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At least 109 records · Page 6Linked to original sources
PubMed2000

Effect of DL-alpha-lipoic acid on tissue nucleic acid contents in aged rats.

We have attempted to evaluate the effect of DL-alpha-lipoic acid on nucleic acid and protein contents in young and aged rats. An age-associated decrease in the deoxyribonucleic acid (DNA), ribonucleic acid (RNA) and protein contents were observed in aged rats. DL-alpha-lipoic acid was administered intraperitoneally (100 mg/kg body weight/day) to young and aged rats from 7 and 14 days. Lipoate administration demonstrated a substantial increase in nucleic acid and protein contents in aged rats. Hence it can be justified that lipoate is functionally efficient in helping the cell to recover from oxidative damage.

Aging↗
PubMed2000

Use of nucleic acids in the mobile phase for the determination of ascorbic acid in foods by high-performance liquid chromatography with electrochemical detection.

The sodium salts of amino acids, nucleic acids and organic acids were examined in a new mobile phase for the determination of ascorbic acid (AA) in foods. It was possible to use disodium guanosine-5'-monophosphate (GMP) (20 mM GMP, pH 2.1) in a new mobile phase after comparison of five mobile phases. The proposed method is simple, rapid (analysis time: ca. 6 min), sensitive (detection limit: ca. 0.1 ng per injection (5 microl) at a signal-to-noise ratio of 3), highly selective and reproducible [relative standard deviation: ca. 2.7% (n=7)]. The calibration graph of AA was linear in the range of 0.1 to 50 ng per injection (5 microl). Recovery of AA was over 90% by the standard addition method.

Ascorbic Acid↗
PubMed2005

Aptamer-derived nucleic acid oligos: applications to develop nucleic acid chips to analyze proteins and small ligands.

The specificity and affinity of aptamers for their cognate ligands are comparable to those of antibodies for antigens. To use aptamers effectively in high-throughput assays in a microarray format, to analyze various analytes, we developed a strategy in which the aptamer was split into two nonfunctional units and allowed to reassemble into the functional aptamer by the cognate ligand. We have named this method "analyte-dependent oligonucleotide modulation assay" (ADONMA). As proof-of-principle, we used oligonucleotides derived from the aptamer RNA against HIV-1 Tat and demonstrated, with both titer plates and plastic slide chips, that specifically in the presence of Tat or its peptide, the two oligos reconstituted the core binding regions of Tat. Thus, these results suggest that ADNOMA has the potential for use in nucleic acid microarrays for detecting various ligands.

Aptamers, Nucleotide↗
PubMed1989

Interactions of the dimethyldiazaperopyrenium dication with nucleic acids. 1. Binding to nucleic acid components and to single-stranded polynucleotides and photocleavage of single-stranded oligonucleotides.

The binding of dimethyldiazaperopyrenium dication (1) with nucleosides, nucleotides, and single-stranded polynucleotides has been studied by photophysical methods. It has been shown that 1 may be a potential selective fluorescent probe for A- and/or T-rich polynucleotides. 1 efficiently cleaves oligonucleotides at guanine sites, under illumination with visible light, and therefore may be used as a sequence-specific artificial photonuclease.

Base Sequence↗
PubMed2003

Difference in conformational diversity between nucleic acids with a six-membered 'sugar' unit and natural 'furanose' nucleic acids.

Natural nucleic acids duplexes formed by Watson-Crick base pairing fold into right-handed helices that are classified in two families of secondary structures, i.e. the A- and B-form. For a long time, these A and B allomorphic nucleic acids have been considered as the 'non plus ultra' of double-stranded nucleic acids geometries with the only exception of Z-DNA, a left-handed helix that can be adopted by some DNA sequences. The five-membered furanose ring in the sugar-phosphate backbone of DNA and RNA is the underlying cause of this restriction in conformational diversity. A collection of new Watson-Crick duplexes have joined the 'original' nucleic acid double helixes at the moment the furanose sugar was replaced by different types of six-membered ring systems. The increase in this structural and conformational diversity originates from the rigid chair conformation of a saturated six-membered ring that determines the orientation of the ring substituents with respect to each other. The original A- and B-form oligonucleotide duplexes have expanded into a whole family of new structures with the potential for selective cross-communication in a parallel or antiparallel orientation, opening up a new world for information storage and for molecular recognition-directed self-organization.

Base Pairing↗
PubMedDate not supplied

Ab initio conformational analysis of nucleic acid components: intrinsic energetic contributions to nucleic acid structure and dynamics.

In recent years, the use of high-level ab initio calculations has allowed for the intrinsic conformational properties of nucleic acid building blocks to be revisited. This has provided new insights into the intrinsic conformational energetics of these compounds and its relationship to nucleic acids structure and dynamics. In this article we review recent developments and present new results. New data include comparison of various levels of theory on conformational properties of nucleic acid building blocks, calculations on the abasic sugar, known to occur in vivo in DNA, on the TA conformation of DNA observed in the complex with the TATA box binding protein, and on inosine. Tests of the Hartree-Fock (HF), second-order Møller-Plesset (MP2), and Density Functional Theory/Becke3, Lee, Yang and Par (DFT/B3LYP) levels of theory show the overall shape of backbone torsional energy profiles (for gamma, epsilon, and chi) to be similar for the different levels, though some systematic differences are identified between the MP2 and DFT/B3LYP profiles. The east pseudorotation energy barrier in deoxyribonucleosides is also sensitive to the level of theory, with the HF and DFT/B3LYP east barriers being significantly lower (approximately 2.5 kcal/mol) than the MP2 counterpart (approximately 4.0 kcal/mol). Additional calculations at various levels of theory suggest that the east barrier in deoxyribonucleosides is between 3.0 and 4.0 kcal/mol. In the abasic sugar, the west pseudorotation energy barrier is found to be slightly lower than the east barrier and the south pucker is favored more than in standard nucleosides. Results on the TA conformation suggest that, at the nucleoside level, this conformation is significantly destabilized relative to the global energy minimum, or relative to the A- and B-DNA conformations. Deoxyribocytosine would destabilize the TA conformation more than other bases relative to the A-DNA conformation, but not relative to the B-DNA conformation.

DNA↗
PubMed2006

Postcolumn nucleic acid intercalation for the fluorescent detection of nucleic acids using ion pair reverse phase high-performance liquid chromatography.

Here we report a simple and effective procedure enabling the fluorescent detection of nucleic acids following the rapid, high-resolution separation using ion pair reverse phase chromatography. This approach uses postcolumn nucleic acid intercalation of fluorescent dyes with subsequent fluorescent detection, demonstrating more than a 1000-fold increase in sensitivity in the detection of nucleic acids when compared with traditional UV detection. Moreover, a wide range of intercalating dyes can be incorporated, including those known to disrupt the structure of the nucleic acids, thereby enabling the sensitive detection of DNA and RNA with no adverse effect on resolution of the nucleic acids during ion pair reverse phase chromatography. In addition, such approaches allow one to readily distinguish single-stranded DNA from double-stranded DNA following their separation using ion pair reverse phase high-performance liquid chromatography.

Chromatography, High Pressure Liquid↗
PubMed2001

Influences of non-selective interactions of nucleic acids on response rates of nucleic acid fiber optic biosensors.

The immobilization of oligonucleotides to solid surfaces can provide a platform of chemistry that is suitable for the development of biosensor and microarray technologies. Experiments were performed using a fiber optic nucleic acid biosensor based on total internal reflection fluorescence to examine the effects of the presence of non-complementary DNA on the detection of hybridization of complementary target DNA. The work has focused on the rates and extent of hybridization in the presence and absence of non-selective adsorption using fluorescein-labeled DNA. A stop-flow system of 137 microL volume permitted rapid introduction and mixing of each sample. Response times measured were on the order of seconds to minutes. Non-selective adsorption of non-complementary oligonucleotides (ncDNA) was found to occur at a significantly faster rate than hybridization of complementary oligomers (cDNA) in all cases. The presence of ncDNA oligonucleotides did not inhibit selective interactions between immobilized DNA and cDNA in solution. The presence of high concentrations of non-complementary genomic DNA had little effect on the extent of hybridization of complementary oligonucleotides, but actually reduced the response times of sensors to cDNA oligonucleotides.

Biosensing Techniques↗
PubMed2000

Extension of biochemical functions by the introduction of nonnatural amino acids and artificial nucleic acid analogs.

Extension of biochemical functions has been attempted by introducing nonatural amino acids and artificial nucleic acid analogs. Nonnatural amino acids have been linked to tRNAs and the amino-acylated tRNAs were added to E. coli in vitro protein synthesizing system to produce nonnatural mutant proteins. The positions of the nonnatural amino acids have been assigned by the 4-base codons, like CGGG and AGGU. The extended codons have been introduced at a specific position or at random positions on a DNA. In the latter case, a DNA library that contains a single 4-base codon at random positions can be obtained. The combination of these new techniques opens a way to the introduction of artificial functions to biochemical systems.

Amino Acids↗
PubMed1998

A theoretical analysis of specificity of nucleic acid interactions with oligonucleotides and peptide nucleic acids (PNAs).

We treat theoretically the problem of the specificity of interaction between nucleic acid and an oligonucleotide, its analog or its mimic (such as peptide nucleic acid, or PNA). We consider simplest models with only essential details using numerical solutions of kinetic equations and the kinetic Monte Carlo method. In our first model, describing the formation of complementary duplex, we demonstrate anti-correlation between specificity and affinity for nucleic acid/oligonucleotide interaction. We analyze in detail one notable exception. Homopyrimidine PNAs exhibit very high affinity to DNA forming extraordinarily stable DNA/(PNA)2 triplexes with the complementary DNA strand. At the same time, such PNAs show remarkable sequence specificity of binding to duplex DNA. We formulate a theoretical model for the two-step process of PNA interaction with DNA. The calculations demonstrate that two-stage binding may secure both high affinity and very high specificity of PNA interaction with DNA. Our computer simulations define the range of parameter values in which high specificity is achieved. These findings are of great importance for numerous applications of PNA and for design of future drugs which specifically interact with DNA.

Base Composition↗