DNA Chain Length Research Articles

Nanoscale surface defects of goethite governing DNA adsorption process and formation of the Goethite-DNA conjugates

In urbanized areas, extracellular DNA (exDNA) is suspected of carrying genes with undesirable traits like virulence genes (VGs) or antibiotic resistance genes (ARGs), which can spread through horizontal gene transfer (HGT). Hence, it is crucial to develop novel approaches for the mitigation of exDNA in the environment. Our research explores the role of goethite, a common iron mineral with high adsorption capabilities, in exDNA adsorption processes. We compare well-crystalline, semi-crystalline, and nano goethites with varying particle sizes to achieve various specific surface areas (SSAs) (18.7–161.6 m2/g) and porosities. We conducted batch adsorption experiments using DNA molecules of varying chain lengths (DNA sizes: <11 Kb, <6 Kb, and <3 Kb) and assessed the impact of Ca2+ and biomacromolecules on the adsorption efficacy and mechanisms. Results show that porosity and pore structure significantly influence DNA adsorption capacity. Goethite with well-developed meso- and macroporosity demonstrated enhanced DNA adsorption. The accumulation of DNA on the goethite interface led to substantial aggregation in the system, thus the formation of DNA-goethite conjugates, indicating the bridging between mineral particles. DNA chain length, the presence of Ca2+, and the biomacromolecule matrix also affected the adsorption capacity and mechanism. Interactions between DNA and positively charged biomacromolecules or Ca2+ led to DNA compaction, allowing greater DNA accumulation in pores. However, a high concentration of biomacromolecules led to the saturation of the goethite surface, inhibiting DNA adsorption. AFM imaging of goethite particles after adsorption suggested the formation of the DNA multilayer. The study advances understanding of the environmental behavior of exDNA and its interaction with iron oxyhydroxides, offering insights into developing more effective methods for ARGs removal in wastewater treatment plants. By manipulating the textural properties of goethite, it's possible to enhance exDNA removal, potentially reducing the spread of biocontamination in urban and industrial environments.

π‐Conjugated polyfluorenes with o‐phenylenediamine unit: Synthesis, optical and electrochemical properties, charge transfer complexation, and DNA sensing

Abstractπ‐Conjugated polyfluorenes (PPs) comprising 2,3‐diaminobenzene‐1,4‐diyl (unit A) and 9,9‐dihexylfluorene‐2,7‐diyl (polymer‐1) or 9,9‐bis(6‐N,N,N,‐trimethylammoniumhexyl)fluorene‐2,7‐diyl (unit B) (polymer‐2) units were synthesized using Suzuki‐Miyaura coupling polycondensation. To compare the chemical properties and functionality of polymer‐2, a water‐soluble PP comprising benzene‐1,4‐diyl and unit B (polymer‐3) was synthesized. Polymer‐1 exhibited solvatochromism: the photoluminescence (PL) peak of the polymer in solutions shifted to a longer wavelength with an increase in the dielectric constants of solvents. Polymer‐1 formed charge transfer (CT) complexes with organic electron acceptors. The CT complexation behavior was systematically elucidated by the PL measurements using Stern–Volmer and Benesi–Hildebrand methods. Water‐soluble polymer‐2 could be used as a sensor for the chain length of telomere DNA by monitoring the changes in its PL intensity upon the addition of the analyte. The DNA sensing performance of polymer‐2 surpassed that of polymer‐3, attributed to the presence of unit A in polymer‐2. This unit brought polymer‐2 closer to DNA through hydrogen bonding between the amino group of polymer‐2 and nucleic acids in DNA. This interaction facilitated the occurrence of CT from the polymer backbone to DNA.

Water‐soluble π‐conjugated polyfluorene bearing 6‐N1‐hexylcytosine and 6‐trimethylammoniumhexyl side chains: Synthesis, chemical properties, and sensing ability for nucleoside and telomere DNA

AbstractWater‐soluble π‐conjugated polyfluorene bearing 6‐N1‐cytosinehexyl and 6‐trimethylammoniumhexyl bromide side chains, namely polymer‐1, was synthesized by Suzuki polycondensation. The absorption onset wavelength (λonset) of the polymer was longer than that of the monomer and confirmed the presence of the π‐conjugated system along the polymer chain. The cyclic voltammetry and UV–vis analyses showed that the highest occupied molecular orbital and lowest unoccupied molecular orbital energy levels of the polymer were −5.5 and −2.6 eV, respectively. The photoluminescence (PL) intensity of the polymer decreased with increasing DNA chain length (m) upon adding (TTAGGG)m (T = thymine, A = adenine, and G = guanine; m = 2, 4, 6, and 8), indicating that the polymer could detect telomere DNA chain lengths with higher precision than previously reported DNA sensors. Similarly, the PL intensity decreased with the addition of nucleosides. Photoinduced charge transfer in the complex between the polymer and DNA or nucleoside played an important role in the PL response of the polymer toward analytes. The sensing behavior was analyzed using the Stern–Volmer and Benesi–Hildebrand methods.

Optimizing the dynamic and thermodynamic properties of hybridization in DNA-mediated nanoparticle self-assembly.

DNA-directed nanoparticle (DNA-NP) systems provide various applications in sensing, medical diagnosis, data storage, plasmonics and photovoltaics. Bonding probability and melting properties are helpful to evaluate the selectivity, thermostability and thermosensitivity of these applications. We investigated the influence of temperature, nanoparticle size, DNA chain length and surface grafting density of DNA on one nanoparticle on the DNA dynamic hybridization percentage and melting properties of DNA-NP assembly systems by molecular dynamics simulation. The high degree of consistency of free energy estimations for DNA hybridization via our theoretical deduction and the nearest-neighbor rule generally used in experiments validates reasonably our DNA model. The melting temperature and thermosensitivity parameter are determined by the sigmoidal melting curves based on hybridization percentage versus temperature. The results indicated that the hybridization percentage presents a downward trend with increasing temperature and nanoparticle size. Applications based on DNA-NP systems with bigger nanoparticle size, such as DNA probes, have better selectivity, thermostability and thermosensitivity. There exist optimal DNA chain length and surface grafting density where the hybridization percentage reaches the maximal value. The melting temperature reaches a maximum at the point of optimal grafting density, while the thermosensitivity parameter presents an upward trend with the increase of grafting density. Several physical quantities consisting of the radial density function, root mean square end-to-end distance, contact distance parameter and effective volume fraction are used to analyse DNA chain conformations and DNA-NP packing in the assembly process. Our findings provide the theoretical basis for the improvement and optimization of applications based on DNA-NP systems.

Divalent metal ions and intermolecular interactions facilitate DNA network formation

The interactions between divalent metal ions and DNA are crucial for basic life processes. These interactions are also important in advanced technological products such as DNA-based ion sensors. Current polyelectrolyte theories cannot describe these interactions well and do not consider the corresponding dynamics. In this study, we report the single-molecule dynamics of the binding of divalent metal ions to a single DNA molecule and the morphology characterization of the complex. We found that most of the divalent metal ions (Mn2+, Zn2+, Co2+, Ni2+, and Cd2+), except Mg2+ and Ca2+, could cause monomolecular DNA condensation. For transition metal ions, different ionic strengths were required to induce the compaction, and different shortening speeds were displayed in the dynamics, indicating ionic specificity. Atomic force microscopy revealed that the morphologies of the metal ion–DNA complexes were affected by the ionic strength of the metal ion, DNA chain length, and DNA concentration. At low metal ion concentration, DNA tended to adopt a random coil conformation. Increasing the ionic strength led to network-like condensed structures, suggesting that divalent metal ions can induce attraction between DNA molecules. Furthermore, higher DNA concentration and longer chain length enhanced intermolecular interactions and consequently resulted in network structures with a higher degree of interconnectivity.

Controlling Droplet Motion on an Organogel Surface by Tuning the Chain Length of DNA and Its Biosensing Application

Summary Controllable droplet motion has attracted extensive attention but still faces the challenges of an uncontrollable sliding speed and a slow response rate. Here, controllable sliding speed and critical sliding angle (CSA) of a droplet on an oil-swollen organogel surface are achieved with a fast response rate via modulation of the DNA chain length. Comprehensive investigations ranging from macroscopic wetting behavior to molecular mechanism suggest that short single-stranded DNA (ssDNA) could act as a hydrotrope to interact with oil molecules via interfacial hydrophobic interactions while increasing the interfacial thickness and adhesion, thus hindering the movement of droplets. Conversely, long ssDNA generated from rolling-circle amplification tend toward a curled conformation, minimizing nucleobase exposure and leading to weak interfacial adhesion, allowing the droplets to slide easily. With a significant CSA gradient, biosensing applications for ATP, microRNA, and thrombin detection are demonstrated, indicating the potential for the detection of a broad range of targets.

Electrostatic Force Triggering Elastic Condensation of Double-Stranded DNA for High-Performance One-Step Immunoassay.

Current strategies for high-performance immunoassay generally require a sandwich structure for signal amplification. This strategy is limited to multivalent antigens and complicates the detection scheme. Herein we demonstrate a class of simple one-step ultrasensitive immunoassay with the adoption of double-stranded DNA (dsDNA) as "conductive spring" to bridge the electrode and redox-reporter/antibody-receptor comodified gold nanoparticles (AbFc@AuNPs). Upon biorecognition between antigen and antibody, the charge of the AuNPs changes, enhancing the electrostatic interaction between the AuNPs and Au electrode surface, and condensing the dsDNA chain. For the first time, the sensitive response of the electrochemical redox current to the DNA chain length is utilized to achieve an ultrahigh sensitivity down to fM level. Only the primary antibody needed in the recognition interface ensures the one-step immunoreaction works well with monovalent antigens, which ensure this method as a promising general alternative means for fast, high-throughput or point-of-care clinical applications even for very challenging clinically relevant samples.

Label-Free Optical Detection of Mycotoxins Using Specific Aptamers Immobilized on Gold Nanostructures.

This work focuses on the development of the novel label-free optical apta-sensors for detection of mycotoxins. A highly sensitive analytical method of total internal reflection ellipsometry (TIRE) combined with Localized Surface Plasmon Resonance (LSPR) phenomenon in nano-structured gold films was exploited here for the first time for detection of aflatoxin B1 and M1 in direct assay with specific aptamers immobilized on the surface of gold. The achieved detection of low molecular weight molecules, such as aflatoxin B1 and M1, in a wide range of concentrations from 100 ng/mL down to 0.01 ng/mL is remarkable for the LSPR method. The study of binding kinetics of aflatoxin molecules to their respective aptamers using dynamic TIRE measurements yielded the values of affinity constants in the range of 10−8–10−7 mol, which is characteristic for highly specific aptamer/target interactions similar to that for monoclonal antibodies. The effect of aptamers’ DNA chain length on their binding characteristics was analyzed.

DNA: New materials for substrate selective catalysis

ABSTRACTWe discovered that random DNA fragments (RDF) could selectively catalyze the oxidation of peroxidase substrates under the H2O2-TMB system. The activity is closely related with the length of DNA chain. Taking advantage of simplicity and efficiency, the RDF would have potential applications in biotechnology and clinical diagnosis as enzymatic mimetics.

Influence of Divalent Counterions on the Dynamics in DNA as Probed by Using a Minor-Groove Binder.

DNA dynamics, to which water, counterions, and DNA motions contribute, is a topic of considerable interest because it is closely related to the efficiency of biological functions performed by it. Simulation studies and experiments suggest that the counterion dynamics in DNA probed by a minor-groove binder are similar for various monovalent counterions. To date, the influence on DNA dynamics of higher-valence counterions, which are also present around DNA and are known to bind more strongly to it than monovalent ions, has not been studied. Herein we investigated DNA dynamics in the presence of Mg2+ and Ca2+ , chosen for their relative abundance in cells, by using minor-groove binder 4',6-diamidino-2-phenylindole (DAPI) as a fluorescence probe. The dynamics, as measured from the time-resolved fluorescence Stokes shifts of DAPI bound to calf thymus DNA on a subpicosecond-to-nanosecond timescale, were found to be very similar in the presence of both the divalent ions and Na+ ions. The observation is explained by considering the screening of the electric field of the divalent ion by its hydration shell, preferential binding of the ions to the phosphate groups, and displacement of ions from the minor groove by DAPI due to the stronger binding interaction of the latter. Furthermore, the similarity of our results in the presence of Na+ to those reported for smaller oligonucleotides suggests that the chain length of DNA does not influence the DNA dynamics.

A molecule that detects the length of DNA by using chain fluctuations

A class of nucleosome remodelling motors translocates the nucleosomes, to which they are attached, towards the middle of the DNA chain in the presence of ATP during in vitro experiments. This biological activity is likely based on a physical mechanism for detecting and comparing the lengths of the flanking polymer chains. Here we propose that a pivoting mode of DNA fluctuations near the surface of the nucleosome coupled with a binding reaction with a DNA binding site of the motor provides a physical basis for length detection. Since the mean frequency of the fluctuations is higher for a shorter chain than a longer one due to its lower drag coefficient, a shorter chain has a higher rate of receptor binding, which triggers the ATP-dependent activity of the remodelling motor. The dimerisation of these units allows the motor to compare the length of the flanking DNA chains, enabling the translocation of the nucleosome towards the centre of the DNA.

A New Mathematical Model for Calculating the Electronic Coupling of a B-DNA Molecule

The charge transport properties of DNA have made this molecule very important for use in nanoscale electronics, molecular computing, and biosensoric devices. Early findings have suggested that DNA can behave as a conductor, semiconductor, or an insulator. This variation in electrical behavior is attributed to many factors such as environmental conditions, base sequence, DNA chain length, orientation, temperature, electrode contacts, and fluctuations. To better understand the charge transport characteristics of a DNA molecule, a more thorough understanding of the electronic coupling between base pairs is required. To achieve this goal, two mathematical methods for calculating the electronic interactions between base pairs of a DNA molecule have been developed, which utilize the concepts from Molecular Orbital Theory (MOT) and Electronic Band Structure Theory (EBST). The electronic coupling characteristics of a B-DNA molecule consisting of two Guanine-Cytosine base pairs have been examined for variation in the twist angle between the base pairs, the separation between base pairs, and the separation between base molecules in a given base pair, for both the HOMO and LUMO states. Comparison of results to published literature reveals similar outcomes. The electronic properties (metallic, semi-conducting, insulating) of a B-DNA molecule are also determined.

Copper(II) Complexes with N,O-Donor Ligands and Ofloxacin Drug as Antibacterial, DNA Interacting, Cytotoxic and SOD Mimic Agent.

The N,O-donor bidentate ligands (L (1) -L (7) ) derived from the reaction between chalcones and pyridinium salt of 2-acetyl furan were synthesized and characterized by IR and NMR spectroscopic techniques. Their complexes [1-7] of Cu(II) were synthesized and characterized by elemental analysis, magnetic measurements, TG analyses, IR and mass spectroscopy. Synthesized complexes were carried out for their biological elucidation using different biological experiments like minimum inhibitory concentration, DNA binding and cleavage study, cytotoxicity, and antiradical activity. Efficient cleavage of pUC19 DNA was observed for all the test complexes than the reference drug. Increase in DNA chain length and hence the relative viscosity as the complexes binds to DNA via intercalative mode and involves a strong stacking interaction between an aromatic chromophore and the DNA base pair.

Kinetic adsorption profile and conformation evolution at the DNA-gold nanoparticle interface probed by dynamic light scattering.

The kinetic adsorption profile at the DNA–gold nanoparticle (AuNP) interface is probed by following the binding and organization of thiolated linear DNA and aptamers of varying chain lengths (15, 30, 44, and 51 mer) to the surface of AuNPs (13.0 ± 1.0 nm diameter). A systematic investigation utilizing dynamic light scattering has been performed to directly measure the changes in particle size during the course of a typical aging-salting thiolated DNA/AuNP preparation procedure. We discuss the effect of DNA chain length, composition, salt concentration, and secondary structure on the kinetics and conformation at the DNA–AuNP interface. The adsorption kinetics are chain-length dependent, composition independent, and not diffusion rate limited for the conditions we report here. The kinetic data support a mechanism of stepwise adsorption of thiols to the surface of AuNPs and reorganization of the thiols at the interface. Very interestingly, the kinetic increases of the particle sizes are modeled accurately by the pseudo-second-order rate model, suggesting that DNA could possess the statistically well-defined conformational evolution. Together with other experimental evidence, we propose a dynamic inner-layer and outer-tail (DILOT) model to describe the evolution of the DNA conformation after the initial adsorption of a single oligonucleotide layer. According to this model, the length of the tails that extend from the surface of AuNPs, capable for hybridization or molecular recognition, can be conveniently calculated. Considering the wide applications of DNA/AuNPs, the results should have important implications in sensing and DNA-directed nanoparticle assembly.

DNA-length-dependent fluorescent sensing based on energy transfer in self-assembled multilayers

In this paper, a novel DNA-length-dependent fluorescent sensor was constructed based on the fluorescence resonance energy transfer. In the self-assembled multilayers (Quartz/GO/PDDA/Tx-DNA/PDDA/ZnO@CdS), ZnO@CdS and graphene oxide(GO) were employed as an energy donor and an energy acceptor, respectively. Single-stranded Tx-DNA (x represents different chain length of DNA) and poly(diallydimethylammonium) chloride (PDDA) were used as a linker. In the presence of complementary Px-DNA, the formation of double-stranded DNA leads to a change in chain length and achieves the purpose of changing the distance between ZnO@CdS and GO. Thereby, it enhances the efficiency of energy transfer between ZnO@CdS and GO resulting in the quench of fluorescence of ZnO@CdS, and thus different length DNA sequence was detected.

Surface stress properties of DNA-microcantilever systems

For the first time, the connection between surface stress and nanoscopic interactions of DNA adsorbed on microcantilever is established by combining Strey's mesoscopic liquid crystal theory and Stoney's formula. It is shown that surface stress depends not only on biomolecular interactions of DNA biofilm but also on mechanical properties of cantilever. Considering the correlativity between grafting density and chain length of DNA chain, we discuss the differences between DNA-microcantilever system and DNA solution system. The major theoretical achievement of this model is to identify the main contributions to surface stress under different detection conditions. This provides guidelines for designing new biosensors with high sensitivity and improved reliability.

Antiviral Activity of Sirna UL42 against Herpes Simplex Virus Type 1 in HeLa Cell Culture

RNA interference (RNAi) is a process by which introduced small interfering RNA (siRNA) can cause the specific degradation of mRNA with identical sequences. In this study, we applied siRNAs targeting the UL42 gene of human herpes simplex virus type 1 (HSV-1), which encodes a multifunctional polypeptide that is vital for virus DNA replication, binding to DNA, stably associating with the virus DNA polymerase (Pol), and acting to increase the length of DNA chains synthesized by Pol. HeLa cell line was used for HSV 1 infection and SiRNA transfection was done to suppress UL-42 gene in cell culture. The decrease in titer of HSV 1 was observed by rReal Time PCR to detect the drop in HSV 1 DNA synthesis and translation. The inhibition rates of siRNA1 and siRNA2 on HSV-1 plaque formation were reported and Comparing with virus control, siRNA1 and siRNA2 reduced DNA replication HSV-1. The decision whether the decrease in the number of HSV-1 plaques was due to siRNA silencing expression of the UL42 gene, a real-time PCR indicating that UL42-specific siRNAs blocked the expression of the UL42 gene significantly. Comparing with virus control, siRNA1 and siRNA2 reduced the expression of UL42 gene. In this study the synthetic siRNA silenced UL42 mRNA expression effectively and specifically and inhibited HSV-1 replication and also our data offer new possibilities for RNAi as a genetic tool for inhibition of HSV-1 replication.

Label‐Free Electrical Detection of DNA Hybridization on Graphene using Hall Effect Measurements: Revisiting the Sensing Mechanism

AbstractThere is broad interest in using graphene or graphene oxide sheets as a transducer for label‐free and selective electrical detection of biomolecules such as DNA. However, it is still not well explored how the DNA molecules interact with and influence the properties of graphene during the detection. Here, Hall effect measurements based on the Van der Pauw method are used to perform single‐base sequence selective detection of DNA on graphene sheets, which are prepared by chemical vapor deposition. The sheet resistance increases and the mobility decreases with the addition of either complementary or one‐base mismatched DNA to the graphene device. The hole carrier concentration of the graphene devices increases significantly with the addition of complementary DNA but it is less affected by the one‐base mismatched DNA. It is concluded that the increase in hole carrier density, indicating p‐doping to graphene, is better correlated with the DNA hybridization compared to the commonly used parameters such as conductivity change. The different electrical observations of p‐doping from Hall effect measurements and n‐doping from electrolyte‐gated transistors can be explained by the characteristic morphology of partially hybridized DNA on graphene and the mismatch between DNA chain length and Debye length in electrolytes.

A New Trace Analytic Method for the Determination of Sequence-Specific DNA with Fluorescent Probes

A new method of fluorescence spectrometry detection of single-strand DNA (ssDNA) was established by hybridizing the ssDNA with its complementary ssDNA to form double-stranded DNA (dsDNA). Our results show that the fluorescence intensity increased significantly when the nucleic acid molecular “light switch"(Ru(phen)2dppx2+) or Hoechst 33258 dye interacted with dsDNA, and the fluorescence intensity also increased as the DNA concentration increased. The changing law was also studied about how the fluorescence intensity changed when the two kinds of fluorescent probes interacted with oligonucleotide of different lengths and different sequences, as well as DNA-DNA′ hybridization products. Then, the effect of the bases mismatch, varying length of DNA chain, and different DNA sequences on the fluorescence intensity were explored at the same time, by detecting the specific DNA sequence of avian influenza H1N1 virus, cauliflower mosaic virus, and hepatitis C virus. Additionally, the selectivity, linear range, and sensitivity of the two probes were compared.

Biochemical Analysis of the Human Mismatch Repair Proteins hMutSα MSH2G674A-MSH6 and MSH2-MSH6T1219D

The heterodimeric human MSH2-MSH6 protein initiates DNA mismatch repair (MMR) by recognizing mismatched bases that result from replication errors. Msh2(G674A) or Msh6(T1217D) mice that have mutations in or near the ATP binding site of MSH2 or ATP hydrolysis catalytic site of MSH6 develop cancer and have a reduced lifespan due to loss of the MMR pathway (Lin, D. P., Wang, Y., Scherer, S. J., Clark, A. B., Yang, K., Avdievich, E., Jin, B., Werling, U., Parris, T., Kurihara, N., Umar, A., Kucherlapati, R., Lipkin, M., Kunkel, T. A., and Edelmann, W. (2004) Cancer Res. 64, 517-522; Yang, G., Scherer, S. J., Shell, S. S., Yang, K., Kim, M., Lipkin, M., Kucherlapati, R., Kolodner, R. D., and Edelmann, W. (2004) Cancer Cell 6, 139-150). Mouse embryonic fibroblasts from these mice retain an apoptotic response to DNA damage. Mutant human MutSα proteins MSH2(G674A)-MSH6(wt) and MSH2(wt)-MSH6(T1219D) are profiled in a variety of functional assays and as expected fail to support MMR in vitro, although they retain mismatch recognition activity. Kinetic analyses of DNA binding and ATPase activities and examination of the excision step of MMR reveal that the two mutants differ in their underlying molecular defects. MSH2(wt)-MSH6(T1219D) fails to couple nucleotide binding and mismatch recognition, whereas MSH2(G674A)-MSH6(wt) has a partial defect in nucleotide binding. Nevertheless, both mutant proteins remain bound to the mismatch and fail to promote efficient excision thereby inhibiting MMR in vitro in a dominant manner. Implications of these findings for MMR and DNA damage signaling by MMR proteins are discussed.