Cis-trans Pairs Research Articles

The role of structure in regulatory RNA elements.

Regulatory RNA elements fulfill functions such as translational regulation, control of transcript levels, and regulation of viral genome replication. Trans-acting factors (i.e. RNA-binding proteins) bind the so-called cis elements and confer functionality to the complex. The specificity during protein-RNA complex (RNP) formation often exploits the structural plasticity of RNA. Functional integrity of cis-trans pairs depends on the availability of properly folded RNA elements, and RNA conformational transitions can cause diseases. Knowledge of RNA structure and the conformational space is needed for understanding complex formation and deducing functional effects. However, structure determination of RNAs under in vivo conditions remains challenging. This review provides an overview of structured eukaryotic and viral RNA cis elements and discusses the effect of RNA structural equilibria on RNP formation. We showcase implications of RNA structural changes for diseases, outline strategies for RNA structure-based drug targeting, and summarize the methodological toolbox for deciphering RNA structures.

Evidence for Selection on Gene Expression in Cultivated Rice (Oryza sativa)

Artificial selection has been used throughout plant domestication and breeding to develop crops that are adapted to diverse environments. Here, we investigate whether gene regulatory changes have been widespread targets of lineage-specific selection in cultivated lines Minghui 63 and Zhenshan 97 of rice, Oryza sativa. A line experiencing positive selection for either an increase or a decrease in genes' transcript abundances is expected to have an overabundance of expression quantitative trait locus (eQTL) alleles that increase or decrease those genes' expression, respectively. Results indicate that several genes that share Gene Ontology terms or are members of the same coexpression module have eQTL alleles from one parent that consistently increase gene expression relative to the second parent. A second line of evidence for lineage-specific selection is an overabundance of cis-trans pairs of eQTL alleles that affect gene expression in the same direction (are reinforcing). Across all cis-trans pairs of eQTL, including pairs that both weakly and strongly affect gene expression, there is no evidence for selection. However, the frequency of genes with reinforcing eQTL increases with eQTL strength. Therefore, there is evidence that eQTL with strong effects were positively selected during rice cultivation. Among 41 cis-trans pairs with strong trans eQTL, 31 have reinforcing eQTL. Several of the candidate genes under positive selection accurately predict phenotypic differences between Minghui 63 and Zhenshan 97. Overall, our results suggest that positive selection for regulatory alleles may be a key factor in plant improvement.

Thymidine glycol: the effect on DNA molecular structure and enzymatic processing

Thymine glycol (Tg) in DNA is a biologically active oxidative damage caused by ionizing radiation or oxidative stress. Due to chirality of C5 and C6 atoms, Tg exists as a mixture of two pairs of cis and trans diastereomers: 5R cis-trans pair (5R,6S; 5R,6R) and 5S cis-trans pair (5S,6R; 5S,6S). Of all the modified pyrimidine lesions that have been studied to date, only thymine glycol represents a strong block to high-fidelity DNA polymerases in vitro and is lethal in vivo. Here we describe the preparation of thymine glycol-containing oligonucleotides and the influence of the oxidized residue on the structure of DNA in different sequence contexts, thymine glycol being paired with either adenine or guanine. The effect of thymine glycol on biochemical processing of DNA, such as biosynthesis, transcription and repair in vitro and in vivo, is also reviewed. Special attention is paid to stereochemistry and 5R cis-trans epimerization of Tg, and their relation to the structure of DNA double helix and enzyme-mediated DNA processing. Described here are the comparative structure and properties of other forms of pyrimidine base oxidation, as well as the role of Tg in tandem lesions.

Photochemical nucleophile–olefin combination, aromatic substitution (photo-NOCAS) reaction. Part 9: methanol-2,6-dimethyl-1,6-heptadiene, and 1,4-dicyanobenzene

The photochemical nucleophile–olefin combination, aromatic substitution (photo-NOCAS) reaction of methanol, 2,6-dimethyl-1,6-heptadiene, and 1,4-dicyanobenzene yields three distinct types of 1:1:1 adducts: an acyclic product, 4-(1-methoxymethyl-1,5-dimethyl-5-hexenyl)benzonitrile (8, 5%); a cis–trans pair of cyclohexanes, 4-(3-methoxymethyl-1,3-dimethylcyclohexyl)benzonitrile (9cis (12%) and 9trans (11%)); and a cis–trans pair of cycloheptanes, 4-(4-methoxy-1,4-dimethylcycloheptyl)benzonitrile (10cis (12%) and 10trans (10%)). Variation in the concentration of the nucleophile, methanol, and codonor, biphenyl, affects the product ratio and it has been possible to establish the mechanisms for the formation of these products. The acyclic product is formed by a typical photo-NOCAS reaction, that is, addition (anti-Markovnikov) across one of the heptadiene double bonds. The cyclohexane products are formed following 1,6-endo cyclization of the intermediate β-alkoxy radical. And the cycloheptane products result from 1,7-endo,endo cyclization of the initially formed 2,6-dimethyl-1,6-heptadiene radical cation. Comparison of the relative rates of these cyclization processes can be made with those of the next smaller homolog, 2,5-dimethyl-1,5-hexadiene. Keywords: photochemistry, photoinduced electron transfer, radical ions, radicals, cyclization.

Synthesis of Optically Pure 2-Aziridinemethanols: Versatile Synthetic Building Blocks.

Synthesis of three cis-trans pairs of N-sulfonylated-2-aziridinemethanols starting from (S)-threonine, (R)-allothreonine, a chiral 2-amino alcohol, or enantiomerically enriched 2, 3-epoxy alcohols is described. A synthetic route to N-tosyl- and N-mesyl-2-aziridinemethanols from (R)- and (S)-serines is also presented.

Single electron transfer versus nucleophilic ring opening in reactions of cis-trans pairs of activated 2-phenylaziridines. Strong influence of nitrogen pyramid for N-benzoylaziridines

Activated 2-phenylaziridines with a second substituent R in position 3 were made to react with xanthyl anion X - . Nucleophilic ring opening is the only reaction that occurs with sulfonyl activation. The analogous N-benzoylaziridines (1) undergo this type of ring opening when the two substituents Ph and R are trans. The cis isomers (cis-1, Ph and R cis) react in this manner to a negligible extent if any. The (nearly) exclusive ring cleavage reaction of cis-1 is C-N homolysis of an intermediate ketyl formed by single electron transfer (SET) from X - . This cis-trans phenomenon is in accordance with the hypothesis that the two competing reactions depend in an opposite manner on the steepness of the nitrogen pyramid

The Thermal Decomposition of Styrene-co-acrylonitrile Trimers to Form 2-Amino-3-methyl-1-naphthalenecarbonitrile

Abstract During the spontaneous copolymerization of styrene and acrylonitrile, many different trimer structures are formed. Some of the trimers contain two acrylonitrile units and one styrene unit (An2S). These trimers are composed of three pairs of cis-trans diastereomers, all having a 1-substituted-4-cyanotetralin nucleus. Two of the cis-trans pairs have been found to decompose upon heating resulting in the formation of 2-amino-3-methyl-1-naphthalenecarbonitrile. The mechanism of this rearrangement involves the elimination of ethylene via a retro Diels-Alder reaction. Kinetic investigations show that the reaction is first order in An2S trimer.

Preparative liquid chromatography of hop and beer bitter acids

Methods and liquid chromatographic (LC) systems for the separation on a preparative scale (Prep-LC) of hop alpha acids and of beer iso-alpha acids were developed. The optimization of the selectivity factor for the cis—trans pairs of the iso-alpha acids was particularly studied. The highest values were achieved on reversed-phase packing materials with acetonitrile—water mixtures containing a relatively high proportion of water, to which magnesium salts are added, as eluent. Up to 400 mg of isomerized hop extract could be treated in one run on a laboratory Prep-LC column of dimensions 25 × 2.2 cm I.D. This application illustrates some critical points of Prep-LC, viz., the need for a high selectivity value, the problem of detection at high concentrations and the difficulties of obtaining the separated compounds undegraded from the collected Prep-LC fractions.

Reactions with aziridines, 46. Ring opening of stilbene imines by thiophenolate

AbstractRing opening by thiophenolate of cis‐trans pairs of stilbene imines proceeds stereospecifically irrespective of the kind of mono activation by the phenylsulfonyl group (1), by the benzoyl group (2), or by protonation of the aziridine base (3). In accordance with complete Walden inversion, the sole product from the cis isomer is always a diastereomer of the sole product from the trans isomer. The diastereomers obtained from 3 are correlated with the respective diastereomers obtained from 2.

ChemInform Abstract: Reactivity Difference of cis-trans Pairs: Different Behavior of Stilbene Oxides and Activated Stilbene Imines.

ChemInform Abstract: Reactivity Difference of cis-trans Pairs: Different Behavior of Stilbene Oxides and Activated Stilbene Imines.

Reactions with aziridines. 43. Reactivity difference of cis-trans pairs: different behavior of stilbene oxides and activated stilbene imines

Reactions with aziridines. 43. Reactivity difference of cis-trans pairs: different behavior of stilbene oxides and activated stilbene imines

ChemInform Abstract: REACTIONS OF 3‐ACETYLTROPOLONE METHYL ETHERS WITH 1,2‐CYCLOHEXANEDIAMINE

AbstractDas Tropolon‐Derivat (I) bildet mit dem Diamin (II) die Kondensationsprodukte (IIIa) und (IIIb), die im Reaktionsgemisch z.T. in die Folgeprodukte (IV) und (V) übergehen [bei Anwendung eines (In‐Überschusses nimmt die Ausb. an Sekun ‐ därprodukten aufKosten derjenigen von (III) zu].

Reactions of 3-Acetyltropolone Methyl Ethers with 1,2-Cyclohexanediamine

Abstract 3-Acetyl-2-methoxytropone reacted with 1,2-cyclohexanediamine (2) (a mixture of cis 60% and trans 40%) to give four cis-trans pairs of 6-acetyl-5H-1,2,3,4,4a,11a-hexahydrocyclohepta[b]quinoxaline (3), 6-acetyl-9-formyl-1,2,3,4,4a,5,10,10a-octahydrophenazine (4), 6-acetyl-1,2,3,4,4a,5,10,10a-octahydrophenazine (5), and 1-methyl-6H-6a,7,8,9,10,10a-hexahydropyrrolo[3,2,1-de]phenazine (6). The reaction of 2-acetyl-7-methoxytropone with 2 gave cis- and trans-N,N′-bis(6-acetyl-7-oxo-1,3,5-cycloheptatrienyl)-1,2-cyclohexanediamine, besides the above products. The cis- and trans-isomers of 4, 5, and 6 were secondary products from the cis- and trans-isomers of 3, respectively.

Solution complexes of the aluminum halides in acetonitrile and acetonitrile-water studied by high-field 27AI NMR

The complexes coexisting in acetonitrile upon dissolution of AIX 3 (X = CI, Br, I) are shown to consist essentially of the pure anionic complex AIX 4 − and mixed hexacoordinated species of type [A1X n S 6− n ] 3− n (S = acetonitrile), all exhibiting distinctly different 27 Al shieldings. The presence of both geometric isomers was unambiguously established for [AICl 2S 4] + and AICl 3S 3, which could be identified on the basis of their characteristic linewidths, dictated by the distinctly different electric field gradient tensor invariants acting on the Al nucleus. The relative populations of the various mixed species are found to be highly dependent upon solute concentration, and the more chloride-rich species become appreciably populated only at high dilution. By contrast only three different hexacoordinated species were identified for AIBr 3 whereas ALL 3 provides only AI(CH 3CN) 6 3+ and All 4 −. Addition of small amounts of water consecutively displaces chloride or bromide ions and acetonitrile from the ligand sphere affording mixed solvates of stoichiometry [AlS n H 2O) 6− n ] 3+ and, with AICl 3, probably also chloride-containing species. All of the complexes described are found to be kinetically inert on the 27Al NMR time scale. Nine out of ten theoretically possible mixed solvates including the cis-trans pairs for [AIS 3(H 2O) 3] 3+ and [AIS 4(H 2O) 2] 3+ were identified.

Influence of substituents in the 3-position of cyclohexene oxides on the rates of their reactions with hydrogen chloride in low polarity aprotic solvents

Rates of reactions of cyclohexene oxide and of its cis- and trans-3-methyl and 3-t-butyl derivatives with HCl were measured in toluene and CCl4 by a calorimetric method. Although these rates are very sensitive to trace impurities, satisfactory second-order kinetics were obtained in the presence of small amounts of water or tetrahydrofuran. An equatorial substituent in the 3-position trans to the epoxide oxygen has a rate-retarding effect which is larger for t-butyl than for methyl. The qualitative agreement between the ratios of the rates of formation of the four trans-chlorohydrins from each cis–trans pair of the 3-alkylcyclohexene oxides and the molar ratios of the bromohydrins obtained in the reactions of the corresponding alkylcyclohexenes with NBS in DMSO–water supports the hypothesis that in the latter reaction the nucleophillic step, rather than the electrophilic one, is rate determining.

Differential gas–liquid chromatographic behaviour in diastereoisomeric systems. Part II. Assignment of diastereomer configuration in 2,3-dipentylbutanes and 2,4-dipentylpentanes

During the preparation of the ditoluene-p-sulphonates of 2,3-dipentylbutane-1,4-diols and 2,4-dipentylpentane-1,5-diols, two competing reactions occurred; the ditoluene-p-sulphonylation and the formation of the appropriate cyclic ethers. Each of the meso-isomers produce a mixture of meso-ditoluene-p-sulphonyl derivative and the cis-cyclic ethers while the (±)-isomers from a mixture of the (±)-ditoluene-p-sulphonyl derivatives and the trans-cyclic ethers. As a result of a difference in the activation energy of formation, the cis- and trans-isomers of each cyclic compound are obtained in unequal amounts with the trans in majority; thus the corresponding ditoluene-p-sulphonyl products are obtained proportionally unbalanced with the (±)-form in minority. The ditoluene-p-sulphonyl derivatives are quantitatively reduced to the corresponding hydrocarbons and after chromatography, help to determine the relative retention times and volatilities of the meso-(±) and cis–trans pairs in the 3,4-dipentyltetrahydrofurans, 3,5-dipentyltetrahydropyrans, 2,3-dipentylbutanes, and 2,4-dipentylpentanes.

Analytical methods for phosphamidon.

Phosphamidon, the dimethyl phosphate of N,N-diethyl-2-chloro-3-hydroxy crotonamide, Open image in new window exists as a cis-trans pair. The two isomers can be differentiated by NMR or gas liquid chromatography. The β-isomer corresponds to the cis-form.

A Mössbauer study of structure and bonding in iron(II) low-spin compounds

The Mossbauer spectra of a large number of iron(II) low-spin compounds are reported. Together with the Mossbauer spectra of other low-spin compounds reported in the literature, we have derived partial centre shifts (p.c.s.) for 37 ligands and partial quadrupole splittings (p.q.s.) for 16 ligands. There is an inverse correlation between the p.c.s. values and spectrochemical ranking of ligands. With this correlation the position of hydride in the spectrochemical series has been re-examined. The p.c.s. values should also be helpful in the preparation of compounds in which the iron(II) exhibits intermediate spin or a high-spin–low-spin equilibrium.The p.c.s. values are related to the total σ-donor plus π-acceptor properties of the ligands, while the differences in c.s. between the cis–trans pairs may be used to separate the σ- and π-effects. Our results indicate that SnCl3– is a good π-acceptor (comparable to ArNC) but a rather poor σ-donor.The 2 : 1 trans-cis quadrupole splitting ratio holds for such ligands as Cl–, SnCl3–, RNC, and CN–, and the q.s. values are used, in conjunction with other spectroscopic data, to assign the stereochemistry of many of the isomers in this study. The 2 : 1 q.s. ratio is explained in terms of a simple molecular orbital model. The p.q.s. values can be useful for examining the bonding properties of many ligands, and can provide complementary bonding information to that obtained from the p.c.s. values.Many of the spectra in this study were distinctly asymmetric. With this Goldanskii asymmetry, a method for obtaining the sign of the field gradient in these compounds is tentatively proposed.

Ion pair formation in the separation of metal complexes by paper electrophoresis

Ion pair formation of cobalt complexes was studied by paper electrophoresis in a wide range of electrolytes. Quite strong interactions between divalent anions and complexes of the type Co(NH 3) 6 3+ were observed. The interactions seems to depend on the shape and size of the interacting ions as well as the charge. Cis-trans pairs of complexes separate very readily in sulphate (mobility differences about 40 %) and much less in monovalent electrolytes (mobility differences about 10 %). Optical isomers could not be resolved by paper electrophoresis.

Assignment of the Ultraviolet Mystery Band of Olefins

The weak mystery band found in the mono-olefins at 5–6 eV is here reassigned as a symmetry-allowed π→CH*(1Ag→1B2u) transition in which the CH* sigma upper orbital has considerable ns Rydberg character. Evidence supporting this assignment and militating against the recent CH→π*(1Ag→1B3g) assignment of Berry [J. Chem. Phys. 38, 1934 (1963)], the only other plausible assignment, is drawn from (a) ab initio calculations of the electronic spectrum and orbital energies of ethylene in large Gaussian bases, (b) a study of the intensities and vibronic band shapes of the mystery bands of cis—trans pairs of dialkylethylenes, (c) the observed effect of ring strain on the mystery-band intensity, (d) a measurement of the Cotton effect and rotational strength of the mystery-band transition, and (e) the spectra of olefins in condensed phases which demonstrate the Rydberg nature of the mystery-band upper state. Evidence is also presented that shows that the first electron affinity of ethylene places an electron in the CH* orbital, rather than in the π* orbital, as previously assumed. The implication of this low-lying π→σ* transition for the common assumption of π—σ separability is mentioned, and the importance of the almost certain presence of relatively low-lying π→σ* transitions with out-of-plane polarization in hydrocarbons of all sizes is stressed.