The effects of nested primer binding sites on the reproducibility of PCR: mathematical modeling and computer simulation studies

Talking the talk, but not walking the walk: RT-qPCR as a paradigm for the lack of reproducibility in molecular research

Poorly executed and inadequately reported molecular measurement methods are amongst the causes underlying the lack of reproducibility of much biomedical research. Although several high impact factor journals have acknowledged their past failure to scrutinise adequately the technical soundness of manuscripts, there is a perplexing reluctance to implement basic corrective measures. The reverse transcription real-time quantitative PCR (RT-qPCR) is probably the most straightforward measurement technique available for RNA quantification and is widely used in research, diagnostic, forensic and biotechnology applications. Despite the impact of the minimum information for the publication of quantitative PCR experiments (MIQE) guidelines, which aim to improve the robustness and the transparency of reporting of RT-qPCR data, we demonstrate that elementary protocol errors, inappropriate data analysis and inadequate reporting continue to be rife and conclude that the majority of published RT-qPCR data are likely to represent technical noise.

Validation and estimation of parameters for a general probabilistic model of the PCR process

Earlier work rigorously derived a general probabilistic model for the PCR process that includes as a special case the Velikanov-Kapral model where all nucleotide reaction rates are the same. In this model, the probability of binding of deoxy-nucleoside triphosphate (dNTP) molecules with template strands is derived from the microscopic chemical kinetics. A recursive solution for the probability function of binding of dNTPs is developed for a single cycle and is used to calculate expected yield for a multicycle PCR. The model is able to reproduce important features of the PCR amplification process quantitatively. With a set of favorable reaction conditions, the amplification of the target sequence is fast enough to rapidly outnumber all side products. Furthermore, the final yield of the target sequence in a multicycle PCR run always approaches an asymptotic limit that is less than one. The amplification process itself is highly sensitive to initial concentrations and the reaction rates of addition to the template strand of each type of dNTP in the solution. This paper extends the earlier Saha model with a physics based model of the dependence of the reaction rates on temperature, and estimates parameters in this new model by nonlinear regression. The calibrated model is validated using RT-PCR data.

A general probabilistic model of the PCR process

This work describes a general probabilistic model for the PCR process; this model includes as a special case the Velikanov-Kapral model where all nucleotide reaction rates are the same. In this model the probability of binding of deoxynucleoside triphosphate (dNTP) molecules with template strands is derived from the microscopic chemical kinetics. A recursive solution for the probability distribution of binding of dNTPs is developed for a single cycle and is used to calculate expected yield for a multicycle PCR. The model is able to reproduce important features of the PCR amplification process quantitatively. This model also suggests that the amplification process itself is highly sensitive to initial concentrations and the reaction rates of addition to the template strand of each type of dNTP in the solution.

Polymerase chain reaction: a Markov process approach

A probabilistic approach to the kinetics of the polymerase chain reaction (PCR) is developed. The approach treats the primer extension step of PCR as a microscopic Markov process in which the molecules of deoxy-nucleoside triphosphate (dNTP) are bound to the 3' end of the primer strand one at a time. The binding probability rates are prescribed by combinatorial rules in accord with the microscopic chemical kinetics. As an example, a simple model based on this approach is proposed and analysed, and an exact solution for the probability distribution of lengths of synthesized DNA strands is found by analytical means. Using this solution, it is demonstrated that the model is able to reproduce the main features of PCR, such as extreme sensitivity to the variation of control parameters and the existence of an amplification plateau. A multidimensional optimization technique is used to find numerically the optimum values of control parameters which maximize the yield of the target sequence for a given PCR run while minimizing the overall run time.

Features of DNA fragments obtained by random amplified polymorphic DNA (RAPD) assays

Random amplified polymorphic DNA (RAPD) fragments were prepared from samples of Calonectris diomedea (Cory's shearwater, Aves) and Haemonchus contortus (Nematoda) DNA by polymerase chain reaction (PCR) using decamers containing two restriction enzyme sites as primers. Six of 19 studied RAPD fragments probably originated from traces of commensal microorganisms. Many rearranged fragments, absent in the original genomic DNA, were synthesized and amplified during the processing of all the DNA samples, indicating that interactions occur within and between strands during the annealing step of PCR. The model of interactions between molecular species during DNA amplification with a single arbitrary oligonucleotide primer was modified to include nested primer annealing and interactions within and between strands. The presence of these artefacts in the final RAPD have a major effect on the interpretation of polymorphism studies.

Scanning of nucleic acids by in vitro amplification: new developments and applications

Nucleic acids can be characterized using a variety of "fingerprinting" techniques usually based on nucleic acid hybridization or enzymatic amplification. The scanning of nucleic acids by amplification with arbitrary oligonucleotide primers has become popular because it can generate simple-to-complex patterns from anonymous DNA or RNA templates without requiring prior knowledge of nucleic acid sequence or cloned or characterized probes. Discrete loci are amplified within genomic DNA, DNA complementary to mRNA populations (cDNA), cloned DNA fragments, and even PCR products. The potential and limitations of the various genome scanning techniques, novel improvements, and their recent use in comparative and experimental biology applications, including the analysis of plant and bacterial genomes are discussed.