Museums and pathology collections around the world represent an archive of genetic material to study populations and diseases. For preservation purposes, a large portion of these collections has been fixed in formalin-containing solutions, a treatment that results in cross-linking of biomolecules. Cross-linking not only complicates isolation of nucleic acid but ...

Site-specific modification of nucleic acid is of great significance in the machinery of gene expression. Specific modification of nucleic acids by an oligonucleotide incorporating a S-vinyl thioguanosine analog, has great potential as a useful tool. The specific transfer of the vinyl derivative to the amino group of dC at the ...

The tricyclic cytosine, tC, is a fluorescent base analogue with excellent properties for investigating intrinsic characteristics of nucleic acid as well as interactions between nucleic acids and other molecules. Its unique fluorescence properties and insignificant influence on overall structure and dynamics of nucleic acid after incorporation makes tC particularly interesting ...

Nucleoside analogues are chemical means to investigate hydrogen bonds, base stacking, and solvation as the three predominant forces that are responsible for the stability of secondary structure of nucleic acids. To obtain deeper insight into the contributions of these interactions to RNA stability apart from the ones exerted by the ...

Nucleic-acid-induced polymerisation of prion protein, when monitored by anilino naphthalene sulfonic acid dye, shows, successively, an immediate fluorescence increase of the dye upon mixing of the reactants, followed by a lag period in which the dye fluorescence remains unchanged, and then a phase in which dye fluorescence increases with time. ...

Aptamers are rare nucleic acid ligands, which can be concocted in the laboratory from the randomized pool of molecules by affinity and amplification processes. Aptamers have several properties as they can be applied complementarily to antibodies and have several advantages over antibodies. In the past, several aptamers have been selected ...

The synthesis of backbone-modified nucleic acids has been an area of very intense research over the last two decades. The main reason for this research activity is the instability of nucleic acid based drugs in the intracellular conditions. Changes in the sugar-phosphate backbone invariably bring about the changes in the ...

We newly designed and synthesized a 2'-deoxy type trans-3',4'-bridged nucleic acid (trans-3',4'-BNA) analogues bearing a 4,7-dioxabicyclo[4.3.0]nonane structure. The synthesis of the trans-3',4'-BNA was carried out successfully from thymidine over 21 steps. The structure of trans-3',4'-BNA was confirmed by x-ray crystallographic analysis, indicating that the furanose ring has a typical S-type ...

We herein describe the introduction of gem-dimethyl substitution into the aminoethylglycyl backbone of PNA to impart steric constraint and pre-organise PNA for selective recognition of nucleic acids. Introduction of cyanuric acid and 8-aminoadenine as pyrimidine and purine analogs that can form base pairing from either face is also described to ...

This protocol describes a simplified means of introducing an anomalously scattering atom into oligonucleotides by conventional solid-phase synthesis. Replacement of a nonbridging phosphate oxygen in the backbone with selenium is practically suitable for any nucleic acid. The resulting oligonucleotide P-diastereomers can be separated using anion exchange HPLC to yield diastereomerically ...

Diatoms are unicellular photoautotrophic eukaryotes that play an important role in ecology by fixing large amounts of CO2 in the oceans. Because they evolved by secondary endocytobiosis--a process of uptake of a eukaryotic alga into another eukaryotic cell--they have a rather unusual cell biology and genetic constitution. Diatoms are also ...

Two highly fluorescent compounds, viz. 6-(6-isobutyrylamino-1,3-dioxo-1 H,3H-benzo[de]isoquinolin-2-yl)-hexanoic acid and 6-(6-dimethylamino-1,3-dioxo-1 H,3H-benzo[de]isoqu-inolin-2-yl)-hexanoic acid have been synthesized, characterized, and attached to 12-mer oligodeoxyribonucleotides at their 5'-end using suitable linker molecule. These labeled oligodeoxyribonucleotides have shown appreciable fluorescence even at 0.0019 microM concentrations. Thermal denaturation studies have shown comparatively higher Tm values when ...

The last decade has witnessed an impressive upsurge in the utilization of microarray platforms for biomedical research. However, the application of this emerging technology in medical practice lagged behind. This lag is understandable because there are specific issues pertaining to the utilization of clinical samples, which has to be rigorously ...

BACKGROUND: The Proteomic Code is a set of rules by which information in genetic material is transferred into the physico-chemical properties of amino acids. It determines how individual amino acids interact with each other during folding and in specific protein-protein interactions. The Proteomic Code is part of the redundant Genetic ...

Nucleic acid polymerases have similar structures and motifs. The function of an aspartic acid (conserved in all classes of nucleic acid polymerases) in motif A remains poorly understood in RNA-dependent RNA polymerases. We mutated this residue to alanine in a poliovirus replicon. The resulting mutant could still replicate, although at ...

In site-directed spin labeling (SDSL), a nitroxide moiety containing a stable, unpaired electron is covalently attached to a specific site within a macromolecule, and structural and dynamic information at the labeling site is obtained via electron paramagnetic resonance (EPR) spectroscopy. Successful SDSL requires efficient site-specific incorporation of nitroxides. Work reported ...

Widely used nucleic acid assays are poorly suited for field deployment where access to laboratory instrumentation is limited or unavailable. The need for field deployable nucleic acid detection demands inexpensive, facile systems without sacrificing information capacity or sensitivity. Here we describe a novel microarray platform capable of rapid, sensitive nucleic ...

Nucleic acid double helices are stabilized by hydrogen bonding and stacking forces (a combination of hydrophobic, dispersive and electrostatic forces) of the base pairs in the helix. One would predict the hydrogen bonding contributions to increase and the stacking contributions to decrease as the water activity in the medium decreases. ...

Some selected amino acids, in particular L-aspartic acid (L-Asp) and L-histidine (L-His), can function as leaving group during polymerase-catalyzed incorporation of deoxyadenosine monophosphate (dAMP) in DNA. Although L-Asp-dAMP and L-His-dAMP bind, most probably, in a different way in the active site of the enzyme, aspartic acid and histidine can be ...

Copy of author's previously published work, inserted.

The emergence and re-emergence of transboundary animal diseases (TADs), e.g., foot-and-mouth disease, classical swine fever and the highly pathogenic avian influenza strongly indicate the need for the development of powerful and robust new diagnostic methods. The experiences of an OIE-Collaborating Centre and of two EU project consortia are summarised on ...

Novel organic sensitizers comprising donor, electron-conducting, and anchoring groups were engineered at molecular level and synthesized. The functionalized unsymmetrical organic sensitizers 3-{5-[N,N-bis(9,9-dimethylfluorene-2-yl)phenyl]-thiophene-2-yl}-2-cyano-acrylic acid (JK-1) and 3-{5'-[N,N-bis(9,9-dimethylfluorene-2-yl)phenyl]-2,2'-bisthiophene-5-yl}-2-cyano-acrylic acid (JK-2), upon anchoring onto TiO2 film, exhibit unprecedented incident photon to current conversion efficiency of 91%. The photovoltaic data using an electrolyte having ...

Here, we report a novel method of micropatterning oligonucleotides via aromatic groups as linkers on partially amino-terminated diamond and the inherence on subsequent hybridization. The covalent immobilization of probe oligonucleotides and characterization of immobilized probe oligonucleotides with carboxylic compounds were investigated by X-ray photoelectron spectroscopy (XPS). To confirm the effects ...

Single-stranded nucleic acids, which carry multiple negative charges in an aqueous medium at near neutral pH, are found to induce the aggregation and self-assembly of the positively charged alkynylplatinum(II) terpyridyl complexes via electrostatic binding of the platinum complexes to the single-stranded nucleic acids, as revealed by the appearance of new ...

High hydrostatic pressure (HHP) technique was used to evaluate a mechanism of RNA hydrolysis with RNA. We showed that hammerhead ribozyme specifically cleaves RNA substrate at HHP in the absence of Mg(2+). A deoxyribozyme "10-23" was active in the same conditions. These results pointed out that the hydrolytic activity of ...

The design of modified nucleic acid aptamers is improved by considering thermodynamics and kinetics of their association/dissociation processes. Locked Nucleic Acids (LNA) is a promising class of nucleic acid analogs. In this work the thermodynamic and kinetic properties of a LNA quadruplex formed by the TGGGT sequence, containing only conformationally ...

Biological organisms perform complex information processing and control tasks using sophisticated biochemical circuits, yet the engineering of such circuits remains ineffective compared with that of electronic circuits. To systematically create complex yet reliable circuits, electrical engineers use digital logic, wherein gates and subcircuits are composed modularly and signal restoration prevents ...

Ion pair formation between timolol and sorbic acid was investigated using NMR spectroscopy in order to clarify their interactions within ophthalmic preparation. (13)C and (1)H NMR spectra of timolol, sorbic acid, and a mixture of the two were obtained, and the signal changes induced by pairing were observed. The carbon ...

One of the most prominent amino acids to appear in monomer-generating origin-of-life experiments is aspartic acid. Hugo Schiff found in 1897 that aspartic acid polymerizes when heated to form polyaspartylimide which hydrolyzes in basic aqueous solution to form thermal polyaspartic acid which is a branched polypeptide. We recently reported at ...

Manganese chloride can form large particles with nucleic acids by electrostatic forces, which results in strong enhancement of resonance light scattering (RLS) signals. Based on this phenomenon, a novel and very simple assay of DNA was established. The work conditions have been investigated including the concentration of probe, the acidity ...

The interactions of yttrium with N,N'-ethylenebis[2-(o-hydroxyphenolic)glycine] (EHPG) and N,N'-di(2-hydroxybenzyl)ethylenediamine-N,N'-diacetic acid (HBED) are investigated by using UV difference and fluorescence spectra methods in 0.1M N-2-hydroxyethylpiperazine-N-2-ethanesulfonic acid (Hepes) at pH 7.4. Yttrium binding produces two UV difference peaks near 240 and 294 nm, respectively, that both are the characteristic of phenolic groups ...

Helicases mode of unwinding the nucleic acids and translocation along single stranded nucleic acids is still a subject of great curiosity. Based on the energy transduction and electrophilic interactions, we present a model to explain the mode of action of active helicases. This model considers that both strand separation as ...

BACKGROUND: Nucleic acid isolation, the most technically demanding and laborious procedure performed in molecular diagnostics, harbors the potential for improvements in automation. A recent development is the use of magnetic beads covered with nucleic acid-binding matrices. We adapted this technology with a broad-range 23S rRNA real-time reverse transcription (RT)-PCR assay ...

The CASPT2//CASSCF method with the 6-31G basis set and an active space up to (16,12) was used to calculate the excitation energies for six tautomers of guanine. Our calculations provide further support on the recent reassignment of the near-UV resonant two-photon ionization (R2PI) spectrum, in which two rare tautomers of ...

This contribution reviews some general aspects of the quaternary iminium protoberberine alkaloids. The alkaloids represent a very extensive group of secondary metabolites with diverse structures, distribution in nature, and biological effects. The quaternary protoberberine alkaloids (QPA), derived from the 5,6-dihydrodibenzo[a,g]quinolizinium system, belong to a large class of isoquinoline alkaloids. Following ...

This work reports a kind of novel bilayer lipid membranes (BLMs) nucleic acid biosensor supported by modified patch-clamp pipette electrode was developed to detect staphylococcus enterotoxins B (SEB) gene. BLMs were formed within 15 min and able to be operated at least 24 h. Hydrophobic dodecane tail (C12) modified 18 ...

Because the fluorescence of azur A can be quenched by adding nucleic acid, a sensitive fluorometric method for determination of nucleic acids at nanogram levels was established. Using optimal conditions, the calibration curves were linear in the range of 0-6.0 microg/mL for calf thymus deoxyribonucleic acid (ct DNA) and 0-7.0 ...

The potential of storing complete frozen real-time polymerase chain reactions (PCRs) and real-time reverse transcription PCRs (RT-PCRs), which require only thawing and the addition of template nucleic acid before PCR cycling, was examined. Master mixes containing all necessary reagents at working concentration (except template nucleic acid) were aliquoted into single-reaction ...

There are numerous molecular modifications known to occur in cancer. New nucleic acid-based biomarkers provide a unique approach to patient management in urologic oncology. Malignant transformation of a normal cell requires a series of epigenetic and genetic changes or "hits." Epigenetics produced by deoxyribonucleic acid methylation, adding a methyl group ...

SELEX (systematic evolution of ligands by exponential enrichment) is a process that involves the progressive purification from a combinatorial library of nucleic acid ligands with a high affinity for a particular target by repeated rounds of partitioning and amplification. With the development of aptamer technology over the last decade, various ...

Nucleic acid separation is an increasingly important tool for molecular biology. Before modern technologies could be used, nucleic acid separation had been a time- and work-consuming process based on several extraction and centrifugation steps, often limited by small yields and low purities of the separation products, and not suited for ...

Prions, the infectious agents of transmissible spongiform encephalopathies (TSEs), have defied full characterization for decades. The dogma has been that prions lack nucleic acids and are composed of a pathological, self-inducing form of the host's prion protein (PrP). Recent progress in propagating TSE infectivity in cell-free systems has effectively ruled ...

Nucleic Acids composed of the five natural bases and a phosphate backbone can be designed or evolved to have a wide variety of sequence-dependent functions. Recent in vitro work has addressed some outstanding issues in evolving nucleic acid catalysts, as well as the creation of prescribed shapes and arrays from ...

The absolute proton affinities of the nonprotein amino acids canavanine and canaline have been determined using the extended kinetic method in an electrospray ionization quadrupole ion trap instrument. Canavanine results from the substitution of an oxygen atom for the delta-CH2 group in the side chain of the protein amino acid ...

The present work characterizes the gas-phase stacking interactions between four aromatic amino acid residues (histidine, phenylalanine, tyrosine, and tryptophan) and adenine or 3-methyladenine due to the proposed utilization of these interactions by enzymes that repair DNA alkylation damage. The MP2 potential energy surfaces of the stacked dimers are considered as ...

Immunoassays have been well established for many years as the cornerstone of detection technologies. These assays are sensitive, selective and, in general, highly resistant to interference from complex sample matrices when compared with nucleic acid-based tests. However, both antibody- and nucleic acid-based detection systems require a priori knowledge of the ...

Our work is motivated by the belief that RNA targeted gene silencing agents can be developed into effective drugs for treating hematologic malignancies. In many experimental systems, antisense nucleic acids of various composition, including antisense oligodeoxynucleotides (AS ODNs) and short interfering RNA (siRNA), have been shown to perturb gene expression ...

Clinical studies indicate relationships between dental plaque, a naturally formed biofilm, and oral diseases. The crucial role of nonmicrobial biofilm constituents in maintaining biofilm structure and biofilm-specific attributes, such as resistance to shear and viscoelasticity, is increasingly recognized. Concurrent analyses of the diverse nonmicrobial biofilm components for multiparameter assessments formed ...

Nucleic acids have gained a lot of interest for the treatment of ocular diseases. The first to enter in clinic has been Vitravene an antisense oligonucleotide for the treatment of cytomegalovirus (CMV) infection and more recently, research on aptamers have led to the marketing of anti-vascular endothelial growth factor (VEGF) ...

This article reviews some of the early work that has been performed to investigate the potential roles of circulating nucleic acids as prediction markers in acute illness and injury. Circulating DNA and RNA concentrations are elevated early in patients with trauma, stroke and ACS, and are generally highest in patients ...