DNA Phosphate Research Articles

Signal-on electrochemical aptasensor based on RGO-AuNPs and exonuclease-III with assistance of external probe for Hg2+ determination in shellfish

In this work, a signal-on electrochemical aptasensor, based on RGO-AuNPs and exonuclease-III (Exo-III), is introduced for sensitive Hg2+ determination in shellfish. RGO-AuNPs is one-step electrodeposited on screen-printed electrode (SPE) surface as a high-performance sensing platform. Hg2+ aptamer serves as a molecular recognizer and selectively responds to Hg2+, thus triggering thymine-Hg2+-thymine (T-Hg2+-T) coordination. Exo-III is activated to cleavage the T-Hg2+-T structure, leading to partial aptamer breakage on sensor surface. Particularly, the reduction of DNA phosphate skeletons actuates is sensitively recorded by the external signal probe (I[Fe(CN)6]4-) and further amplified, thus composing a signal-on system. Under optimum conditions, as-fabricated sensor presents a good linear relationship to Hg2+ level in the range of 3.5×10−3 – 5.6×10−1 mg L−1, and the detection limit (LOD) is well found as 1.2×10−3 mg L−1. In certified ICP-MS and recovery tests of shellfish samples, the errors and recovery rates are calculated as 1.5%∼4.4% and 97.5%∼103.5%, respectively.

Structural elucidation of new ferrocene appended scaffold and their metal complexes: Comparative in vitro DNA/BSA binding and antibacterial assay

A new organometallic ligand (L) was designed and synthesized from ferrocenecarboxaldehyde and 2–Aminobenzophenone through the condensation reaction in one step process. The metal complexes of this L with the formula [Zn(L)2](NO3)2 (1), [Cu(L)2](NO3)2 (2) and [Co(L)2](NO3)2 (3) were synthesized in high yield. The ligand (L) and complexes 1–3 were completely characterized by elemental analysis, spectroscopic and spectrometric techniques such as FT–IR, ToF Mass,1H NMR,13C NMR molar conductance and magnetic moment measurements. The spectroscopic interpretation showed that complex 1 and complex 3 prefer tetrahedral geometry whereas complex 2 adopts a square planar arrangement around the copper(II) ion. The in vitro DNA interaction studies of ligand (L) and metal complexes 1–3, were performed by UV–Vis absorption, fluorescence spectral and ethidium bromide displacement experiments. The absorption studies of complexes 1–3 reveal the existence of both hyperchromic and hypochromic effect which indicated the mixed type of binding that is intercalation of the aromatic part and the electrostatic surface interaction of metal ions with DNA phosphate groups. A comparison of binding constant Kb values suggested the stronger binding of complex 2 (Kb = 6.17 × 104 M−1) as compared to L and complexes 1 and 3. Furthermore, in vitro BSA binding studies and FRET also suggests greater interaction of complex 2 with BSA causing modulations in the hydrophobic microenvironment near Trp-212 in the subdomain IIA pocket by static quenching mechanism. Interestingly, all three complexes 1–3 tested showed promising antimicrobial activity as revealed by the disc diffusion assay in all four human pathogenic bacterial species comprising both gram–positive and gram–negative bacteria.

Fast Electron Detachment Dissociation of Oligonucleotides in Electron-Nitrogen Plasma Stored in Magneto Radio-Frequency Ion Traps.

We report "plasma" electron detachment dissociation (EDD), a novel electron-activated dissociation (EAD) method for the fast sequencing of oligonucleotides with a high sequence coverage. To reduce the repulsive Coulombic force between the deprotonated oligonucleotides and the electron beam, we performed EDD in a neutral electron-nitrogen (N2+) plasma stored in a magneto radio-frequency ion trap. We confirmed that plasma EDD accomplished a high sequence coverage (100%) of RNA with 40 mers in the reaction time of 10 ms using the electron beam kinetic energy of 35 eV. This new technique was applied to various modifications in oligonucleotide therapeutics (ONTs). Phosphorothioate (PS) positions showed an extremely high dissociation efficiency, i.e., 100 times higher than the standard phosphate (PO) in DNA. Locked nucleotides did not show intensive dissociation in EDD; however, collision-induced dissociation (CID) helped sequence these portions. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) using a ZenoTOF mass spectrometer equipped with the plasma EDD technique successfully identified impurities in degraded samples.

Biochemical analysis of the replication initiator protein of staphylococcal plasmid pC194

The staphylococcal plasmid pC194 is replicated through the rolling-circle mechanism. Its replication protein RepA has been proposed to initiate replication by making a bond between Y214 and DNA phosphate via transesterification and to terminate it by hydrolyzing DNA with E210 and carrying out strand transfer. We tested this model by examining the catalytic functions of the protein with purified RepA proteins and single-stranded DNA oligomers. The wild-type RepA formed a covalent bond with the DNA phosphate at the predicted initiation site. It hydrolyzed the phosphodiester bond at the site, which activity was found to depend on the presence of a large pseudopalindrome contained in the replication origin. The protein carried out a strand-transfer reaction which mimicked the termination step of replication. A Y214F and an E210A mutant respectively lacked the transesterification and the hydrolytic activity. These results are consistent with the previously proposed model, which was based solely on molecular genetics results. In addition, an E142A mutant was found to lack both activities, suggesting that the residue may coordinate the divalent cation necessary for them. A possible role of the pseudopalindrome in controlling the two activities of RepA during a replication cycle is also discussed.

Structural Characterization of Dendriplexes In Vacuo: A Joint Ion Mobility/Molecular Dynamics Investigation.

The combination between ion mobility mass spectrometry and molecular dynamics simulations is demonstrated for the first time to afford valuable information on structural changes undergone by dendriplexes containing ds-DNA and low-generation dendrimers when transferred from the solution to the gas phase. Dendriplex ions presenting 1:1 and 2:1 stoichiometries are identified using mass spectrometry experiments, and the collision cross sections (CCS) of the 1:1 ions are measured using drift time ion mobility experiments. Structural predictions using Molecular Dynamics (MD) simulations showed that gas-phase relevant structures, i.e., with a good match between the experimental and theoretical CCS, are generated when the global electrospray process is simulated, including the solvent molecule evaporation, rather than abruptly transferring the ions from the solution to the gas phase. The progressive migration of ammonium groups (either NH4+ from the buffer or protonated amines of the dendrimer) into the minor and major grooves of DNA all along the evaporation processes is shown to compact the DNA structure by electrostatic and hydrogen-bond interactions. The subsequent proton transfer from the ammonium (NH4+ or protonated amino groups) to the DNA phosphate groups allows creation of protonated phosphate/phosphate hydrogen bonds within the compact structures. MD simulations showed major structural differences between the dendriplexes in solution and in the gas phase, not only due to the loss of the solvent but also due to the proton transfers and the huge difference between the solution and gas-phase charge states.

Polyethylenimine-DNA Nanoparticles under Endosomal Acidification and Implication to Gene Delivery.

Non-viral gene delivery using polyethylenimine (PEI) has shown tremendous promise as a therapeutic technique. Through the formation of nanoparticles (NPs), PEIs protect genetic material such as DNA from degradation. Escape of the NPs from endosomes and lysosomes is facilitated by PEI's buffering capacity over a wide range of pH. However, little is known about the effects of endosomal acidification on the morphology of the NPs. In this work, large-scale coarse-grained simulations performed to mimic endosomal acidification reveal that NPs undergo a resizing process that is highly dependent on the N/P ratio (ratio of PEI nitrogen to DNA phosphate) at which they are prepared. With a low N/P ratio, NPs further aggregate after endosomal acidification, whereas with a high N/P ratio they dissociate. The mechanisms behind such NP resizing and its consequences on endosomal escape and nuclear trafficking are discussed. Based on the findings, suggestions are made on the PEI architecture that may enhance NP dissociation driven by endosomal acidification.

Nanopore Sequencing for Detection and Characterization of Phosphorothioate Modifications in Native DNA Sequences.

Bacterial DNA is subject to various modifications involved in gene regulation and defense against bacteriophage attacks. Phosphorothioate (PT) modifications are protective modifications in which the non-bridging oxygen in the DNA phosphate backbone is replaced with a sulfur atom. Here, we expand third-generation sequencing techniques to allow for the sequence-specific mapping of DNA modifications by demonstrating the application of Oxford Nanopore Technologies (ONT) and the ELIGOS software package for site-specific detection and characterization of PT modifications. The ONT/ELIGOS platform accurately detected PT modifications in a plasmid carrying synthetic PT modifications. Subsequently, studies were extended to the genome-wide mapping of PT modifications in the Salmonella enterica genomes within the wild-type strain and strains lacking the PT regulatory gene dndB (ΔdndB) or the PT synthetic gene dndC (ΔdndC). PT site-specific signatures were observed in the established motifs of GAAC/GTTC. The PT site locations were in close agreement with PT sites previously identified using the Nick-seq technique. Compared to the wild-type strain, the number of PT modifications are 1.8-fold higher in ΔdndB and 25-fold lower in ΔdndC, again consistent with known regulation of the dnd operon. These results demonstrate the suitability of the ONT platform for accurate detection and identification of the unusual PT backbone modifications in native genome sequences.

Effect of Bis‐Dimethylamine Substitution on DNA Binding Property and Cytotoxic Activity of Polyhydroxyxanthone

AbstractA bis‐dimethylamine substituted xanthone (Xan‐2) was obtained by cationic modification of the free C3 and C6 hydroxy groups of 1,3,6‐trihydroxyxanthone (Xan‐1) which was isolated from Polygala hongkongensis Hemsl.. The results of the spectroscopic analysis, melting profiles, electrophoretic migration, PCR assay and molecular docking indicated that the hydrophobic plane of Xan‐1 and Xan‐2 could intercalate into the DNA base pairs meanwhile the basic amine alkyl chain of Xan‐2 could bind with DNA phosphate framework via electrostatic interaction. Thus, Xan‐2 exhibited higher DNA binding affinity than Xan‐1. Further study showed that Xan‐2 could inhibit the proliferation of HeLa, SGC‐7901 and A549 cells effectively by MTT assay and induce apoptosis of HeLa cells as detected by AO/EB staining and flow cytometry assay. Interestingly, Xan‐2 exhibited selective cytotoxicity to cells, which was proved by its relatively low inhibitory effect on Raw 264.7 cell. What these studies mean is that disubstituted amine alkyl chains will play an important role in DNA binding property and cytotoxic activity, providing a direction for the development of novel potential antitumor agents.

Review of Knowledge of Uranium-Induced Kidney Toxicity for the Development of an Adverse Outcome Pathway to Renal Impairment

An adverse outcome pathway (AOP) is a conceptual construct of causally and sequentially linked events, which occur during exposure to stressors, with an adverse outcome relevant to risk assessment. The development of an AOP is a means of identifying knowledge gaps in order to prioritize research assessing the health risks associated with exposure to physical or chemical stressors. In this paper, a review of knowledge was proposed, examining experimental and epidemiological data, in order to identify relevant key events and potential key event relationships in an AOP for renal impairment, relevant to stressors such as uranium (U). Other stressors may promote similar pathways, and this review is a necessary step to compare and combine knowledge reported for nephrotoxicants. U metal ions are filtered through the glomerular membrane of the kidneys, then concentrate in the cortical and juxtaglomerular areas, and bind to the brush border membrane of the proximal convoluted tubules. U uptake by epithelial cells occurs through endocytosis and the sodium-dependent phosphate co-transporter (NaPi-IIa). The identified key events start with the inhibition of the mitochondria electron transfer chain and the collapse of mitochondrial membrane potential, due to cytochrome b5/cytochrome c disruption. In the nucleus, U directly interacts with negatively charged DNA phosphate, thereby inducing an adduct formation, and possibly DNA strand breaks or cross-links. U also compromises DNA repair by inhibiting zing finger proteins. Thereafter, U triggers the Nrf2, NF-κB, or endoplasmic reticulum stress pathways. The resulting cellular key events include oxidative stress, DNA strand breaks and chromosomal aberrations, apoptosis, and pro-inflammatory effects. Finally, the main adverse outcome is tubular damage of the S2 and S3 segments of the kidneys, leading to tubular cell death, and then kidney failure. The attribution of renal carcinogenesis due to U is controversial, and specific experimental or epidemiological studies must be conducted. A tentative construction of an AOP for uranium-induced kidney toxicity and failure was proposed.

Gallic acid-coated silver nanoparticles as perspective drug nanocarriers: bioanalytical study.

The ability of silver nanoparticles (AgNPs) to be used as drug nanocarriers has helped rapidly to invent novel strategies to treat diseases, such as cancer. The nanoparticles may offer a valuable tool to novel pH-sensitive drug delivery systems in the present scenario because of their undergoing mechanisms associated with the regulated dissolution, aggregation, and generation of oxygen radicals as well. These processes could be monitored by electrochemical (bio)sensors that are less money and time-consuming compared to other analytical approaches, however, with comparable analytical performance. In this paper, synthesized and microscopically characterized gallic acid-coated AgNPs (GA-AgNPs) are investigated using spectral and electrochemical methods. To investigate the Ag+ release, a 21-day ageing experiment is performed spectrophotometrically, finding that the peak maximum of GA-AgNPs spectra diminished by 24.5%. The highest Ag+ content was electrochemically determined in the supernatant solution after centrifugation (6.97 μmol·L−1), while no significant concentration of silver ions in solution after redispersion was observed (1.26 μmol·L−1). The interaction experiment indicates a stabilization of GA-AgNPs in the presence of long-chain dsDNA as well as a mutual electrostatic interaction with DNA sugar-phosphate backbone. This interaction mechanism is confirmed by FTIR analysis, showing a shift (1049 to 1061 cm−1 and 913 to 964 cm−1) specific to DNA phosphate bands. Finally, doxorubicin-loaded GA-AgNPs are monitored for the specific drug release in the physiological and more reactive weakly acidic microenvironment. Hereby, electrochemical (bio)sensing of GA-AgNPs undergoing mechanisms shows a huge potential to be used for monitoring of drug delivery systems at cancer therapy.Graphical abstract

Study of the DNA binding mechanism and in vitro activity against cancer cells of iron(III) and aluminium(III) kojic acid derivative complexes.

Metal ions have unique electrochemical and spectroscopical properties that cannot be attained by purely organic compounds. Most of the metal ions are toxic to humans, but paradoxically, metallodrugs are used in medicine as therapeutics and theranostics. Metallodrugs are eliminated in urine and faeces, and therefore release toxic metals and ligands into aquatic ecosystems, thereby raising concerns regarding environmental risks. The use of metallodrugs based on essential metal ions (i.e., iron, copper and zinc), instead of toxic ions, is a new alternative with minor hazards. Kojic acid is an Asperigillus oryzae metabolite of low toxicity used in the food and cosmetics industries. Its derivatives form stable complexes with iron(III) ions, which bind effectively to DNA and inhibit DNA polymerization. The iron(III)/S2 ligand complexes reduce in vitro colon carcinoma (Caco2) cell viability and significantly decrease the cell number. The kojic acid derivative complexes with iron(III) presented here are an alternative to the currently used platinum complexes in cancer therapy.

Uniform iron oxide nanoparticles reduce the required amount of polyethylenimine in the gene delivery to mesenchymal stem cells

Cationic polyethylenimine (PEI) is regarded as the ‘golden standard’ of non-viral gene vectors. However, the superiority of PEI with high positive charge density also induces its major drawback of cytotoxicity, which restricts its application for an effective and safe gene delivery to stem cells. To redress this shortcoming, herein, a magnetic gene complex containing uniform iron oxide nanoparticles (UIONPs), plasmid DNA, and free PEI is prepared through electrostatic interactions for the gene delivery to bone marrow-derived mesenchymal stem cells (BM-MSCs). Results show that UIONPs dramatically promote the gene delivery to BM-MSCs using the assistance of magnetic force. In addition, decreasing the free PEI nitrogen to DNA phosphate (N/P) ratio from 10 to 6 has little adverse impact on the transgene expression levels (over 300 times than that of PEI alone at the N/P ratio of 6) and significantly reduces the cytotoxicity to BM-MSCs. Further investigations confirmed that the decrease of free PEI has little influence on the cellular uptake after applying external magnetic forces, but that the reduced positive charge density decreases the cytotoxicity. The present study demonstrates that magnetic gene delivery not only contributes to the enhanced gene expression but also helps to reduce the required amount of PEI, providing a potential strategy for an efficient and safe gene delivery to stem cells.

Tuning DNA Supramolecular Polymers by the Addition of Small, Functionalized Nucleobase Mimics.

Nucleobase mimicking small molecules able to reconfigure DNA are a recently discovered strategy that promises to extend the structural and functional diversity of nucleic acids. However, only simple, unfunctionalized molecules such as cyanuric acid and melamine have so far been used in this approach. In this work, we show that the addition of substituted cyanuric acid molecules can successfully program polyadenine strands to assemble into supramolecular fibers. Unlike conventional DNA nanostructure functionalization, which typically end-labels DNA strands, our approach incorporates functional groups into DNA with high density using small molecules and results in new DNA triple helices coated with alkylamine or alcohol units that grow into micrometer-long fibers. We find that small changes in the small molecule functional group can result in large structural and energetic variation in the overall assembly. A combination of circular dichroism, atomic force microscopy, molecular dynamics simulations, and a new thermodynamic method, transient equilibrium mapping, elucidated the molecular factors behind these large changes. In particular, we identify substantial DNA sugar and phosphate group deformations to accommodate a hydrogen bond between the phosphate and the small-molecule functional groups, as well as a critical chain length of the functional group which switches this interaction from intra- to interfiber. These parameters allow the controlled formation of hierarchical, hybrid DNA assemblies simply through the addition and variation of small, functionalized molecules.

The Ad‐MD method to calculate NMR shift including effects due to conformational dynamics: The 31P NMR shift in DNA

A method for averaging of NMR parameters by molecular dynamics (MD) has been derived from the method of statistical averaging in MD snapshots, benchmarked and applied to structurally dynamic interpretation of the 31 P NMR shift (δ31P ) in DNA phosphates. The method employs adiabatic dependence of an NMR parameter on selected geometric parameter(s) that is weighted by MD-calculated probability distribution(s) for the geometric parameter(s) (Ad-MD method). The usage of Ad-MD for polymers is computationally convenient when one pre-calculated structural dependence of an NMR parameter is employed for all chemically equivalent units differing only in dynamic behavior. The Ad-MD method is benchmarked against the statistical averaging method for δ31P in the model phosphates featuring distinctively different structures and dynamic behavior. The applicability of Ad-MD is illustrated by calculating 31 P NMR spectra in the Dickerson-Drew DNA dodecamer. δ31P was calculated with the B3LYP/IGLO-III/PCM(water) and the probability distributions for the torsion angles adjacent to the phosphorus atoms in the DNA phosphates were calculated using the OL15 force field.

New Hybrid Compounds Combining Fragments of Usnic Acid and Thioether Are Inhibitors of Human Enzymes TDP1, TDP2 and PARP1.

Tyrosyl-DNA phosphodiesterase 1 (TDP1) catalyzes the cleavage of the phosphodiester bond between the tyrosine residue of topoisomerase 1 (TOP1) and the 3′ phosphate of DNA in the single-strand break generated by TOP1. TDP1 promotes the cleavage of the stable DNA–TOP1 complexes with the TOP1 inhibitor topotecan, which is a clinically used anticancer drug. This article reports the synthesis and study of usnic acid thioether and sulfoxide derivatives that efficiently suppress TDP1 activity, with IC50 values in the 1.4–25.2 μM range. The structure of the heterocyclic substituent introduced into the dibenzofuran core affects the TDP1 inhibitory efficiency of the compounds. A five-membered heterocyclic fragment was shown to be most pharmacophoric among the others. Sulfoxide derivatives were less cytotoxic than their thioester analogs. We observed an uncompetitive type of inhibition for the four most effective inhibitors of TDP1. The anticancer effect of TOP1 inhibitors can be enhanced by the simultaneous inhibition of PARP1, TDP1, and TDP2. Some of the compounds inhibited not only TDP1 but also TDP2 and/or PARP1, but at significantly higher concentration ranges than TDP1. Leader compound 10a showed promising synergy on HeLa cells in conjunction with the TOP1 inhibitor topotecan.

Revealing the binding properties between resorcinol and DNA

Resorcinol (1,3-dihydroxybenzene) is a common coupling agent in permanent hair dyes, and has arrested people's attention for its potential hazard to human health. However, the action mechanism of resorcinol and human DNA has not been elucidated. In this research, the binding properties between resorcinol and calf thymus DNA (ct-DNA) were studied for the first time through various spectral and molecular docking techniques. Spectral studies showed that the initial fluorescence quenching of resorcinol against DNA was a static one. The result of ΔH < 0 and ΔS > 0 was produced from thermodynamic experimental data, therefore it could be concluded that electrostatic force was the major driving force, while binding constant Kb was 1.56 × 104 M-1 at 298 K. The electrostatic binding network between resorcinol and ct-DNA was established explicitly through competitive substitution analysis and other spectral approaches. The results of FT-IR absorption spectra indicated that resorcinol had bound to the DNA phosphate skeleton. Molecular docking clearly revealed that binding occurred between hydroxyl groups of resorcinol and phosphorus oxygen bonds (P-O) of the DNA skeleton. These findings may deepen our understanding of the action mechanism between resorcinol and ct-DNA and provide some useful data on the effect of resorcinol on human diseases.

The DNA Recognition Motif of GapR Has an Intrinsic DNA Binding Preference towards AT-rich DNA.

The nucleoid-associated protein GapR found in Caulobacter crescentus is crucial for DNA replication, transcription, and cell division. Associated with overtwisted DNA in front of replication forks and the 3′ end of highly-expressed genes, GapR can stimulate gyrase and topo IV to relax (+) supercoils, thus facilitating the movement of the replication and transcription machines. GapR forms a dimer-of-dimers structure in solution that can exist in either an open or a closed conformation. It initially binds DNA through the open conformation and then undergoes structural rearrangement to form a closed tetramer, with DNA wrapped in the central channel. Here, we show that the DNA binding domain of GapR (residues 1–72, GapRΔC17) exists as a dimer in solution and adopts the same fold as the two dimer units in the full-length tetrameric protein. It binds DNA at the minor groove and reads the spatial distribution of DNA phosphate groups through a lysine/arginine network, with a preference towards AT-rich overtwisted DNA. These findings indicate that the dimer unit of GapR has an intrinsic DNA binding preference. Thus, at the initial binding step, the open tetramer of GapR with two relatively independent dimer units can be more efficiently recruited to overtwisted regions.

First Principles Dynamics Study of Excited Hole Relaxation in DNA.

A recent theoretical work showed that ion irradiation generates excited holes deep within the valence band of DNA. In this work, we investigate the excited hole relaxation toward HOMO using a first-principles computational method following such ionization events. The excited hole relaxation is found to depend significantly on the energetic position of the excited hole generated. The relaxation process is found to be an order of magnitude slower for holes that are generated deeper than 20 eV than those generated within 10 eV, where the probability for the initial ionization events is the highest. However, the excited holes that are generated in different spatial moieties such as DNA nucleotide bases and phosphate backbones do not show noticeable differences in terms of the relaxation time. Our work also shows that decoherence due to nuclei dynamics slows down the relaxation by a factor of two or more. At the same time, the relaxation time is found to be less than a couple of picoseconds, much shorter than typical timescales associated with chemical bond dissociation.

The importance of hydrophobic interactions in the structure of transcription systems.

Hydrophobic forces play a crucial role in both the stability of B DNA and its interactions with proteins. In the present study, we postulate that the hydrophobic effect is an essential component in establishing specificity in the interaction transcription factor proteins with their consensus DNA sequence partners. The PDB coordinates of more than 50 transcription systems have been used to analyze the hydrophobic attraction of proteins towards their DNA consensus. This analysis includes computing the hydrophobic energy of the interacting molecules by means of their hydrophobic moments. Hydrophobic moments have successfully been used in previous studies involving self-assembly protein systems. In the present case, in spite of some variability, we found specificity in transcription factors when interacting with their respective consensus DNA sequences. By applying our model of biological membrane pattern for hydrophobic interactions, we postulate that hydrophobic forces constitute the necessary intermediate interaction between the unspecific electrostatic attraction for DNA phosphate groups and the very short-range interaction promoting hydrogen bonds. We conclude that hydrophobic interactions serve as the intermediate force guiding transcriptions factors towards the proper hydrogen bonds to their DNAs.

Identification of Thioflavin T Binding Modes to DNA: A Structure-Specific Molecular Probe for Lasing Applications.

The binding mechanism of thioflavin T (ThT) to DNA was studied using polarized light spectroscopy and fluorescence-based techniques in solutions and in solid films. Linear dichroism measurements showed that ThT binds to DNA duplex by intercalation. Time-resolved fluorescence studies revealed a second binding mode which is the external binding to the DNA phosphate groups. Both binding modes represent the nonspecific type of interactions. The studies were complemented with the analysis of short oligonucleotides having DNA cavities. The results indicate that the interplay between three binding modes—intercalation, external binding, and binding inside DNA cavities—determines the effective fluorescence quantum yield of the dye in the DNA structures. External binding was found to be responsible for fluorescence quenching because of energy transfer between intercalated and externally bound molecules. Finally, amplified spontaneous emission (ASE) was successfully generated in the ThT-stained films and used for detecting different DNA structures. ASE measurements show that ThT-stained DNA structures can be used for designing bioderived microlasers.