DNA sequencing by denaturation: principle and thermodynamic simulations

Evaluation of current methods to detect the mutations of epidermal growth factor receptor in non-small cell lung cancer patients

Many different methods were developed to detect commonly known mutations and to screen new mutations of the epidermal growth factor receptor in non-small cell lung cancer patients. Some of these methods are so sensitive as to be able to detect even one epidermal growth factor receptor mutant tumor cell among up to 1000–2000 normal cells. We have considered current methods chronologically reported to detect mutations in epidermal growth factor receptor in patients with non-small cell lung cancer. We also gave a short preview of their significance for routine clinical works. A Pub Med literature search was performed in order to demonstrate what methods are mostly used in mutation detection and to show their distribution through the last 10 years.

Multifractal analysis of thermal denaturation based on the Peyrard-Bishop-Dauxois model

The theory of DNA dynamics is exceedingly complex and not easily explained. In the past two decades, by adapting methods of statistical physics, the dynamics of DNA in contact with a thermal bath is widely studied. In this paper, the thermal denaturation of DNA in the framework of the Peyrard-Bishop-Dauxois (PBD) model through the Rényi dimension is investigated. As a result, the Rényi dimension spectrum of the melting transition process reveals the multifractal nature of the dynamics of the Peyrard-Bishop-Dauxois model. Also, it can be concluded that the Rényi dimension (D(q)) at negative values of q is the characteristic signature of pre-melting and thermal denaturation of DNA. Furthermore, this approach is in excellent agreement with previous experimental studies.

Non-contact fluorescent bleaching-independent method for temperature measurement in microfluidic systems based on DNA melting curves

This report introduces a bleaching-independent temperature measurement method based on the analysis of the fluorescence emitted during the melting of DNA molecules with the SYBR-Green I intercalator, in a microvolume where the strong non-linearity of the signal is used to eliminate the photobleaching effect as well as to determine the heat transfer rate between a heater and the sample and the temperature non-uniformity within the sample.

Nucleotide extension genotyping by high-resolution melting

One limitation of small amplicon melting is the inability to genotype certain nearest-neighbor symmetric variations without manipulating the sample. We have developed a method for these exceptions: a high-resolution melting single nucleotide extension assay. Single nucleotide extension was performed in a new instrument, the LightScanner 32 (LS32), which uses capillary reaction tubes and is capable of real-time PCR and sequential high-resolution melting of 32 samples. Asymmetric PCR used Platinum Taq and LC Green Plus in the master mix for target amplification. Dideoxynucleotides and extension oligonucleotides were sequestered in the tube cap and added post-PCR, maintaining a closed system. One dideoxynucleotides was used per capillary tube. Samples were cycled five times to incorporate dideoxynucleotides into the extension products using ThermoSequenase, followed by high-resolution melting. Single nucleotide polymorphisms from the RET proto-oncogene (n = 7), hemochromatosis (HFE, n = 30), coagulation factor 2 (F2, n = 29), coagulation factor 5 (F5, n = 30), and methylenetetrahydrofolate reductase (MTHFR, n = 60) genes were genotyped. The DNA melting profiles identified the target single nucleotide polymorphisms by the lowest melting temperature transition. All genotypes had a distinctive melting pattern. The method was 100% concordant with samples previously genotyped at HFE, MTHFR, and F2 and 90% concordant with F5. F5 discordants were genotyped correctly by redesigning the assay. Our results demonstrate that although single nucleotide polymorphisms can be successfully differentiated using this methodology, the method requires careful optimization.

DNA sequencing by denaturation: experimental proof of concept with an integrated fluidic device

We report the proof of concept of a novel DNA sequencing technology called sequencing by denaturation (SBD). SBD is based on the Sanger sequencing reaction performed on amplified target templates immobilized on a solid surface followed by the denaturation of these Sanger fragments. As these fluorescently labeled fragments denature sequentially, the fluorescence intensities in the four channels corresponding to the four base types are monitored in a flow cell. A sequencing instrument with a microfluidic flowcell has been custom-designed to integrate automated fluidics, temperature control, and fluorescence imaging. The denaturation profiles of several synthetic oligonucleotides were measured with this system and our data demonstrated the ability to sequence short DNA by SBD. SBD is a simple and fast method with the potential to improve the speed and cost of large-scale genome re-sequencing.

Classification of DNA sequences based on thermal melting profiles

A new classification scheme based on the melting profile of DNA sequences simulated thermal melting profiles. This method was applied in the classification of (a) several species of mammalian - β globin and (b) α-chain class II MHC genes. Comparison of the thermal melting profile with the molecular phylogenetic trees constructed using the sequences shows that the melting temperature based approach is able to reproduce most of the major features of the sequence based evolutionary tree. Melting profile method takes into account the inherent structure and dynamics of the DNA molecule, does not require sequence alignment prior to tree construction, and provides a means to verify the results experimentally. Therefore our results show that melting profile based classification of DNA sequences could be a useful tool for sequence analysis.