Protonated primary amines induced thymine quintets studied by electrospray ionization mass spectrometry and density functional theory calculations

As the novel magic number clusters of nucleobases, the thymine quintets induced by ammonium ion (NH₄⁺), and particularly by its derivatives such as protonated alkyl amines and protonated aryl amines, have been studied by electrospray ionization mass spectrometry (ESI‐MS) and density functional theory (DFT) calculations. The DFT‐optimized geometry of NH₄⁺ induced thymine quintet ([T₅ + NH₄]⁺) reveals some new features including three additional hydrogen bonds between NH₄⁺ and its surrounding thymine molecules when compared with that of the alkali metal ions induced thymine quintets. In addition, the fourth hydrogen atom of NH₄⁺ is sticking out the assembly, and, thus, it might be replaced by an organic group R to form the protonated primary amine induced thymine quintet ([T₅ + R ? NH₃]⁺), a hypothesis that has been confirmed by both DFT calculations and ESI‐MS experiments. Furthermore, the relative abilities of the different protonated primary amines for inducing the thymine quintets are investigated by ESI‐MS competition experiments, and the results have shown a clear trend of stronger ability as the alkyl chain gets longer or as the aryl ring gets larger for the alkyl amines or the aryl amines. Two basic influence factors are consequently identified: one is the ability of the alkyl amine to accept proton, another is the π–π stacking interaction between the aryl ring and the π‐surface of the thymine molecule(s), whose explanations are strongly supported by multiple types of thermochemical data, various control experiments and DFT calculations. Copyright © 2014 John Wiley & Sons, Ltd.     

Kinetics and mechanism of protection of thymine from phosphate radical anion under anoxic conditions

The rates of photooxidation of thymine in the presence of peroxydiphosphate (PDP) have been determined by measuring the absorbance of thymine at 264 nm spectrophotometrically. The rates and the quantum yields (φ) of oxidation of thymine by phosphate radical anion have been determined in the presence of different concentrations of dithiothreitol (DTT). An increase in DTT is found to decrease the rate of oxidation of thymine, suggesting that DTT acts as an efficient scavenger of PO₄^·2? and protects thymine from it. Phosphate radical anion competes for thymine as well as DTT; the rate constant for the phosphate radical anion with DTT has been calculated to be 2.21 × 10⁹ dm³ mol^?1 s^?1, assuming the rate constant of phosphate radical anion reaction with thymine as 9.6 × 10⁷ dm³ mol^?1 s^?1. The quantum yields of photooxidation of thymine have been calculated from the rates of oxidation of thymine and the light intensity absorbed by PDP at 254 nm, the wavelength at which PDP is activated to phosphate radical anion. From the results of experimentally determined quantum yields (φ_exptl) and the quantum yields calculated (φ_cl), assuming DTT acts only as a scavenger of PO₄^·2? radicals, show that φ_exptl values are lower than φ_cl values. The φ′ values, which are experimentally found quantum yield values at each DTT concentration and corrected for PO₄^·2? scavenging by DTT, are also found to be greater than φ_exptl values. These observations suggest that the thymine radicals are repaired by DTT in addition to scavenging of phosphate radical anions. © 2001 John Wiley & Sons, Inc. Int J Chem Kinet 33: 271–275, 2001     

Kinetics and mechanism of protection of thymine from sulphate radical anion under anoxic conditions

The rates of photooxidation of thymine in presence of peroxydisulphate (PDS) have been determined by measuring the absorbance of thymine at 264 nm spectrophotometrically. The rates and the quantum yields (φ) of oxidation of thymine by sulphate radical anion have been determined in the presence of different concentrations of caffeic acid. Increase in [caffeic acid] is found to decrease the rate of oxidation of thymine suggesting that caffeic acid acts as an efficient scavenger of SO ₄ ^•- and protects thymine from it. Sulphate radical anion competes for thymine as well as for caffeic acid. The rate constant of sulphate radical anion with caffeic acid has been calculated to be 1.24 x 10¹⁰ dm³ mol^-1s^-1. The quantum yields of photooxidation of thymine have been calculated from the rates of oxidation of thymine and the light intensity absorbed by PDS at 254 nm, the wavelength at which PDS is activated to sulphate radical anion. From the results of experimentally determined quantum yields (φ_expt1) and the quantum yields calculated (φ_cl) assuming caffeic acid acting only as a scavenger of SO ₄ ^•- radicals show that φ_expt1 values are lower than φ_cl values. The φ ’ values, which are experimentally found quantum yield values at each caffeic acid concentration and corrected for SO ₄ ^•- scavenging by caffeic acid, are also found to be greater than φ_expt1 values. These observations suggest that the thymine radicals are repaired by caffeic acid in addition to scavenging of sulphate radical anions.     

Oxidation of nucleic acid bases by hexavalent manganese in aqueous alkaline medium: a kinetic study

Oxidation of uracil or thymine by Mn^VI in aqueous alkali shows first order dependence on [MnO ₄ ²⁻ ] and fractional order dependence on [uracil] or [thymine]. The effect of ionic strength is negligible on the rate of oxidation. The product of oxidation is the 5,6-dihydroxy compound. A mechanism is proposed involving the formation of a 5-membered cyclic complex between the substrate and manganate in a fast step, which subsequently disproportionates to give the final products. The large negative values of the entropy of activation suggest the formation of an intermediate complex. The formation constants of the latter and the rate of its disproportionation have been calculated from the derived rate law. The rate of oxidation of thymine is faster than that of uracil.     

Design and stereoselective synthesis of four peptide nucleic acid monomers with cyclic structures in backbone

Four isomers of the monomer of peptide nucleic acid (PNA) were derived from (2S,4R)‐4‐hydroxyproline; they had different stereochemistries at the C² and C⁴ positions in the pyrrolidine ring. These different backbone conformations corresponding to four different stereochemistries were realized through a combination of inversions at the C² and the C⁴ positions in pyrrolidine ring. The obtained backbone frameworks were reacted with N‐benzoyl thymine to give the corresponding PNA monomers. Spectroscopic comparison of the resultant monomers confirmed their stereochemistries. J. Heterocyclic Chem., (2011).     

End-labeling of peptide nucleic acid with osmium complex. Voltammetry at carbon and mercury electrodes

Peptide nucleic acid (PNA), the DNA mimic with electrically neutral pseudopeptide backbone, is intensively used in biotechnologies and particularly in single-base mismatch detection in DNA hybridization sensors. We propose a simple method of covalent end-labeling of PNA with osmium tetroxide, 2,2′-bipyridine (Os,bipy). Os,bipy-modified PNA (PNA–Os,bipy) produces voltammetric stripping peaks at carbon and mercury electrodes. Peak potential (E_p) of one of the anodic peaks of PNA–Os,bipy at the pyrolytic graphite electrode (PGE) differs from E_p of the reagent, allowing PNA–Os,bipy analysis directly in the reaction mixture. At the hanging mercury drop electrode (HMDE) the PNA–Os,bipy yields a catalytic peak Cat_p, in addition to the redox couples. Using Cat_p it is possible to detect purified PNA–Os,bipy down to 1 pM concentration at accumulation time 60 s. To our knowledge this is the highest sensitivity of the electrochemical detection of PNA.     

Design of a new oligotriazole peptide nucleic acid analogue (oT-PNA)

We describe in this Letter the synthesis of an original thymine azido-heterotrimer generated by Click Chemistry. This trimer has been obtained from an azido-thymidine and a new chloroethyl-propargylated PNA monomer analogue, after two azidation/click-reaction cycles. Conformational preferences of a rotameric intermediate have also been studied     

1,8-Dimercuri-6-Phenyl-1H-Carbazole as a Monofacial Dinuclear Organometallic Nucleobase

A C-nucleoside with 6-phenyl-1H-carbazole as the base moiety has been synthesized and incorporated in the middle of an oligonucleotide. Mercuration of this modified residue at positions 1 and 8 gave the first example of an oligonucleotide featuring a monofacial dinuclear organometallic nucleobase. The dimercurated oligonucleotide formed stable duplexes with unmodified oligonucleotides placing either cytosine, guanine, or thymine opposite to the organometallic nucleobase. A highly stabilizing (ΔT_m=7.3 °C) Hg^II-mediated base pair was formed with thymine. According to DFT calculations performed at the PBE0DH level of theory, this base pair is most likely dinuclear, with the two Hg^II ions coordinated to O2 and O4 of the thymine base.     

Solubilities of lactic acid and 2-hydroxyhexanoic acid in supercritical CO2

Solubilities of lactic acid and 2-hydroxyhexanoic acid in supercritical CO₂ have been measured at T=(311 or 313, 318, 328 K) in the pressure range from 50 to 200 bar. The measurements have been performed using a flow-type apparatus. The solute solubility in compressed carbon dioxide increased with pressure at all investigated temperatures. At pressures below 130 bar, a solubility decrease on temperature increase was observed. An accurate correlation method for the solubility of low volatile substances in supercritical CO₂ has been applied for the interpolation of the experimental results.     

Thermal properties of poly(methyl methacrylate-co-butyl acrylate-co-acrylic acid) modified with divinyl benzene and vinyltrimethoxysilane

The effect of butyl acrylate (BA), divinyl benzene (DVB) and vinyltrimethoxysilane (TMVS) on the thermal properties of poly(methyl methacrylate-co-butyl acrylate-co-acrylic acid) was investigated. Glass transition temperature (T_g), melting temperature (T_m) and specific heat capacity of the copolymers were investigated using Differential Scanning Calorimetry. Thermal stability of the copolymers which is associated with the degradation temperature (T_d) was studied by Thermogravimetric Analysis. Polyacrylates with T_g ranges between -19°Cand 19°C were obtained. With the incorporation of >7 wt% of DVB, the T_g of the copolymer increases from about ?17°C to ?10°C even though they have not undergone UV irradiation. Gel content results prove that crosslinking has occurred in the copolymers. With increasing amount of TMVS from 0 wt% to 7 wt%, the T_m of the copolymers prepared at acidic pH is about 40-60°C higher than that at the alkaline pH. However, the addition of TMVS gives no significant effect to the T_g and T_d of the copolymer films. The thermal stability of the copolymer has improved with increasing amount of BA and DVB, with DVB being more effective. The highest T_d of 425°C with 8% of DVB has been obtained. Consequently, a polyacrylate copolymer with a T_g of about ?13°C, a T_m of 170 °C and a T_d of about 424°C has been successfully synthesized. Hence, the soft polyacrylate with its relatively high T_m and T_d could serve as a superb material especially to be applied in the areas that require high melting temperature and good thermal stability.     

Synthesis and evaluation of (1S,2R/1R,2S)-aminocyclohexylglycyl PNAs as conformationally preorganized PNA analogues for DNA/RNA recognition

Conformationally constrained cis-aminocyclohexylglycyl PNAs have been designed on the basis of stereospecific imposition of 1,2-cis-cyclohexyl moieties on the aminoethyl segment of aminoethylglycyl PNA (aegPNA). The introduction of the cis-cyclohexyl ring may allow the restriction of the torsion angle beta in the ethylenediamine segment to 60-70 degrees that is prevalent in PNA(2):DNA and PNA:RNA complexes. The synthesis of the optically pure monomers (10a and 10b) is achieved by stereoselective enzymatic hydrolysis of an intermediate ester 2. The chiral PNA oligomers were synthesized with (1S,2R/1R,2S)-aminocyclohexylglycyl thymine monomers in the center and N-terminus of aegPNA. Differential gel shift retardation with one or more units of modified monomer units was observed as a result of hybridization of PNA sequences with complementary DNA sequences. Hybridization studies with complementary DNA and RNA sequences using UV-T(m) measurements indicate that PNA with (1S,2R)-cyclohexyl stereochemistry enhances selective binding with RNA over DNA as compared to control aegPNA and PNA with the other (1R,2S) isomer.     

Kinetics and mechanism of chromic acid oxidation of oxalic acid in absence and presence of different acid media. A kinetic study

Kinetics and mechanism of the reaction of Cr(VI) with oxalic acid have been studied in presence and absence of H₂SO₄, HClO₄, and CH₃COOH by monitoring the formation of Cr(III)-oxalic acid complex at 560 nm. The effect of total [oxalic acid], [Cr(VI)], [H₂SO₄], [HClO₄], and [CH₃COOH] on the reaction rate was determined at 30°C. Formation of carbon dioxide was also confirmed. The oxidation rate increases with [oxalic acid] and [CH₃COOH] while it decreases with [H₂SO₄], [HClO₄], and pH. The rate law governing the oxidation of oxalic acid over a wide range of conditions is rate=k₁ K_es1 [oxalic acid]_T [Cr(VI)]_T 1+K_es1 [oxalic acid]_T, where only undissociated oxalic acid is kinetically active. Kinetic evidence for the formation of a Cr(VI)(SINGLEBOND)oxalic acid 1:1 complex has been obtained and the equilibrium constant for their formation has been determined. The 1:1 complex exists most likely in an open chain form. The rate-limiting step of the oxidation reaction involves the breaking of the C(SINGLEBOND)C bond in the 1:2 complex. Oxidizing ability of Cr(VI) species have been discussed. Mechanism with the associated reaction kinetics is assigned. © 1998 John Wiley & Sons, Inc. Int J Chem Kinet 30: 335–340, 1998     

Hybridization Study of PNA-DNA in the Solution and Surface-Solution Interface for Biosensor Application

Abstract

Hybridization of 12-mers peptide nucleic acid (PNA) to complementary DNA was investigated in solution and on gold surfaces. The oligomers were designed to improve mismatch discrimination and minimize formation of secondary structures. Thermal denaturation experiments indicate high thermal stabilities for PNA-DNA hybrid with T _m values close to calculated values. Hybridization of PNA-DNA at 45°C and room temperature showed no difference. Hybridization on gold surface was also investigated with complementary and noncomplementary DNAs. The results show that 12-mer PNA and DNA hybridization at room temperature retained high specificity within ～5 ng.     

Peptide Nucleic Acid Immobilized Biocompatible Silane Nanocomposite Platform for Mycobacterium tuberculosis Detection

We have prepared nanocomposite films comprising of 3‐glycidoxypropyltrimethoxysilane (GOPS) and iron‐oxide (Fe₃O₄) onto indium‐tin‐oxide (ITO) glass plate for covalent immobilization of 21‐mer peptide nucleic acid (PNA). These films have been characterized using contact angle, atomic force microscopy (AFM), electrochemical techniques. The electrochemical response of the GOPS/ITO and Fe₃O₄‐GOPS/ITO electrodes has been investigated by hybridization with complementary, non‐complementary and one‐base mismatch using methylene blue as electrochemical indicator. The PNA/Fe₃O₄‐GOPS/ITO bioelectrode exhibits improved specificity and detection limit (0.1 fM) as compared to that of the PNA‐GOPS/ITO bioelectrode (0.1 pM). This PNA/Fe₃O₄‐GOPS/ITO electrode can be utilized for detection of hybridization with the complementary sequence in sonicated M. tuberculosis genomic DNA within 90 s of hybridization time.     

Influence of the Type of Junction in DNA-3′-Peptide Nucleic Acid (PNA) Chimeras on Their Binding Affinity to DNA and RNA

The automated on-line synthesis of DNA-3′-PNA (PNA=Polyamide Nucleic Acids) chimeras 1 – 3 is described, in which the 3′-terminal part of the oligonucleotide is linked to the aminoterminal part of the PNA either via a N-(2-mercaptoethyl)- (X=S), a N-(2-hydroxyethyl)- (X=O), or a N-(2-aminoethyl)- (X=NH) N-[(thymin-1-yl)acetyl]glycine unit. Furthermore, the DNA-3′-PNA chimera 4 without a nucleobase at the linking unit was prepared. The binding affinities of all chimeras were directly compared by determining their T_m values in the duplex with complementary DNA, RNA, or DNA containing a mismatch or abasic site opposite to the linker unit. We found that all investigated chimeras with a nucleobase at the junction form more stable duplexes with complementary DNA and RNA than the corresponding unmodified DNA. The influence of X on duplex stabilization was determined to be in the order O>S≈NH, rendering the phosphodiester bridge the most favored linkage at the DNA/PNA junction. The observed strong duplex-destabilizing effects, when base mismatches or non-basic sites were introduced opposite to the nucleobase at the DNA/PNA junction, suggest that the base at the linking unit contributes significantly to duplex stabilization.     

Detection of hydrogen-bonded adenine-thymine base-pair complexes by electrospray mass spectrometry

Abstract

Bibracchial lariat ether compounds having three-carbon sidearms terminated in either adenine or thymine have the potential to form a molecular box in which the “ends” are crown ethers and the “sides” are hydrogen-bonded base pairs. Previous solution studies relying upon NMR and vapor pressure osmometry confirmed the formation of complexes. In the present study, four diaza-18-crown-6 derivatives having either one or two sidearms each terminated in either adenine or thymine have been studied in a mixture of CHCl₃ and CH₃OH. Either acetic acid or sodium chloride was added to the solutions. For the two-armed systems, the preferred complex was the dimer involving adenines on one monomer and thymines on the other. Homodimers and other complexes were detected as well. The preferred single-armed complex was that occurring between the monomer whose sidearm was terminated in thymine and either H⁺ or Na⁺.     

Glass transition temperatures of poly(itaconic acid ester)s containing pendant cycloalkyl rings

A series of poly(itaconic acid ester)s with pendant cycloalkyl rings, ranging in size from cyclopropyl to cyclododecyl, have been prepared. Two distinct groups have been synthesized; Group I derivatives have the ring attached directly to the main chain through an oxycarbonyl group and Group II polymers have a methylene unit inserted between the ring and the oxycarbonyl group. The glass transition temperatures, T_g, have been measured for polymers in each group. In Group I, T_g increased with ring size up to the dicyclohexyl derivative, but it then decreased with further increase in ring size. The decrease in T_g is due to the inherent flexibility of the ring which leads to internal plasticization of the sample. This effect appears to predominate over ring size in determining the magnitude of T_g, for 7–12 membered rings. Similar trends have been found in the Group II polymers, but the effect of the ring becomes less important the further it is moved away from the chain backbone.     

Photochemical studies of thymine in ice

Abstract— Solutions containing various concentrations of thymine have been irradiated (254 nm) at — 196°, and the corresponding absorbance changes at 315 nm due to thymine-thymine adduct formation have been followed as a function of dose. The maximum yield of the adduct is about 3–2 per cent. Additional irradiation leads to a reduction in the yield of adduct and to an increase in the yield of the proposed trimer, which shows a sigmoid dose response curve. Not more than 10 per cent of the thymine is converted to trimer. Irradiation of the trimer in solution converts it into adduct plus thymine. Fluorescence due to the adduct does not appear directly after irradiation at — 196°, but comes about upon annealing at elevated temperatures (T > - 80°).     

The Electrocatalytic Oxidation of Thymine at α‐Cyclodextrin Incorporated Carbon Nanotube‐Coated Electrode

Electrocatalytic oxidation of thymine at α‐cyclodextrin (α‐CD) incorporated carbon nanotube‐coated electrode (CNT/CE) was thoroughly studied in alkaline media. CNT showed an electrocatalytic effect on the oxidation of thymine, formation of a supramolecular inclusion complex between α‐CD and thymine at CNT/CE further enhanced the sensitivity to thymine. The electrocatalytic behavior was further developed as a sensitive detection scheme for thymine by differential pulse voltammetry. A linear calibration over the concentration range from 2.5×10^?5 to 1.8×10^?3 mol/L in pH 10.8 NaHCO₃‐Na₂CO₃ buffer solution was obtained with a detection limit of 5×10^?6 mol/L.     

Studies on kinetics and mechanism of oxidation of D‐sorbitol and D‐mannitol by cerium(IV) in aqueous micellar sulfuric acid media

The kinetics and mechanism of cerium(IV) oxidation of hexitols, i.e. D ‐sorbitol and D ‐mannitol, in aqueous sulfuric acid media have been studied in the presence and absence of surfactants. Under the kinetic conditions, [S]_T ? [Ce(IV)]_T, where [S]_T is the total substrate (D ‐sorbitol or D ‐mannitol) concentration, the overall process shows a first‐order dependence on [Ce(IV)]_T and [S]_T. The process is acid catalyzed and inhibited by [HSO]. From the [HSO] dependence, it has been noted that the both Ce(SO₄)²⁺ and Ce(SO₄)₂ have been found kinetically active. The different rate constants in the presence and absence of surfactants have been estimated with the activation parameters. N‐cetylpyridinium chloride has been found to retard the oxidation process of hexitols, whereas sodium dodecyl sulfate has been found to accelerate the rate process. All these findings including the micellar effects have been interpreted in terms of the proposed reaction mechanism and partitioning behavior of the kinetically active different species of Ce(IV) between the aqueous and pseudomicellar phase. © 2008 Wiley Periodicals, Inc. 40: 445–453, 2008