolecular direct arylation reactions

The influence of ligand, stoichiometric base, and additive has been evaluated in the context of intramolecular direct arylation reactions. Under the optimal conditions, arylation of simple arenes can be performed under very mild conditions, with heating to 50 °C. The role of the pivalic acid additive is rationalized by invoking a concerted palladation–deprotonation pathway where the pivalate is behaving as either an intramolecular base from the palladium metal or through an intermolecular deprotonation in a similar manner as that previously described by Echavarren and Maseras.

Activation of Carbon−Hydrogen Bonds via 1,2-Addition across M−X (X = OH or NH2) Bonds of d6Transition Metals as a Potential Key Step in Hydrocarbon Functionalization: A Computational Study

Recent reports of 1,2-addition of C-H bonds across Ru-X (X = amido, hydroxo) bonds of TpRu(PMe3)X fragments {Tp = hydridotris(pyrazolyl)borate} suggest opportunities for the development of new catalytic cycles for hydrocarbon functionalization. In order to enhance understanding of these transformations, computational examinations of the efficacy of model d6 transition metal complexes of the form [(Tab)M(PH3)2X]q (Tab = tris-azo-borate; X = OH, NH2; q = -1 to +2; M = TcI, Re(I), Ru(II), Co(III), Ir(III), Ni(IV), Pt(IV)) for the activation of benzene C-H bonds, as well as the potential for their incorporation into catalytic functionalization cycles, are presented. For the benzene C-H activation reaction steps, kite-shaped transition states were located and found to have relatively little metal-hydrogen interaction. The C-H activation process is best described as a metal-mediated proton transfer in which the metal center and ligand X function as an activating electrophile and intramolecular base, respectively. While the metal plays a primary role in controlling the kinetics and thermodynamics of the reaction coordinate for C-H activation/functionalization, the ligand X also influences the energetics. On the basis of three thermodynamic criteria characterizing salient energetic aspects of the proposed catalytic cycle and the detailed computational studies reported herein, late transition metal complexes (e.g., Pt, Co, etc.) in the d6 electron configuration {especially the TabCo(PH3)2(OH)+ complex and related Co(III) systems} are predicted to be the most promising for further catalyst investigation.

Kinetic Evidence for the Formation of Monocationic N,N‘-Disubstituted Phthalamide in Tertiary Amine-Catalyzed Hydrolysis of N-Substituted Phthalimides

A kinetic study on the aqueous cleavage of N-(2-methoxyphenyl)phthalimide (1) and N-(2-hydroxyphenyl)phthalimide (2), under the buffers of N-methylmorpholine, reveals the equilibrium presence of monocationic amide (Ctam) formed due to nucleophilic reactions of N-methylmorpholine with 1 and 2. Pseudo-first-order rate constants for the reactions of water and HO- with Ctam (formed through nucleophilic reaction of N-methylmorpholine with 1) are 4.60 x 10(-5) s-1 and 47.9 M-1 s-1, respectively. But the cleavage of Ctam, formed through nucleophilic reaction of N-methylmorpholine with 2, involves intramolecular general base (2'-O- group of Ctam)-assisted water attack at carbonyl carbon of cationic amide group of Ctam in or before the rate-determining step.

Intramolecular general base catalysis exerted by the carboxilate group in the spontaneous dehydration of the carbinolamine formed from benzoylformic anion and hydroxylamine at early values of pH

AbstractData obtained from the reaction of oxime formation from benzoylformic anion lead to the suggestion that the spontaneous dehydration observed after pH ∼ 5.0, proceeds through a transition state in which an intramolecular general base catalysis is exerted by the carboxylate group. Copyright © 2007 John Wiley & Sons, Ltd.

Stabilizing effect of intramolecular lewis base toward racemization of optically active selenoxides

Abstract2‐(Methylchalcogenomethyl)diphenyl selenoxides 1 and 2‐{2′‐(N,N‐dimethylamino)ethyl}phenyl alkyl (or aryl) selenoxides 2, which were expected to be stabilized toward racemization by intramolecular coordination, were synthesized and optically resolved into their enantiomers on an optically active column using high‐performance liquid chromatography. Relationship between the absolute configurations and the chiroptical properties of the enantiomers was clarified by comparing with those of sulfur analogues. Stabilities toward racemization of optically active selenoxides 1a and 1b were nearly equal to that of 2‐{(N,N‐dimethylamino)methyl}diphenyl selenoxide and mesityl phenyl selenoxide. The rates of racemization for optically active selenoxides 2 were found to be faster than that of 2‐{(N,N‐dimethylamino)methyl}phenyl alkyl (or aryl) selenoxides. © 2007 Wiley Periodicals, Inc. Heteroatom Chem 18:301–311, 2007; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/hc.20299

Efficient Rate Enhancement Due to Intramolecular General Base (IGB) Assistance in the Hydrolysis of N-(o-Hydroxyphenyl)phthalimide

The rates of the hydrolyses of N-(o-hydroxyphenyl)phthalimide (1) and N-(o-methoxyphenyl)phthalimide (2), studied at different pH, show that the hydrolysis of 1 involves intramolecular general base (IGB) assistance where the o-O- group of ionized 1 acts as IGB and H2O as the reactant. The rate enhancement due to the IGB-assisted reaction of H2O with ionized 1 is>8x10(4)-fold. Pseudo-first-order rate constant for the reaction of water with 2 is approximately 2x10(3)-fold smaller than the first-order rate constant (0.10 s-1) for pH-independent hydrolysis of 1 within the pH range of 9.60-10.10. Second-order rate constants (kOH) for hydroxide ion-assisted hydrolysis of ionized 1 and 2 are 3.0 and 29.1 M-1 s-1, respectively. The solvent deuterium kinetic isotope effect (dKIE) on the rate of alkaline hydrolysis of 1 and 2 reveals that the respective values of kOH/kOD are 0.84 and 0.78, where kOD represents the second-order rate constant for DO--assisted cleavage of these imides (1 and 2). The value of kwH2O/kdD2O is 2.04, with kwH2O and kdD2O representing pseudo-first-order rate constants for the reactions of ionized 1 with H2O and D2O, respectively.

Hydroxyl radical scavenging by edaravone derivatives: Efficient scavenging by 3-methyl-1-(pyridin-2-yl)-5-pyrazolone with an intramolecular base

We synthesized various 3-methyl-1-phenyl-5-pyrazolone (edaravone) derivatives and evaluated their oxidation potential and hydroxyl radical scavenging activity. It was found 3-methyl-1-(pyridin-2-yl)-5-pyrazolone had a much higher ability to scavenge the radical than did edaravone itself. Its efficient radical scavenging activity was assumed to be due to the increase of its anion form, an active form, by a hydrogen-bonded intramolecular base.