Nucleic Acid Base Derivatives Research Articles

A nucleic acid base derivative tethered to a ruthenium carbene complex: hydrogen bonded dimers in both the solid state and solution?

A ruthenium carbene bearing a uracil (Ur) substituent has been prepared and has a dimeric structure in the solid state-the dimer being held together by hydrogen bonds between two uracil groups on neighbouring molecules: evidence for the persistence of this interaction in solution has been obtained.

Computer‐Aided Molecular Design of Hydrogen Bond Equivalents of Nucleobases: Theoretical Study of Substituent Effects on the Hydrogen Bond Energies of Nucleobase Pairs

AbstractSubstituent effects on the hydrogen bond energies of Watson−Crick‐type base pairs, formed between a chemically modified nucleic acid base derivative and an unmodified one, were evaluated by ab initio molecular orbital theory. Different trends were observed in the relationship between the substituent and the hydrogen bond energy in each base pair. The predicted hydrogen bond energies correlated well with the experimentally measured binding properties, and so ab initio calculation appears to be an effective method with which to estimate the stabilities of base pairs between chemically modified nucleic acid bases. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003)

Study on the inhibition of protein production by L-cysteine derivatives of nucleic acid bases.

Isopoly (S-carboxymethyl-L-cysteine) derivatives of nucleic acids bases were prepared as antisense compounds. In previous studies, we investigated the properties of these compounds in vitro, and revealed that these compounds in vivo regulated the cell death presumably due to the inhibition of protein production. In this study, western and northern blots were carried out in order to reveal the mechanism of this inhibition for N-methyl-D-aspartate receptor in neuroblastoma x glioma hybrid NG108-15 cell line. In addition, we investigated the resistance of these compounds against cell extract and the metabolism. In conclusion, we proved that these compounds inhibited the protein production by antisense mechanism.

Application of L-cystein derivative to DNA microarray.

S-carboxymethyl-L-cystein derivatives of nucleic acid bases were prepared as DNA chip probe. These compounds in vitro have been found to form stable complex with oligo-DNA and RNA. This paper deals with preparing new DNA chip using L-cystein derivative synthetic nucleotides as probe and immobilized it to quartz plate by photosensitive PVA. Then the chip exposed with FITC labeled target DNA was observed by confocal fluorescence microscope.

Study about the inhibition of L-cysteine derivatives of nucleic acid bases in protein production.

Isopoly (S-carboxymethyl-L-cysteine) derivatives of nucleic acids bases were prepared as antisense compounds. In past study, we investigated the properties of these compounds in vitro, and revealed that these compounds in vivo regulated the cell death presumably due to the inhibition of protein production. In this study, western and northern blots were carried out in order to reveal the mechanism of this inhibition for N-methyl-D-aspartate receptor in neuroblastoma x glioma hybrid NG108-15 cell line. In addition, we investigated the resistance of these compounds against cell extract and the metabolism. In conclusion, we proved that these compounds inhibited the protein production by antisense mechanism.

Transfection of fluorescent probed antisense compounds: L-cysteine derivatives of nucleic acid bases.

Antisense with L-cysteine derivative (CAS) can recognize DNA and forms the complementary duplex with DNA. So the properties of CAS in vitro and in vivo were examined in this study. CAS was resistant to proteinase K and stabilized RNA against RNase HI. Moreover using fluorescent CAS, the localization was observed by fluorescence microscope and confocal microscope. As a result, CASs were accumulated inside the nucleus in NG108-15.

The behavior and effect of isopoly (S-carboxymethyl-L-cysteine) derivatives of nucleic acid bases

Isopoly(S-carboxymethyl-L-cysteine) derivatives of nucleic acid bases were prepared as antisense compounds. These compounds in vitro have been found to form stable complex with oligo-DNA or RNA. This paper deals with effect of antisense compounds in vivo. The target in this paper is the sequence of the PSD-95 protein linked with NMDA receptor. Excess passing of calcium ions through the loss of the signal pathway without PSD-95 proteins caused by antisense compound. The cells detailing with L-cysteine derivatives showed the lowest percentage of 19.1%. The data were compared with that of phosphotioate antisense compound.

Electrochemical responses of cytochrome c on gold electrodes modified with nucleic acid base derivatives–electrochemical and quartz crystal microbalance studies

The electrochemical responses of cytochrome c on the gold electrodes modified with nucleic acid base derivatives such as 2-amino-6-purinethiol, 2-amino-6-mercaptopurine riboside, 6-amino-8-purinethiol and 2-thiouracil were investigated. The monolayers of 2-amino-6-purinethiol and 6-amino-8-purinethiol on gold can promote the electron transfer between cytochrome c in solution and gold electrode like that of well-known promoters such as pyridylthiol derivatives and carboxylic acid terminated alkanethiols, as reported previously. However, in the case of 2-amino-6-mercaptopurine riboside modified gold electrode, the redox response of cytochrome c was completely inhibited, because a bulky ribose group inhibited the promoting ability. We also confirmed that the 2-thiouracil on gold electrode can facilitate the electron transfer between cytochrome c and gold electrode. The redox response of cytochrome c on 6-amino-8-purinethiol modified gold electrode was inhibited effectively by forming a hydrogen bonded complex with a complementary nucleic acid base derivative, thymidine. However, in the cases of 2-amino-6-purinethiol and 2-thiouracil modified gold electrodes, the redox response of cytochrome c was not inhibited by thymidine treatment. These phenomena should reflect the difference of adsorbed direction between 2-amino-6-purinethiol and 6-amino-8-purinethiol on gold and the unsuitable matching of thiouracil adsorbed on gold with thymidine in solution.

Density functional theory studies of methylated uracil: geometries and energies

Density functional theory studies on the geometries and energies of the methylated derivatives of uracil yield two stable conformations, α and β, for each single-methylated uracil. They are different in the spatial orientation of the substituting methyl group and the molecular total energy. Analyzing the calculated structural parameters, we also found an elongation effect in the methylated uracil, which contributes to the increase of dipole moment and molecular size of molecules such as the methylated derivatives of nucleic acid bases.

A new family of high-affinity transporters for adenine, cytosine, and purine derivatives in Arabidopsis.

In many organisms, including plants, nucleic acid bases and derivatives such as caffeine are transported across the plasma membrane. Cytokinins, important hormones structurally related to adenine, are produced mainly in root apices, from where they are translocated to shoots to control a multitude of physiological processes. Complementation of a yeast mutant deficient in adenine uptake (fcy2) with an Arabidopsis cDNA expression library enabled the identification of a gene, AtPUP1 (for Arabidopsis thaliana purine permease1), belonging to a large gene family (AtPUP1 to AtPUP15) encoding a new class of small, integral membrane proteins. AtPUP1 transports adenine and cytosine with high affinity. Uptake is energy dependent, occurs against a concentration gradient, and is sensitive to protonophores, potentially indicating secondary active transport. Competition studies show that purine derivatives (e.g., hypoxanthine), phytohormones (e.g., zeatin and kinetin), and alkaloids (e.g., caffeine) are potent inhibitors of adenine and cytosine uptake. Inhibition by cytokinins is competitive (competitive inhibition constant K(i) = 20 to 35 microM), indicating that cytokinins are transported by this system. AtPUP1 is expressed in all organs except roots, indicating that the gene encodes an uptake system for root-derived nucleic acid base derivatives in shoots or that it exports nucleic acid base analogs from shoots by way of the phloem. The other family members may have different affinities for nucleic acid bases, perhaps functioning as transporters for nucleosides, nucleotides, and their derivatives.

Fluorescent probe and permeability to cells of isopoly (S-carboxymethyl-L-cysteine) derivative of nucleic acid bases.

Isopoly(S-carboxymethyl-L-cysteine) derivatives of nucleic acid bases were found to form stable complex with oligo-DNA in vitro. Fluorescent probed isopoly(S-carboxymethyl cysteine) derivatives of nucleic acid bases were prepared as antisense oligomers. The transfection of the oligomer into cells was carried out by HVJ-liposome method. Fluorescence was observed from the cells treated with HVJ-liposome including fluorescent probed oligomers.

Isopoly(S-carboxymethyl-L-cysteine) derivatives of nucleic acid bases: effects of D-cysteine derivatives on the interaction with DNA.

Isopoly(S-carboxymethyl-D-cysteine) derivatives of nucleic acid bases were prepared to study the effect of chirality on the complex formation with oligo-DNA. The D-cysteine unit in the L-cysteine oligomer caused decrease of Tm for the complex with DNA.

Synthesis and characterization of new chiral peptide nucleic acid (PNA) monomers.

PNAs are DNA analogues in which the nucleic acid's backbone is replaced by a chiral or achiral pseudopeptide backbone and nucleobases are attached to the backbone by methylene carbonyl linkers. The easy to modify PNA structure gives the possibility to obtain monomers, and subsequently oligomers, with improved properties. We have synthesised several new PNA monomers, starting from a series of 2'-substituted methyl N-(2-Boc-aminoethyl)glycinates. The pseudodipeptides were obtained using modified Kosynkina's method, based on the reductive amination of N-Boc-protected alpha-amino aldehydes [glycinal, isoleucinal, valinal, tryptophanal, serinal(Bzl), prolinal] with methyl glycinate. The compounds were then acylated with nucleic acid base derivatives by simplified procedure, and the purification was limited to the last step of the synthesis. The applied procedure is useful in synthesis of various chiral PNA monomers.

Electrochemical behavior of gold electrodes modified with aminopurinethiol derivatives

The electrochemical properties of gold electrodes modified with 2-amino-6-purinethiol and 6-amino-8-purinethiol were investigated. The aminopurinethiolate monolayers could facilitate the electron transfer between cytochrome c in solution and a gold electrode in the same way as well-known promoters such as pyridylthiol derivatives and carboxylic acid terminated alkanethiols as reported previously. The redox response of cytochrome c on a 6-amino-8-purinethiol modified gold electrode was inhibited effectively by forming a hydrogen bonded complex with a complementary nucleic acid base derivative, thymidine. However, in the case of a 2-amino-6-purinethiol modified gold electrode, an inhibition of the redox response of cytochrome c by thymidine treatment was not observed. These phenomena reflect the difference of direction of each of the adsorbed molecules.

Preparation of zinc organometallics derived from nucleosides and nucleic acid bases and Pd(0) catalyzed coupling with aryl iodides

5-lodouracil and 6-iodopurine derivatives readily insert zinc dust (25 °C or 70 °C) in THF or DMAC affording zincated nucleic acid base derivatives which undergo efficient palladium catalyzed cross-coupling reactions with aryl iodides in good yields. This reaction sequence has been extended to two nucleosides (a purine and an uridine derivative).

Thermochemistry of aqueous solutions of nucleic acid bases and their alkylated derivatives

Enthalpy of solution, ΔH sol o , enthalpy of sublimation, ΔH subl o , apparent partial molar volume and heat capacities,V 2 o andC p,2 o were determined for aqueous solutions of thirty alkylated derivatives of uracyl and adenine, eight derivatives of cytosine and guanine. Calculated accessible surface areas and molar volumes are presented, too. The values of enthalpy of solution, enthalpy of sublimation can be useful in the studies on the nature of interaction between these compounds and water molecules. Apparent partial molar volume and heat capacity give a new aspect on hydrophob properties of the examined nucleic acid base derivatives.

Transport Performance of Nucleosides through Nucleic Acid Bases Conjugated Hyaluronan

Abstract The transport performance of nucleosides through the membranes of hyaluronic acid and deacetylated hyaluronan conjugated with nucleic acid base derivatives has been studied under varied temperature. Partition coefficient values of the permeants and permeabilities of the membranes showed the selectivity of nucleosides due to the effect of specific interaction between the permeants and nucleic acid base moiety in the membrane.

Synthesis of Sulfonated Hyaluronan Derivatives Containing Nucleic Acid Bases

Abstract The conjugation of nucleic acid base with sulfonated hyaluronan was achieved by the ring opening reaction of 1,2-O-ethano derivatives of nucleic acid bases. The conditions of sulfonation of sodium hyaluronate were studied. Thymine and 5-bromouracil base were quantitatively conjugated to sulfonated hyaluronan in 15% and 24%, respectively.

Low-Frequency Vibrations of a Nucleoside Analog

This paper reports on the first coherent neutron scattering measurements ever carried out on the vibrational spectrum of a nucleoside analog. Frequencies up to 3.5 Thz belonging to some half-dozen dispersion curves have been measured in a plane normal to the [1 10] direction in a triclinic crystal of 5-iodo-2'-deoxyuridine (5-iodouridine). The number of phonon branches observed suggests that the deoxyribose sugar and pyrimidine in this molecule are the vibrating entities at low frequencies. Comparisons, notably of elastic properties, are made with previous measurements on crystalline forms of DNA and various nucleic acid base derivatives. The observed frequencies are discussed with reference to a simple force constant model.

ChemInform Abstract: Synthesis of Optically Active α‐(Imidazol‐1‐yl, Purin‐9‐yl or Uracil‐1‐yl) Propanoic and Succinic Acid Derivatives.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.