Characterization of the binding interactions between EvaGreen dye and dsDNA

Optical-fiber sensor for 17β-Estradiol-binding aptamer evaluation and specific detection of 17β-Estradiol in serum at physiological concentrations

Methods for evaluation of immobilized-small molecule-binding aptamers are rare. In this study, taking the evaluation of 17β-Estradiol (E2) aptamers as an example, we first summarized the reported affinity and specificity results of 16 E2 aptamers, highlighting the issues of insufficient and inconsistent results and the lacking of evaluation of immobilized aptamers. We further exemplified the limited application scope of current affinity techniques by testing the two most widely-applied E2 aptamers, Kim76 and Alsa35, using the three label-free fluorescence assays and two nuclease protection assays. Subsequently, we evaluated the affinity of immobilized-E2 aptamers, Alsa35 and E09, using fiber optic evanescent wave aptasensor (FOEW) based on the competitive binding of target and fluorophore-labeled complementary strand with the fiber surface immobilized-aptamer. The results revealed that Alsa35 had the better affinity and specificity than E09. Using Alsa35-based FOEW, the enzyme-free detection of E2 spiked in river water and human serum was respectively realized with the unprecedented limits of detection (LOD, S/N = 3) of 4.75 (undiluted river water) and 206 pM (undiluted serum). FOEW is a valuable addition to analytical approaches for evaluation of immobilized-aptamers and a general platform for ultrasensitive target detection.

Ultra-sensitive fluorescence-activated droplet single-cell sorting based on Tetramer-HCR-EvaGreen amplification

The current single-cell analysis technologies such as fluorescence-activated cell sorting (FACS) and fluorescence-activated droplet sorting (FADS) could decipher the cellular heterogeneity but were constrained by low sorting performance and cell viability. Here, an ultra-sensitive single-cell sorting platform has been developed by integrating the FADS technology with Tetramer-HCR-EvaGreen (THE) fluorescence signal amplification. The THE system produced much higher fluorescence signal than that of the single Tetramer or Tetramer-HCR signal amplification. Upon application to target MCF-7 cells, the platform exhibited high efficacy and selectivity while maintaining more than 95% cell viability. The THE-FADS achieved sorting efficiencies of 55.5% and 50.3% with purities of 91% and 85% for MCF-7 cells in PBS solutions and simulated serum samples, respectively. The sorted MCF-7 cells showed similar proliferation together with CK19 and EGFR mRNA expression compared with the control cells. The established THE-FADS showed the promising prospects to cellular heterogeneity understanding and personalized medicine.

Digital Melting Curve Analysis for Multiplex Quantification of Nucleic Acids on Droplet Digital PCR

We present a cost-effective and simple multiplex nucleic acid quantification method using droplet digital PCR (ddPCR) with digital melting curve analysis (MCA). This approach eliminates the need for complex fluorescent probe design, reducing both costs and dependence on fluorescence channels. We developed a convolutional neighborhood search algorithm to correct droplet displacement during heating, ensuring precise tracking and accurate extraction of melting curves. An experimental protocol for digital MCA on the ddPCR platform was established, enabling accurate quantification of six target pathogen genes using a single fluorescence channel, with an average accuracy of 85%. Our method overcomes the multiplexing limitations of ddPCR, facilitating its application in multi-target pathogen detection.

Nucleic acid-binding bis-acridine orange dyes with improved properties for bioimaging and PCR applications

Understanding the intricate interactions of molecular dyes with nucleic acids is pivotal for advancing medical and biochemical applications. In this work, we present a comprehensive study of the interplay between a novel series of bis-acridine orange (BAO) dyes and double-stranded DNA (dsDNA). These BAO dyes were intentionally designed as two acridine orange units connected by neutral linkers featuring a 2,5-disubstituted thiophene moiety. Comparative analysis of BAO compounds with the widely utilized DNA-binding dye EvaGreen (EG) was carried out for fibroblast staining and qPCR analysis. The results show that BAO dyes outperform EG by supporting PCR amplification over a broader concentration range (0.5-5.0 μM). Furthermore, they exhibit an exceptional capability to generate consistent DNA melting curves regardless of DNA concentration fluctuations. Molecular dynamics simulations showed that BAO dyes when interacting with dsDNA unfold from the stacked conformation to the elongated one. The difference in the energy between the conformations is shown to be concomitant with fluorescence enhancement. This study enriches our understanding of the intricate interplay between innovative BAO dyes and dsDNA, fostering their applications in medical and biochemical research, particularly in qPCR methodologies and bioimaging techniques.

Staining Properties of Selected Commercial Fluorescent Dyes Toward B- and Z-DNA

The properties of six commonly used, commercially available, fluorescent dyes were compared in staining right-handed B-DNA and left-handed Z-DNA. All showed different degree of fluorescence turn-on in the presence of B-DNA, but very little in the presence of Z-DNA. The optimal range of dye-DNA ratios of DNA was determined. While these dyes do not provide a turn-on type probe for Z-DNA, staining between B- and Z-DNA using dyes such as SYBR Green I was shown to be useful in tracking the kinetics of conformational changes between these two forms of DNA. Finally, SYBR Green I showed unique circular dichroism patterns in 4 M NaCl that change in the presence of double stranded DNA, both in the visible and UV range.

Test Article for automation purposes

Digital recombinase polymerase amplification (dRPA) aims to quantify the initial amount of nucleic acid by dividing nucleic acid and all reagents required for the RPA reaction evenly into numerous individual reaction units, such as chambers or droplets. dRPA turns out to be a prominent technique for quantifying the absolute quantity of target nucleic acid because of its advantages including low equipment requirements, short time consumption, as well as high sensitivity and specificity. dRPA combined with microfluidics are recognized as simple, various, and high-throughput nucleic acid quantization systems. This paper classifies the microfluidic dRPA systems over the last decade. We analyze and summarize the vital technologies of various microfluidic dRPA systems (e.g., chip preparation process, segmentation principle, microfluidic control, and statistical analysis methods), and major efforts to address limitations (e.g., prevention of evaporation and contamination, accurate initiation, and reduction of manual operation). In addition, this paper summarizes key factors and potential constraints to the success of the microfluidic dRPA to help more researchers, and possible strategies to overcome the mentioned challenges. Lastly, actual suggestions and strategies are proposed for the subsequent development of microfluidic dRPA.

Enabling programmable dynamic DNA chemistry using small-molecule DNA binders

The binding of small molecules to the double helical structure of DNA, through either intercalation or minor groove binding, may significantly alter the stability and functionality of DNA, which is a fundamental basis for many therapeutic and sensing applications. Here, we report that small-molecule DNA binders can also be used to program reaction pathways of a dynamic DNA reaction, where DNA strand displacement can be tuned quantitatively according to the affinity, charge, and concentrations of a given DNA binder. The binder-induced nucleic acid strand displacement (BIND) thus enables innovative technologies to accelerate the discovery and characterization of bioactive small molecules. Specifically, we demonstrate the comprehensive characterization of existing and newly discovered DNA binders, where critical parameters for binding affinity and sequence selectivity can be obtained in a single, unbiased molecular platform without the need for any specialized equipment. We also engineer a tandem BIND system as a high-throughput screening assay for discovering DNA binders, through which 8 DNA binders were successfully discovered from a library of 700 compounds.

Analysis of aptamer-target binding and molecular mechanisms by thermofluorimetric analysis and molecular dynamics simulation

Introduction: Aptamers are valuable for bioassays, but aptamer-target binding is susceptible to reaction conditions. In this study, we combined thermofluorimetric analysis (TFA) and molecular dynamics (MD) simulations to optimize aptamer-target binding, explore underlying mechanisms and select preferred aptamer. Methods: Alpha-fetoprotein (AFP) aptamer AP273 (as the model) was incubated with AFP under various experimental conditions, and melting curves were measured in a real-time PCR system to select the optimal binding conditions. The intermolecular interactions of AP273-AFP were analysed by MD simulations with these conditions to reveal the underlying mechanisms. A comparative study between AP273 and control aptamer AP-L3-4 was performed to validate the value of combined TFA and MD simulation in selecting preferred aptamers. Results: The optimal aptamer concentration and buffer system were easily determined from the dF/dT peak characteristics and the melting temperature (Tm) values on the melting curves of related TFA experiments, respectively. A high Tm value was found in TFA experiments performed in buffer systems with low metal ion strength. The molecular docking and MD simulation analyses revealed the underlying mechanisms of the TFA results, i.e., the binding force and stability of AP273 to AFP were affected by the number of binding sites, frequency and distance of hydrogen bonds, and binding free energies; these factors varied in different buffer and metal ion conditions. The comparative study showed that AP273 was superior to the homologous aptamer AP-L3-4. Conclusion: Combining TFA and MD simulation is efficient for optimizing the reaction conditions, exploring underlying mechanisms, and selecting aptamers in aptamer-target bioassays.

Plasmon-Exciton Coupling Effect in Nanostructured Arrays for Optical Signal Amplification and SARS-CoV-2 DNA Sensing

A surface plasmon resonance (SPR)-enhanced optical signal using a nanoslit array and acridine orange (AO) dye system at a flexible poly(dimethylsiloxane) (PDMS) substrate was achieved in this work and demonstrated a simple sensing scheme to directly detect SARS-CoV-2 nucleic acid via DNA hybridization. A simple nanoimprinting pattern transfer technique was introduced to form uniform reproducible nanoslit arrays where the dimensions of the slit array were controlled by the thickness of the gold film. The plasmon-exciton coupling effect on the optical enhancement of different dye molecules, i.e., AO, propidium iodide (PI), or dihydroethidium (DHE) attached to the nanoslit surfaces, was examined thoroughly by measuring the surface reflection and fluorescence imaging. The results indicate that the best overlap of the plasmon resonance wavelength to the excitation spectrum of AO presented the largest optical enhancement (∼57×) compared to the signal at flat gold surfaces. Based on this finding, a sensitive assay for detecting DNA hybridization was generated using the interaction of the selected SARS-CoV-2 ssDNA and dsDNA with AO to trigger the metachromatic behavior of the dye at the nanoarray surfaces. We found strong optical signal amplification on the formation of acridine-ssDNA complexes and a quenched signal upon hybridization to the complementary target DNA (ct-DNA) along with a blue shift in the fluorescence of AO-dsDNAs. A quantitative evaluation of the ct-DNA concentration in a range of 100-0.08 nM using both the reflection and emission imaging signals demonstrated two linear regimes with a lowest detection limit of 0.21 nM. The sensing method showed high sensitivity and distinguished signals from 1-, 2-, and 3-base mismatched DNA targets, as well as high stability and reusability. This approach toward enhancing optical signal for DNA sensing offers promise in a general, rapid, and direct vision detection method for nucleic acid analytes.

Two novel "release-on-demand" fluorescent biosensors for probing UV-induced DNA damage induced in single stranded and double stranded DNA: Comparative study

Light in the UVC spectral region damages both single-strand (ssDNA) and double-strand DNA (dsDNA), and contributes to the formation of mutagenic photoproducts. In-vivo studies show greater damage for ssDNA compared to dsDNA. However, excited-state spectroscopy shows that dsDNA has longer excited-state lifetime than ssDNA, which increases the probability of damage for dsDNA. However, lack of a direct comparison of in-vitro ssDNA and dsDNA damage rates precludes the development of a model that elucidates the molecular factors responsible for damage. In this work, two novel sensitive "release-on-demand" biosensors are developed for the selective probing of DNA-damage and comparing the rate of DNA damage in ssDNA and dsDNA. The two biosensors involve the use of EvaGreen and Hoechst dyes for the sensitive probing of DNA-damage. The results show that ssDNA is damaged at a faster rate than dsDNA in the presence of UVC light (200-295 nm). Furthermore, we examined the effect of G/C composition on the damage rate for mostly A/T ssDNA and dsDNA oligonucleotides. Our results show that DNA damage rates are highly dependent on the fraction of guanines in the sequence, but that in-vitro dsDNA always exhibits an overall slower rate of damage compared to ssDNA, essentially independent of sequence.

Kinetics of Isothermal Dumbbell Exponential Amplification: Effects of Mix Composition on LAMP and Its Derivatives

Loop-mediated isothermal amplification (LAMP) is an exponential amplification method of DNA strands that is more and more used for its high performances. Thanks to its high sensitivity and selectivity, LAMP found numerous applications from the detection of pathogens or viruses through their genome amplification to its incorporation as an amplification strategy in protein or miRNA biomarker quantification. The LAMP method is composed of two stages: the first one consists in the transformation of the DNA strands into dumbbell structures formed of two stems and loops thanks to four primers; then, in the second stage, only two primers are required to amplify the dumbbells exponentially in numerous hairpins of increasing lengths. In this paper, we propose a theoretical framework to analyze the kinetics of the second stage of LAMP, the isothermal dumbbell exponential amplification (IDEA) as function of the physico-chemical parameters of the amplification reaction. Dedicated experiments validate the models. We believe these results may help the optimization of LAMP performances by reducing the number of experiments necessary to find the best parameters.

Overview and Future Perspectives of Microfluidic Digital Recombinase Polymerase Amplification (dRPA)

Digital recombinase polymerase amplification (dRPA) aims to quantify the initial amount of nucleic acid by dividing nucleic acid and all reagents required for the RPA reaction evenly into numerous individual reaction units, such as chambers or droplets. dRPA turns out to be a prominent technique for quantifying the absolute quantity of target nucleic acid because of its advantages including low equipment requirements, short time consumption, as well as high sensitivity and specificity. dRPA combined with microfluidics are recognized as simple, various, and high-throughput nucleic acid quantization systems. This paper classifies the microfluidic dRPA systems over the last decade. We analyze and summarize the vital technologies of various microfluidic dRPA systems (e.g., chip preparation process, segmentation principle, microfluidic control, and statistical analysis methods), and major efforts to address limitations (e.g., prevention of evaporation and contamination, accurate initiation, and reduction of manual operation). In addition, this paper summarizes key factors and potential constraints to the success of the microfluidic dRPA to help more researchers, and possible strategies to overcome the mentioned challenges. Lastly, actual suggestions and strategies are proposed for the subsequent development of microfluidic dRPA.

Investigation of nucleic acid damage induced by a novel ruthenium anti-cancer drug using multiple analytical techniques: Sequence specificity and damage kinetics

Cis-diacetonitrilo-bis(bipyridine) ruthenium(II) chloride is a recently introduced cis-platin analogue that has anti-cancer properties with lower side effects. However, the sequence dependence of its DNA damaging mechanism is unclear. Here, we present a simple, sensitive, multiplexed mix-and-read assay for ascertaining the molecular mechanism of DNA damage induced by the studied ruthenium complex (Ru-complex). The damage kinetics and sequence specificity for the Ru-complex induced DNA damage are examined by studying the induced damage in various oligonucleotide sequences by EvaGreen-DNA intercalator probe. High-through-put measurements were established using a 96-well microplate platform that allows multiple sequences to be measured simultaneously. The results show that the extent of damage increases with an increasing number of guanines, with considerable amount of damage at GA, GT and GC sites, in particular. Furthermore, the interaction of Ru-complex with DNA was confirmed using thermal analysis and MALDI-TOF-MS. Results indicate that the activated Ru-complex preferentially binds via both mono- and di-adduct formation at G and GG sites, respectively. Moreover, the developed method was successfully applied for the determination of the potency of the studied Ru-complex to induce DNA damage in K-Ras and N-Ras family of genes, one of the most common oncogenic events in cancer.

Single nucleotide polymorphism genotyping of ALDH2 gene based on asymmetric PCR and fluorescent probe-mediated melting curves

Detection of single nucleotide polymorphisms (SNPs) is of great value in precision medicine. The polymorphism of the aldehyde dehydrogenase 2 (ALDH2) gene is caused by a G1510A transition, resulting in the substitution of glutamic acid by lysine at position 487. People of different ALDH2 genotypes show different susceptibility to cancer, metabolic diseases, etc. SNP analysis based on fluorescent probe-mediated melting curves is a relatively efficient and cost-effective method. Genomic DNA extracted from 100 whole blood samples was subjected to polymorphisms mutational analysis using asymmetric PCR and probe-mediated melting curves. Then a certain number of samples from each genotype were randomly selected for direct sequencing verification. The new assay can be performed in 2 h without post-PCR processing such as gel electrophoresis and validated by direct sequencing in a blind study with 100% concordance. Moreover, comparing the detection of polymorphisms of ALDH2 with the clinics, and an overall agreement of 100% (100/100) was demonstrated. Our study has shown a high level of concordance between DNA sequencing, which is suitable for the detection of clinical specimens. Based on the concept of probe-mediated melting curves, we further developed this platform as a universal strategy for the detection of polymorphisms related to folate metabolism.

Determination of Advantages and Limitations of qPCR Duplexing in a Single Fluorescent Channel

Real-time (quantitative) polymerase chain reaction (qPCR) has been widely applied in molecular diagnostics due to its immense sensitivity and specificity. qPCR multiplexing, based either on fluorescent probes or intercalating dyes, greatly expanded PCR capability due to the concurrent amplification of several deoxyribonucleic acid sequences. However, probe-based multiplexing requires multiple fluorescent channels, while intercalating dye-based multiplexing needs primers to be designed for amplicons having different melting temperatures. Here, we report a single fluorescent channel-based qPCR duplexing method on a model containing the sequence of chromosomes 21 (Chr21) and 18 (Chr18). We combined nonspecific intercalating dye EvaGreen with a 6-carboxyfluorescein (FAM) probe specific to either Chr21 or Chr18. The copy number (cn) of the target linked to the FAM probe could be determined in the entire tested range from the denaturation curve, while the cn of the other one was determined from the difference between the denaturation and elongation curves. We recorded the amplitude of fluorescence at the end of denaturation and elongation steps, thus getting statistical data set to determine the limit of the proposed method in detail in terms of detectable concentration ratios of both targets. The proposed method eliminated the fluorescence overspilling that happened in probe-based qPCR multiplexing and determined the specificity of the PCR product via melting curve analysis. Additionally, we performed and verified our method using a commercial thermal cycler instead of a self-developed system, making it more generally applicable for researchers. This quantitative single-channel duplexing method is an economical substitute for a conventional rather expensive probe-based qPCR requiring different color probes and hardware capable of processing these fluorescent signals.

Display of functional nucleic acid polymerase on Escherichia coli surface and its application in directed polymerase evolution

We report a first of its kind functional cell surface display of nucleic acid polymerase and its directed evolution to efficiently incorporate 2'-O-methyl nucleotide triphosphates (2'-OMe-NTPs). In the development of polymerase cell surface display, two autotransporter proteins (Escherichia coli adhesin involved in diffuse adherence and Pseudomonas aeruginosa esterase A [EstA]) were employed to transport and anchor the 68-kDa Klenow fragment (KF) of E. coli DNA polymerase I on the surface of E. coli. The localization and function of the displayed KF were verified by analysis of cell outer membrane fractions, immunostaining, and fluorometric detection of synthesized DNA products. The EstA cell surface display system was applied to evolve KF for the incorporation of 2'-OMe-NTPs and a KF variant with a 50.7-fold increased ability to successively incorporate 2'-OMe-NTPs was discovered. Expanding the scope of cell-surface displayable proteins to the realm of polymerases provides a novel screening tool for tailoring polymerases to diverse application demands in a polymerase chain reaction and sequencing-based biotechnological and medical applications. Especially, cell surface display enables novel polymerase screening strategies in which the heat-lysis step is bypassed and thus allows the screening of mesophilic polymerases with broad application potentials ranging from diagnostics and DNA sequencing to replication of synthetic genetic polymers.

Clip-to-release on amplification (CRoA): a novel DNA amplification enhancer on and off microfluidics

Despite its high sensitivity, low cost, and high efficiency as a DNA amplification indicator with a yes/no answer, dsDNA-binding dye encounters incompatibility when used in microfluidic systems, resulting in problems such as false negative amplification results. Besides, its inhibition of amplification at high concentrations hinders its application both on-chip and off-chip. In this study, we propose a novel DNA amplification enhancer to counteract the drawbacks of dsDNA-binding dyes. It acts as a temporary reservoir for the free-floating dyes in solution and releases them on demand during the amplification process. Through this clip-to-release on amplification mechanism, the enhancer lowered the background fluorescence of sample droplets before amplification, enhanced the signal-to-background ratio of positive samples, and eliminated the false negative signal of on-chip PCR. Moreover, the enhancer increased the off-chip polymerase chain reaction (PCR) efficiency, boosted the fluorescence signal up to 10-fold, and made less nonspecific amplification product. All the factors affecting the enhancer's performance are investigated in detail, including its structure and concentration, and the types of dsDNA-binding dye used in the reaction. Finally, we demonstrated the broad application of the proposed amplification enhancer in various DNA amplification systems, for various genes, and on various amplification platforms. It would reignite the utilization of dsDNA dyes for wider applications in DNA analysis both on-chip and off-chip.

PCR inhibition in qPCR, dPCR and MPS-mechanisms and solutions

DNA analysis has seen an incredible development in terms of instrumentation, assays and applications over the last years. Massively parallel sequencing (MPS) and digital PCR are now broadly applied in research and diagnostics, and quantitative PCR is used for more and more practises. All these techniques are based on in vitro DNA polymerization and fluorescence measurements. A major limitation for successful analysis is the various sample-related substances that interfere with the analysis, i.e. PCR inhibitors. PCR inhibition affects library preparation in MPS analysis and skews quantification in qPCR, and some inhibitors have been found to quench the fluorescence of the applied fluorophores. Here, we provide a deeper understanding of mechanisms of specific PCR inhibitors and how these impact specific analytical techniques. This background knowledge is necessary in order to take full advantage of modern DNA analysis techniques, specifically for analysis of samples with low amounts of template and high amounts of background material. The classical solution to handle PCR inhibition is to purify or dilute DNA extracts, which leads to DNA loss. Applying inhibitor-tolerant DNA polymerases, either single enzymes or blends, provides a more straightforward and powerful solution. This review includes mechanisms of specific PCR inhibitors as well as solutions to the inhibition problem in relation to cutting-edge DNA analysis.

Progress in loop-mediated isothermal amplification assay for detection of Schistosoma mansoni DNA: towards a ready-to-use test

Schistosomiasis is one of the most prevalent Neglected Tropical Disease, affecting approximately 250 million people worldwide. Schistosoma mansoni is the most important species causing human intestinal schistosomiasis. Despite significant efforts in recent decades, the global disease burden of schistosomiasis remains extremely high. This could partly be attributed to the absence of accurate diagnostic tools, primarily in endemic areas. Loop-mediated isothermal amplification (LAMP) is increasingly used in molecular diagnostics as a field-friendly alternative to many other complex molecular methods and it has been proposed as an ideal candidate for revolutionizing point-of-care molecular diagnostics. In a previous work, a LAMP-based method to detect S. mansoni DNA (SmMIT-LAMP) was developed by our research group for early diagnosis of active schistosomiasis in an experimental infection murine model. The SmMIT-LAMP has been further successfully evaluated in both human stool and snail samples and, recently, in human urine samples. In this study, we developed an important improvement for SmMIT-LAMP molecular assay, transforming it into a cold maintenance dry format suitable for potentially manufacturing as kit for ready-to-use for schistosomiasis diagnosis. This procedure could be applied to create dry LAMP kits for a laboratory setting and for diagnostic applications for other neglected tropical diseases.

Hybrid Soft Nanomaterials Composed of DNA Microspheres and Supramolecular Nanostructures of Semi-artificial Glycopeptides

Aqueous hybrid soft nanomaterials consisting of plural supramolecular architectures with a high degree of segregation (orthogonal coexistence) and precise hierarchy at the nano- and microscales, which are reminiscent of complex biomolecular systems, have attracted increasing attention. Remarkable progress has been witnessed in the construction of DNA nanostructures obtained by rational sequence design and supramolecular nanostructures of peptide derivatives through self-assembly under aqueous conditions. However, orthogonal self-assembly of DNA nanostructures and supramolecular nanostructures of peptide derivatives in a single medium has not yet been explored in detail. In this study, DNA microspheres, which can be obtained from three single-stranded DNAs, and three different supramolecular nanostructures (helical nanofibers, straight nanoribbons, and flowerlike microaggregates) of semi-artificial glycopeptides were simultaneously constructed in a single medium by a simple thermal annealing process, which gives rise to hybrid soft nanomaterials. Fluorescence imaging with selective staining of each supramolecular nanostructure uncovered the orthogonal coexistence of these structures with only marginal impact on their morphology. Additionally, the biostimuli-responsive degradation propensity of each supramolecular architecture is retained, and this may allow the construction of active soft nanomaterials exhibiting intelligent biofunctions.

Comparison of K-Ras and N-Ras Mutagenic Hot Spots for UVC Damage

It has been well established that mutations in K-Ras and N-Ras proto-oncogenes can convert them into active oncogenes. Current molecular cancer research has been focused on determining the key steps by which cellular genes become oncogenes and not on the underlying and fundamental chemical damage mechanism and susceptibility to damage. In this study, we investigate the damage hot spots present in the N-Ras and K-Ras genes upon exposure to UVC radiation. Detection of damage is accomplished by a simple, sensitive, mix-and-read assay using an EvaGreen probe in a 96-well microtiter plate. Our results show that, although there is high degree of sequential similarities among K-Ras and N-Ras genes, they show different degrees of UV damage in different portions of their genomes. Our experiments demonstrate that overall, the K-Ras genome is more prone to UVC damage than the N-Ras genome. We observe that the extent of damage increases with increasing number of TTs in a sequence, consistent with previous results that show that thymine cyclobutyl photodimers are the primary DNA damage photoproducts upon UVC irradiation. This understanding of the effect of UVC radiation on various codons of K-Ras and N-Ras genes will help to increase our understanding about hot spots of DNA damage and the chemical damage mechanism.