Quantitative fluorescence method for continuous measurement of DNA hybridization kinetics using a fluorescent intercalator

SHARPIN is a novel gene of colorectal cancer that promotes tumor growth potentially via inhibition of p53 expression

Colorectal cancer (CRC) is widely prevalent and represents a significant contributor to global cancer‑related mortality. There remains a pressing demand for advancements in CRC treatment modalities. The E3 ubiquitin ligase is a critical enzyme involved in modulating protein expression levels via posttranslational ubiquitin‑mediated proteolysis, and it is reportedly involved in the progression of various cancers, making it a target of recent interest in anticancer therapy. In the present study, using comprehensive expression analysis involving spatial transcriptomic analysis with single‑cell RNA sequencing in clinical CRC datasets, the ubiquitin‑associated protein Shank‑associated RH domain interactor (SHARPIN) was identified, located on amplified chromosome 8q, which could promote CRC progression. SHARPIN was found to be upregulated in tumor cells, with elevated expression observed in tumor tissues. This heightened expression of SHARPIN was positively associated with lymphatic invasion and served as an independent predictor of a poor prognosis in patients with CRC. In vitro and in vivo analyses using SHARPIN‑overexpressing or ‑knockout CRC cells revealed that SHARPIN overexpression upregulated MDM2, resulting in the downregulation of p53, while SHARPIN silencing or knockout downregulated MDM2, leading to p53 upregulation, which affects cell cycle progression, tumor cell apoptosis and tumor growth in CRC. Furthermore, SHARPIN was found to be overexpressed in several cancer types, exerting significant effects on survival outcomes. In conclusion, SHARPIN represents a newly identified novel gene with the potential to promote tumor growth following apoptosis inhibition and cell cycle progression in part by inhibiting p53 expression via MDM2 upregulation; therefore, SHARPIN represents a potential therapeutic target for CRC.

Dicationic styryl dyes for colorimetric and fluorescent detection of nucleic acids

Nucleic acid staining dyes are important tools for the analysis and visualizing of DNA/RNA in vitro and in the cells. Nevertheless, the range of commercially accessible dyes is still rather limited, and they are often very costly. As a result, finding nontoxic, easily accessible dyes, with desirable optical characteristics remains important. Styryl dyes have recently gained popularity as potential biological staining agents with many appealing properties, including a straightforward synthesis procedure, excellent photostability, tunable fluorescence, and high fluorescence quantum yield in the presence of nucleic acid targets with low background fluorescence signals. In addition to fluorescence, styryl dyes are strongly colored and exhibit solvatochromic properties which make them useful as colorimetric stains for low-cost and rapid testing of nucleic acids. In this work, novel dicationic styryl dyes bearing quaternary ammonium groups are designed to improve binding strength and optical response with target nucleic acids which contain a negatively charged phosphate backbone. Optical properties of the newly synthesized styryl dyes have been studied in the presence and absence of nucleic acid targets with the aim to find new dyes that can sensitively and specifically change fluorescence and/or color in the presence of nucleic acid targets. The binding interaction and optical response of the dicationic styryl dyes with nucleic acid were superior to the corresponding monocationic styryl dyes. Applications of the developed dyes for colorimetric detection of DNA in vitro and imaging of cellular nucleic acids are also demonstrated.

Fluorescent probes based on side-chain chlorinated benzo[a]phenoxazinium chlorides: Studies of interaction with DNA

The interaction of DNA with six water soluble benzo[a]phenoxazinium chlorides mono- or di-substituted with 3-chloropropyl groups at the O and N of 2- and 9-positions, along with methyl, hydroxyl and amine terminal groups at 5-positions, was investigated by photophysical techniques. The results indicated that almost all compounds intercalated in DNA base pairs at phosphate to dye ratio higher than 5. At lower values of this ratio, electrostatic binding mode with DNA was observed. Groove binding was detected mainly for the benzo[a]phenoxazinium dye with NH₂·HBr terminal. The set of six benzo[a]phenoxazinium chlorides proved successful to label the migrating DNA in agarose gel electrophoresis assays. These finding proves the ability of these benzo[a]phenoxazinium dyes to strongly interact with DNA.

Enhanced nonlinear optical characteristics of copper-ion-doped double crossover DNAs

The modification of deoxyribonucleic acid (DNA) samples by sequencing the order of bases and doping copper ions opens the possibility for the design of novel nanomaterials exhibiting large optical nonlinearity. We investigated the nonlinear characteristics of copper-ion doped double crossover DNA samples for the first time to the best of our knowledge by using Z-scan and four-wave mixing methods. To accelerate the nonlinear characteristics, we prepared two types of unique DNA nanostructures composed of 148 base pairs doped with copper ions with a facile annealing method. The outstanding third-order nonlinear optical susceptibility of the copper-ion-doped DNA solution, 1.19 × 10(-12) esu, was estimated by the conventional Z-scan measurement, whereas the four-wave mixing experiment was also investigated. In the visible spectral range, the copper-ion-doped DNA solution samples provided competent four-wave mixing signals with a remarkable conversion efficiency of -4.15 dB for the converted signal at 627 nm. The interactions between DNA and copper ions contribute to the enhancement of nonlinearity due to structural and functional changes. The present study signifies that the copper-ion-doped double crossover DNA is a potential candidate as a highly efficient novel material for further nonlinear optical applications.

Ethidium bromide as a marker of mtDNA replication in living cells

Mitochondrial DNA (mtDNA) in tumor cells was found to play an important role in maintaining the malignant phenotype. Using laser scanning confocal fluorescence microscopy (LSCFM) in a recent work, we reported a variable fluorescence intensity of ethidium bromide (EB) in mitochondria nucleoids of living carcinoma cells. Since when EB is bound to nucleic acids its fluorescence is intensified; a higher EB fluorescence intensity could reflect a higher DNA accessibility to EB, suggesting a higher mtDNA replication activity. To prove this hypothesis, in the present work we studied, by LSCFM, the EB fluorescence in mitochondria nucleoids of living neuroblastoma cells, a model system in which differentiation affects the level of mtDNA replication. A drastic decrease of fluorescence was observed after differentiation. To correlate EB fluorescence intensity to the mtDNA replication state, we evaluated the mtDNA nascent strands content by ligation-mediated real-time PCR, and we found a halved amount of replicating mtDNA molecules in differentiating cells. A similar result was obtained by BrdU incorporation. These results indicate that the low EB fluorescence of nucleoids in differentiated cells is correlated to a low content of replicating mtDNA, suggesting that EB may be used as a marker of mtDNA replication in living cells.

Photophysics and binding constant determination of the homodimeric dye BOBO-3 and DNA oligonucleotides

The interactions between single- and double-stranded DNA and the trimethine cyanine homodimer dye, BOBO-3 (1,1'-(4,4,7,7-tetramethyl-4,7-diazaundecamethylene)-bis-4-[3-methyl-2,3-dihydro-(benzo-1,3-thiazole)-2-methylidene]pyridinium tetraiodide), have been investigated in detail using absorption and steady-state and time-resolved fluorescence spectroscopy. The dye interacts with both single-stranded and double-stranded DNA, under a variety of conditions, with changes in its spectral characteristics. Our results indicated that the complex formed between BOBO-3 dye and DNA oligonucleotides could not be explained with a simple, single intercalation mechanism; therefore, different modes of interaction were proposed. By using time-resolved fluorescence methodology and in-depth analysis of the fluorescence decay traces, we obtained the contribution of the different forms of BOBO-3: free in solution, a low affinity, electrostatically driven interaction with DNA, and a full bis-intercalation mechanism within the DNA double helix. With this information, we applied the McGhee-Von Hippel theory for two overlapping, noncooperative binding modes to obtain equilibrium binding constants and the number of sites occupied for each binding mode. Binding constants for dye/dsDNA complexes in complete bis-intercalation and externally bound were (8.8 +/- 1.1) x 10(5) and (2.6 +/- 0.3) x 10(5) M(-1), respectively. The corresponding recovered number of base pairs covered were 5.9 +/- 0.2 and 3.5 +/- 0.5 sites for each mode.

Hybridization kinetics and thermodynamics of DNA adsorbed to individually dispersed single-walled carbon nanotubes

Hybridization of DNA adsorbed to single-walled carbon nanotubes in solution has much slower kinetics than free solution DNA, and can be detected through a blue shift in the near-infrared nanotube fluorescence. Adsorption of the receptor DNA strand to the nanotube surface is consistent with models of polyelectrolyte adsorption on charged surfaces, introducing both entropic (46.8 cal mol(-1) K(-1)) and activation energy (20.4 kcal mol(-1)) barriers to the hybridization, which are greater than free solution values (31.9 cal mol(-1) K(-1) and 12.9 kcal mol(-1)) at 25 degrees C. The increased hybridization barriers on the nanotube result in exceedingly slow kinetics for hybridization with t(1/2)=3.4 h, compared to the free solution value of t(1/2)=4 min. These results have significant implications for nanotube and nanowire biosensors.

Label-Free Single-Nucleotide Polymorphism Detection Using a Cationic Tetrahedralfluorene and Silica Nanoparticles

We developed a simple method that is able to provide label-free sequence-specific DNA detection with single-nucleotide polymorphism (SNP) detection selectivity. This method makes use of both DNA probe immobilized silica nanoparticles and optically amplifying light harvesting molecules. The recognition is accomplished by sequence-specific hybridization between the DNA probes on the silica nanoparticles and the targets of interest. After subsequent treatment with ethidium bromide (EB), a cationic tetrahedralfluorene was added to electrostatically associate with the DNA molecules on the nanoparticle surface, leading to sensitized EB emission via fluorescence resonance energy transfer (FRET). Because of the selective response of the tetrahedralfluorene to intercalated EB, the perfectly matched DNA targets were distinctively differentiated from those with mutations. The presence of tetrahedralfluorene provides improved detection sensitivity and selectivity, as compared to the use of EB alone as a signal reporter. The demonstrated highly selective label-free detection method laid the ground work for the future development of disposable and real-time testing kits in SNP screenings.

Direct measurement of T-cell receptor repertoire diversity with AmpliCot

Many studies require the measurement of nucleic acid sequence diversity. Here we describe a method, called AmpliCot, that measures the sequence diversity of PCR products on the basis of DNA hybridization kinetics, thereby avoiding the time, expense and biases associated with cloning and sequencing. SYBR Green dye is used to measure DNA hybridization kinetics in a homogeneous, automated fashion. PCR products are prepared in wholly double-stranded homoduplex form for a baseline measurement of DNA concentration. The DNA is melted and then reannealed under stringent conditions that allow only homoduplexes to form. The sequence diversity of a sample is proportional to the product of its concentration and the time required for it to anneal. After validating AmpliCot with a library of diverse sequences, we use it to measure the diversity of expressed rearrangements of the gene encoding the T-cell antigen receptor (TCR) beta chain. AmpliCot measurements are in good agreement with previous estimates of murine TCR repertoire diversity that required extensive cloning and sequencing.

Determination of nucleic acids with a near infrared cyanine dye using resonance light scattering technique

A new method for the determination of nucleic acids has been developed based on the enhancement effect of resonance light scattering (RLS) with a cationic near infrared (NIR) cyanine dye. Under the optimal conditions, the enhanced RLS intensity at 823 nm is proportional to the concentration of nucleic acids in the range of 0-400 ng mL-1 for both calf thymus DNA (CT DNA) and fish sperm DNA (FS DNA), 0-600 ng mL-1 for snake ovum RNA (SO RNA). The detection limits are 3.5 ng mL-1, 3.4 ng mL-1 and 2.9 ng mL-1 for CT DNA, FS DNA and SO RNA, respectively. Owing to performing in near infrared region, this method not only has high sensitivity endowed by RLS technique but also avoids possible spectral interference from background. It has been applied to the determination of nucleic acids in synthetic and real samples and satisfactory results were obtained.

Two-dimensional strandness-dependent electrophoresis: A method to characterize single-stranded DNA, double-stranded DNA, and RNA–DNA hybrids in complex samples

We describe two-dimensional strandness-dependent electrophoresis (2D-SDE) for quantification and length distribution analysis of single-stranded (ss) DNA fragments, double-stranded (ds) DNA fragments, RNA-DNA hybrids, and nicked DNA fragments in complex samples. In the first dimension nucleic acid molecules are separated based on strandness and length in the presence of 7 M urea. After the first-dimension electrophoresis all nucleic acid fragments are heat denatured in the gel. During the second-dimension electrophoresis all nucleic acid fragments are single-stranded and migrate according to length. 2D-SDE takes about 90 min and requires only basic skills and equipment. We show that 2D-SDE has many applications in analyzing complex nucleic acid samples including (1) estimation of renaturation efficiency and kinetics, (2) monitoring cDNA synthesis, (3) detection of nicked DNA fragments, and (4) estimation of quality and in vitro damage of nucleic acid samples. Results from 2D-SDE should be useful to validate techniques such as complex polymerase chain reaction, subtractive hybridization, cDNA synthesis, cDNA normalization, and microarray analysis. 2D-SDE could also be used, e.g., to characterize biological nucleic acid samples. Information obtained with 2D-SDE cannot be readily obtained with other methods. 2D-SDE can be used for preparative isolation of ssDNA fragments, dsDNA fragments, and RNA-DNA hybrids.

Kinetic measurements of DNA hybridization on an oligonucleotide-immobilized 27-MHz quartz crystal microbalance

A highly sensitive 27-MHz quartz-crystal microbalance, on which a 10-30-mer oligonucleotide was immobilized as a probe molecule, was employed to detect hybridization of complementary oligonucleotides in aqueous solution. From frequency decreases (mass increases due to the hybridization) with passage of time, kinetic parameters such as association constants (K(a)) and binding and dissociation rate constants (k(1) and k(-1)) could be obtained, as well as binding (hybridization) amount at the nanogram level (delta m). Kinetic studies were carried out by changing various parameters: (i) the immobilization method of a probe oligonucleotide on Au electrode, (ii) number of mismatching bases in sequences of target oligonucleotides, (iii) length of both probe and target oligonucleotides, (iv) hybridization temperature, and (v) ionic strength in solution. The obtained results were compared with those obtained by a surface plasmon resonance method using a BIAcore system.

Species-differentiable sensing of phosphate-containing anions in neutral aqueous solution based on coordinatively unsaturated lanthanide complex probes

A new chromogenic/fluorogenic molecular probe was developed for highly selective and species-differentiable detection of phosphate-containing anions in neutral aqueous solution. The coordinatively unsaturated lanthanide complex, made from Eu(III) ion and 2-[(8-hydroxy-5-sulfo-7-quinoline)azo]-1,8-dihydroxy-3,6-naphthalene disulfonic acid, changed its conformation when binding to the incoming target anions, which resulted in differential absorption or fluorescence responses. It was demonstrated that not only phosphate and pyrophosphate but also DNA and RNA could be clearly distinguished by visible absorption or fluorescence spectra. Also, differential responses in absorption spectra were observed when AMP, ADP, and ATP were added into the sensing system. Selective quantitation of these phosphate-containing anions in aqueous solutions, therefore, can be easily available. DNA and RNA were distinguished by different colors and independent fluorescence emissions due to their intrinsic differences in beta-D-ribose residues. Simultaneous or independent quantitation of DNA and RNA in a mixture sample, therefore, is possible without pretreatment with nuclease. Furthermore, the influence from the base selectivity can be eliminated by the use of the probe. The detection limits of phosphate and 5'-ATP in neutral water were 6.0 x 10(-7) and 9.0 x 10(-7)M, respectively, by the UV/Vis spectrophotometric method; the detection limits were 12.3 ng/mL for DNA by fluorimetry and 2.3mg/L for RNA by UV/Vis spectrophotometry.

Determination of nucleic acids based on shifting the association equilibrium between tetracarboxy aluminum phthalocyanine and poly-lysine

A new method based on near-infrared (near-IR) fluorescence recovery was presented for the determination of nucleic acids. This method employed a two-reagent system composed of anionic tetracarboxy aluminum phthalocyanine (AlC4Pc) and polycationic poly-lysine. The fluorescence of AlC4Pc, with the maximum excitation and emission wavelengths at 620 and 701 nm, respectively, was quenched by poly-lysine with a proper concentration, but recovered by adding nucleic acids. Under optimal conditions, the recovered fluorescence was in proportional to the concentration of nucleic acids. The linear ranges of the calibration curves were 5-200 ng mL(-1) for both calf thymus DNA (ctDNA) and fish sperm DNA (fsDNA) with the detection limit of 2.6 ng mL(-1) for ctDNA and 2.1 ng mL(-1) for fsDNA. The relative standard deviation (n = 6) was 1.9 and 1.3% for 50 ng mL(-1) ctDNA and fsDNA, respectively. The proposed method was applied to the determination of nucleic acids in synthetic samples with satisfactory results.

Modeling of DNA hybridization kinetics for spatially resolved biochips

The marriage of microfluidics with detection technologies that rely on highly selective nucleic acid hybridization will provide improvements in bioanalytical methods for purposes such as detection of pathogens or mutations and drug screening. The capability to deliver samples in a controlled manner across a two-dimensional hybridization detection platform represents a substantial technical challenge in the development of quantitative and reusable biochips. General theoretical and numerical models of heterogeneous hybridization kinetics are required in order to design and optimize such biochips and to develop a quantitative method for online interpretation of experimental results. In this work we propose a general kinetic model of heterogeneous hybridization and develop a technique for estimating the kinetic coefficients for the case of well-spaced, noninteracting surface-bound probes. The experimentally verified model is then incorporated into the BLOCS (biolab-on-a-chip simulation) 3D microfluidics finite element code and used to model the dynamic hybridization on a biochip surface in the presence of a temperature gradient. These simulations demonstrate how such a device can be used to discriminate between fully complementary and single-base-pair mismatched hybridization using fluorescence detection by interpretation of the unique spatially resolved intensity pattern. It is also shown how the dynamic transport of the targets is likely to affect the rate and location of hybridization as well as that, although nonspecific hybridization is present, the change in the concentration of hybridized targets over the sensor platform is sufficiently high to determine if a fully complementary match is present. Practical design information such as the optimum transport speed, target concentration, and channel height is presented. The results presented here will aid in the interpretation of results obtained with such a temperature-gradient biochip.

Fluorescence energy transfer between fluorescein label and DNA intercalators to detect nucleic acids hybridization in homogeneous media

A general approach to detecting nucleic acid sequences in homogeneous media by means of steady-state fluorescence measurements is proposed. The methodology combines the use of a fluorescence-labeled single-strand DNA model probe, the complementary single-strand DNA target, and a DNA intercalator. The probe was fluorescein labeled to a spacer arm at the N4 position of the cytosine amino groups in polyribocytidylic acid (5'), poly(C), which acts as a model DNA probe. The complementary strand was polyriboinosinic acid (5'), poly(I), as a model of the target, and the energy transfer acceptor was an intercalator, either ethidium bromide or ethidium homodimer. In previous papers we have shown that the fluorescence intensity of the fluorescein label decreases when labeled poly(C) hybridizes with poly(I), and this fluorescence quenching can be used to detect DNA hybridization or renaturation in homogeneous media. In this paper we demonstrate that fluorescence resonance energy transfer (FRET) between fluorescein labeled to poly(C) and an intercalator agent takes place when single-stranded poly(C) hybridizes with poly(I), and we show how the fluorescence energy transfer further decreases the steady-state fluorescence intensity of the label, thus increasing the detection limit of the method. The main aim of this work was to develop a truly homogeneous detection system for specific nucleic acid hybridization in solution using steady-state fluorescence and FRET, but with the advantage of only having to label the probe with the energy donor since the energy acceptor is intercalated spontaneously. Moreover, the site label is not critical and can be labeled randomly in the DNA strand. Thus, the method is simpler than those published previously based on FRET. The experiments were carried out in both direct and competitive formats.

A continuous kinetic assay for RNA-cleaving deoxyribozymes, exploiting ethidium bromide as an extrinsic fluorescent probe

We describe a rapid and inexpensive method to monitor the kinetics of small RNA-cleaving deoxyribozymes, based on the exogenous fluorophore ethidium bromide. Ethidium binds preferentially to double-stranded nucleic acids, and its fluorescence emission increases dramatically upon intercalation. Thus, ethidium can be used in single-turnover experiments to measure both annealing of the deoxyribozyme to its substrate and release of the products. Under conditions in which dissociation of the product is fast compared with cleavage, the apparent rate of product release reflects the cleavage step. The method was developed for characterizing the so-called 8-17 catalytic DNA, but its general applicability in the deoxyribozyme field was verified using the 10-23 RNA-cleaving construct. Catalysis by both deoxyribozymes was not inhibited in the presence of substoichiometric amounts of ethidium, and the rates obtained through the ethidium assay were virtually identical to the rates determined using radiolabeled substrates. In contrast, the assay cannot be applied to the large, structured ribozymes, and its use to study the kinetics of the small hammerhead ribozyme was hampered by the presence on the catalyst of at least one high-affinity ethidium binding site.

Study of the interaction of cis-dichloro-(1,2 diethyl-3-aminopyrrolidine)Pt(II) complex with poly(I), poly(C) and poly(I) x poly(C)

The interaction of cis-dichloro-(1,2 diethyl-3-aminopyrrolidine)platinum(II) (Ptpyrr) with the polynucleotides poly(I), poly(C) and poly(I) x poly(C) acids was studied by circular dichroism, molecular fluorescence and (1)H NMR spectroscopies. Multivariate Curve Resolution, a factor analysis method, was applied for the analysis and interpretation of spectroscopic data obtained in mole ratio and kinetics studies. This procedure allows the determination of the number of different interaction complexes present during the experiments and the resolution of both concentration profiles and pure spectra for all of them. Two different interaction complexes were observed at the experimental conditions studied. The first one, at low Ptpyrr:polynucleotide ratio (r(Ptpyrr:poly)) values, corresponds to the interaction of Ptpyrr with hypoxanthine bases in the poly(I) moiety. This interaction leads to the destabilization and dissociation of the double-stranded conformation. The second complex was observed at higher r(Ptpyrr:poly) values and corresponds to the interaction of Ptpyrr to cytosine bases in poly(C) moiety. The formation of both complexes showed that the interaction of Ptpyrr with hypoxanthine bases occurred at the first stages of the reaction and with cytosine bases at longer reaction times. The results obtained show the utility of the Multivariate Curve Resolution approach for the analysis of data obtained by monitoring spectroscopically the interaction equilibria of platinum compounds with nucleic acids.

Analytical characterization of the conformational transitions of polynucleotides by means of different molecular spectroscopies and multivariate curve resolution

A general procedure for the study of conformational transitions of polynucleotides is described. The equilibria between different conformations induced by salt, ethidium bromide, and temperature of poly(dG-dC). poly(dG-dC) and induced by salt and temperature of poly(A). poly(U) are investigated using molecular absorption, circular dichroism, and fluorescence spectroscopies. Spectral data obtained from experiments are analyzed by means of a factor analysis method, namely, multivariate curve resolution, which allows possible intermediate states to be detected and the pure spectra and the concentration profiles of all species present in the system to be estimated. This work shows the application of this procedure for the analysis of data matrices obtained in individual experiments but also for the analysis of several data matrices simultaneously.

Fluorescence-labelled DNA probes to detect complementary sequences in homogeneous media

Sensitive, safe and easy-to-use probes for the detection of nucleic acids are urgently called for. To this end we are in the process of developing a fluorescence-based technique to work in homogeneous assay media. We have examined pyrene and fluorescein as fluorescent labels for natural DNA probes. A fraction of the cytosine residues of a single-stranded cDNA was randomly labelled with either pyrene or fluorescein using the bisulfite-catalyzed diamine reaction. Both fluorophores showed fluorescence quenching when the labelled probe was hybridized with its complementary strand and we describe the changes in steady-state fluorescence intensity that occurred upon hybridization. Our results demonstrate that pyrene quenching is more efficient than fluorescein quenching and thus pyrene-labelled probes are more sensitive for detecting and quantifying DNA from natural sources.

Photophysics of ethidium bromide complexed to ct-DNA: a maximum entropy study

Time-integrated and time-resolved fluorescence spectroscopies have been used to probe the photophysical properties of ethidium bromide (Eb) complexed to calf thymus DNA (ct-DNA). Fluorescence decay profiles are obtained using the technique of time-correlated single photon counting (TCSPC), and subsequently analysed using conventional sum-of-exponential (SOE) routines and also the maximum entropy method (MEM). Through use of these methods and simulated decay data, it is demonstrated that the kinetics of Eb in the presence of ds-DNA are best described by a generic model consisting of three exponential terms. At all DNA:Eb ratios and NaCl concentrations studied, free Eb is detected. Furthermore, Eb is found to interact with ds-DNA through two mechanisms, each distinguishable by its fluorescence decay time. Eb is shown to interact with DNA through classic intercalation, and also through binding at secondary sites. The component decay times are shown to be a function of NaCl concentration but independent of DNA:Eb molar ratio.

Product differentiation by analysis of DNA melting curves during the polymerase chain reaction

A microvolume fluorometer integrated with a thermal cycler was used to acquire DNA melting curves during polymerase chain reaction by fluorescence monitoring of the double-stranded DNA specific dye SYBR Green I. Plotting fluorescence as a function of temperature as the thermal cycler heats through the dissociation temperature of the product gives a DNA melting curve. The shape and position of this DNA melting curve are functions of the GC/AT ratio, length, and sequence and can be used to differentiate amplification products separated by less than 2 degrees C in melting temperature. Desired products can be distinguished from undesirable products, in many cases eliminating the need for gel electrophoresis. Analysis of melting curves can extend the dynamic range of initial template quantification when amplification is monitored with double-stranded DNA specific dyes. Complete amplification and analysis of products can be performed in less than 15 min.