A method for quantification of absolute amounts of nucleic acids by (RT)–PCR and a new mathematical model for data analysis

Accurate quantification of nucleic acids by competitive (RT)–PCR requires a valid internal standard, a reference for data normalization and an adequate mathematical model for data analysis. We report here an effective procedure for the generation of homologous RNA internal standards and a strategy for synthesizing and using a reference target RNA in quantification of absolute amounts of nucleic acids. Further, a new mathematical model describing the general kinetic features of competitive PCR was developed. The model extends the validity of quantitative competitive (RT)–PCR beyond the exponential phase. The new method eliminates the errors arising from different amplification efficiencies of the co-amplified sequences and from heteroduplex formation in the system. The high accuracy (relative error <2%) is comparable to the recently developed real time detection 5′-nuclease PCR. Also, corresponding computer software has been devised for practical data analysis.     

Electric chips for rapid detection and quantification of nucleic acids

A silicon chip-based electric detector coupled to bead-based sandwich hybridization (BBSH) is presented as an approach to perform rapid analysis of specific nucleic acids. A microfluidic platform incorporating paramagnetic beads with immobilized capture probes is used for the bio-recognition steps. The protocol involves simultaneous sandwich hybridization of a single-stranded nucleic acid target with the capture probe on the beads and with a detection probe in the reaction solution, followed by enzyme labeling of the detection probe, enzymatic reaction, and finally, potentiometric measurement of the enzyme product at the chip surface. Anti-DIG-alkaline phosphatase conjugate was used for the enzyme labeling of the DIG-labeled detection probe. p-Aminophenol phosphate (pAPP) was used as a substrate. The enzyme reaction product, p-aminophenol (pAP), is oxidized at the anode of the chip to quinoneimine that is reduced back to pAP at the cathode. The cycling oxidation and reduction of these compounds result in a current producing a characteristic signal that can be related to the concentration of the analyte. The performance of the different steps in the assay was characterized using in vitro synthesized RNA oligonucleotides and then the instrument was used for analysis of 16S rRNA in Escherichia coli extract. The assay time depends on the sensitivity required. Artificial RNA target and 16S rRNA, in amounts ranging from 10(11) to 10(10) molecules, were assayed within 25 min and 4 h, respectively.     

Protein standard absolute quantification (PSAQ) method for the measurement of cellular ubiquitin pools

The protein ubiquitin is an important post-translational modifier that regulates a wide variety of biological processes. In cells, ubiquitin is apportioned among distinct pools, which include a variety of free and conjugated species. Although maintenance of a dynamic and complex equilibrium among ubiquitin pools is crucial for cell survival, the tools necessary to quantify each cellular ubiquitin pool have been limited. We have developed a quantitative mass spectrometry approach to measure cellular concentrations of ubiquitin species using isotope-labeled protein standards and applied it to characterize ubiquitin pools in cells and tissues. Our method is convenient, adaptable and should be a valuable tool to facilitate our understanding of this important signaling molecule.     

Nucleic acid capture assay,a new method for direct quantitation of nucleic acids

Technologies allowing direct detection of specific RNA/DNA sequences occasionally serve as an alternative to amplification methods for gene expression studies. In these direct methods the hybridization of probes takes place in complex mixtures, thus specificity and sensitivity still limit the use of current technologies. To address these challenges, we developed a new technique called the nucleic acid capture assay, involving a direct multi-capture system. This approach combines a 3′-ethylene glycol scaffolding with the incorporation of 2′-methoxy deoxyribonucleotides in the capture sequences. In our design, all nucleotides other than those complementary to the target mRNA have been replaced by an inert linker, resulting in significant reductions in non-specific binding. We also provide a versatile method to detect the presence of captured targets by using specific labeled probes with alkaline phosphatase-conjugated anti-label antibodies. This direct, flexible and reliable technique for gene expression analysis is well suited for high-throughput screening and has potential for DNA microarray applications.     

Quantitative determination method of nucleic acids by enzymatic amplification (PCR method) to saturation]

We describe here conditions under which the enzymatic amplification of DNA using the polymerase chain reaction (PCR) is quantitative, even when the amplification reaction is run to saturation. DNA in the sample to analyze is co-amplified with known quantities of an internal standard, namely a DNA molecule whose sequence or length differs from that of the sample DNA by only a few base pairs. The two amplification products are detected as run-off products elongated from one or several additional labelled, primers. The ratio between the two signals provides a precise estimate of the amount of specific DNA in the sample to analyze.     

A perturbation method for the analysis of impulse propagation in a mathematical neuron model

A perturbation method is presented for the calculation of signal propagation velocities in a mathematical neuron model. Impulse frequencies and waveforms are also determined. The method uses a non-linear conduction model containing a small parameter, such that analytical solutions are possible, yet the inherently non-linear physiological phenomena involved, can be explained. A simple two-variable membrane equation is used, but the method is generally applicable to various more complete systems.     

A mathematical analysis of a model for tumour angiogenesis

In order to accomplish the transition from avascular to vascular growth, solid tumours secrete a diffusible substance known as tumour angiogenesis factor (TAF) into the surrounding tissue. Neighbouring endothelial cells respond to this chemotactic stimulus in a well-ordered sequence of events comprising, at minimum, of a degradation of their basement membrane, migration and proliferation. A mathematical model is presented which takes into account two of the most important events associated with the endothelial cells as they form capillary sprouts and make their way towards the tumour i.e. cell migration and proliferation. The numerical simulations of the model compare very well with the actual experimental observations. We subsequently investigate the model analytically by making some relevant biological simplifications. The mathematical analysis helps to clarify the particular contributions to the model of the two independent processes of endothelial cell migration and proliferation.     

A fluorimetric method for the determination of nucleic acids using Ce(IV) and sodium triphosphate.

A novel and stable fluorimetric method was established for the determination of nucleic acids. The proposed method is based on the reduction by nucleic acids of Ce(IV) to fluorescent Ce(III). The fluorescence intensity can be greatly increased by sodium triphosphate. The enhanced fluorescence intensity is proportional to the concentration of nucleic acids in the range 4.2 x 10(-8)-4.2 x 10(-6) g/mL for fish sperm DNA and 5.0 x 10(-8)-6.5 x 10(-6) g/mL for yeast RNA, and the detection limits (S/N = 3) are 13.5 ng/mL and 45 ng/mL, respectively. The reaction mechanism of the hydrolytic scission of nucleic acids by Ce(IV) is discussed.     

The peptide nucleic acids (PNAs): a new generation of probes for genetic and cytogenetic analyses

Peptide nucleic acids (PNAs) are synthetic homologs of nucleic acids in which the phosphate-sugar polynucleotide backbone is replaced by a flexible pseudo-peptide polymer to which the nucleobases are linked. This structure gives PNAs the capacity to hybridize with high affinity and specificity to complementary sequences of DNA and RNA, and also confers remarkable resistance to DNAses and proteinases. The unique physico-chemical characteristics of PNAs have led to the development of a wide range of biological assays. Several exciting new applications of PNA technology have been published recently in genetics and cytogenetics. Also, PNA-based hybridization technology is developing rapidly within the field of in situ fluorescence hybridization, pointing out the great potential of PNA probes for chromosomal investigations.     

Interactions in the metabolism of polyunsaturated fatty acids: analysis by a simple mathematical model

Interactions in the metabolism of polyunsaturated fatty acids have been simulated in a simple model system. In the development of this system it was assumed that simple competitive inhibition occurs between parent acids as they are transformed (via dehydrogenation and chain lengthening) to their derivative acids. Numerical solutions of this model system give the composition of the tissue pool of polyunsaturated acids as a function of the proportion of the parent acids in the diet. Experimental data have been analyzed in the light of relations generated by the model system and the parallels observed substantiate the assumptions postulated in the development of the model system.     

Synthesis and nucleic acids binding properties of diastereomeric aminoethylprolyl peptide nucleic acids (aepPNA)

A general synthetic method for Fmoc-protected monomers of all four diastereomeric aminoethyl peptide nucleic acid (aepPNA) has been developed. The key reaction is the coupling of nucleobase-modified proline derivatives and Fmoc-protected aminoacetaldehyde by reductive alkylation. Oligomerization of the aepPNAs up to 10mer was achieved by Fmoc-solid phase peptide synthesis methodology. Preliminary binding studies of these aepPNA oligomers with nucleic acids suggested that the "cis-" homothymine aepPNA decamers with (2'R,4'R) and (2'S,4'S) configurations can bind, albeit with slow kinetics, to their complementary RNA [poly(adenylic acid)] but not to the complementary DNA [poly(deoxyadenylic acid)]. On the other hand, the trans homothymine aepPNA decamers with (2'R,4'S) and (2'S,4'R) configurations failed to form stable hybrid with poly(adenylic acid) and poly(deoxyadenylic acid). No hybrid formation could be observed between a mixed-base (2'R,4'R)-aepPNA decamer with DNA and RNA in both antiparallel and parallel orientations.     

The peptide nucleic acids (PNAs): introduction to a new class of probes for chromosomal investigation

Peptide nucleic acids (PNAs) are synthetic DNA mimics in which the sugar phosphate backbone is replaced by repeating N-(2-aminoethyl) glycine units linked by an amine bond and to which the nucleobases are fixed. Peptide nucleic acids hybridize with complementary nucleic acids with remarkably high affinity and specificity, essentially because of their uncharged and flexible polyamide backbone. The unique physicochemical properties of PNAs have led to the development of a large variety of biological research assays, and, over the last few years, PNAs have proved their powerful usefulness in genetic and cytogenetic diagnostic procedures. Several sensitive and robust PNA-dependent methods have been designed for modulating polymerase chain reactions, detecting genomic mutation or capturing nucleic acids. The more recent applications of PNA involve their use as molecular hybridization probes. Thus, the in situ detection of several human chromosomes has been reported in various types of tissues.Communicated by E.A. Nigg     

A method for the recovery of nucleic acids from polyacrylamide gels

A method is described for the recovery of RNA from ethylene diacrylate cross-linked polyacrylamide gels. The RNA is recovered undergraded in good yields under mild conditions and is free of soluble polyacrylamide gels.