Adsorption Of ssDNA Research Articles

Understanding Oligonucleotide Hybridization and the Role of Anchoring on the Single-Walled Carbon Nanotube Corona Phase for Viral Sensing Applications

Semiconducting single-walled carbon nanotubes (SWCNTs) with tailored corona phases (CPs), or surface adsorbed molecules, have emerged as a promising interface for sensing applications. The adsorption of an analyte can be specifically transduced as a modulation of their band gap near-infrared (nIR) photoluminescence (PL). One such CP ideal for this purpose is single-stranded DNA (ssDNA), where subsequent sequence dependent hybridization can result in PL emission wavelength shifts. Due to ssDNA adsorption to the SWCNT surface, the resultant non-canonical hybridization and its effect on SWCNT photophysical properties are not well understood. In this work, we study 20- and 21-mer DNA and RNA hybridization on the complementary ssDNA-SWCNT CP in the context of nucleic acid sensing for SARS-CoV-2 sequences as model analytes. We found that the van’t Hoff transition enthalpy of hybridization on SWCNT CP was -11.9 kJ mol-1, much lower than that of hybridization in solution (-707 kJ mol-1). We used SWCNT solvatochromism to calculate the solvent exposed surface area to indicate successful hybridization. We found that having a 30-mer anchor region in addition to the complementary region significantly improved PL response sensitivity and selectivity, with (GT)15 anchor preferred for RNA targets. Coincubation of ssDNA-SWCNT with analyte at 37°C resulted in faster hybridization kinetics without sacrificing specificity. Other methods aimed to improve CP rearrangement kinetics such as bath sonication and surfactant additions were ineffective. We also determined that target sequence choice is important as secondary structure formation in target is negatively correlated with hybridization. Best performing CPs showed detection limits of 11 nM and 13 nM for DNA and RNA targets respectively. Finally, we simulated sensing conditions using saliva environment, showing sensor compatibility in biofluids. In total, this work elucidates key design features and processing to enable sequence specific hybridization on ssDNA-SWCNT CP.

Facilitation of Dye-Based Quantitative Real-Time Polymerase Chain Reaction with Poly(ethylene glycol)-Engrafted Graphene Oxide.

Quantitative real-time polymerase chain reaction (qPCR) is an important and extensively utilized technique in medical and biotechnological applications. qPCR enables the real-time detection of nucleic acid during amplification, thus surpassing the necessity of post-amplification gel electrophoresis for amplicon detection. Despite being widely employed in molecular diagnostics, qPCR exhibits limitations attributed to nonspecific DNA amplification that compromises the efficiency and fidelity of qPCR. Herein, we demonstrate that poly(ethylene glycol)-engrafted nanosized graphene oxide (PEG-nGO) can significantly improve the efficiency and specificity of qPCR by adsorbing single-stranded DNA (ssDNA) without affecting the fluorescence of double-stranded DNA binding dye during DNA amplification. PEG-nGO adsorbs surplus ssDNA primers in the initial phase of PCR, having lower concentrations of DNA amplicons and thus minimizing the nonspecific annealing of ssDNA and false amplification due to primer dimerization and erroneous priming. As compared to conventional qPCR, the addition of PEG-nGO and the DNA binding dye, EvaGreen, in the qPCR setup (dubbed as PENGO-qPCR) significantly enhances the specificity and sensitivity of DNA amplification by preferential adsorption of ssDNA without inhibiting DNA polymerase activity. The PENGO-qPCR system for detection of influenza viral RNA exhibited a 67-fold higher sensitivity than the conventional qPCR setup. Thus, the performance of a qPCR can be greatly enhanced by adding PEG-nGO as a PCR enhancer as well as EvaGreen as a DNA binding dye to the qPCR mixture, which exhibits a significantly improved sensitivity of the qPCR.

Reversed Regulation Effects of ssDNA on the Mimetic Oxidase and Peroxidase Activities of Covalent Organic Frameworks.

Nanomaterials with enzyme mimetic activity have attracted extensive attention, especially in the regulation of their catalytic activities by biomolecules or other polymers. Here, a covalent organic framework (Tph-BT COF) with excellent photocatalytic activity is constructed by Schiff base reaction, and its mimetic oxidase activity and peroxidase activity is inversely regulated via single-stranded DNA (ssDNA). Under light-emitting diode (LED) light irradiation, Tph-BT exhibited outstanding oxidase activity, which efficiently catalyzed oxidation of 3,3',5,5'-tetramethylbenzidine (TMB) to produce blue oxTMB, and ssDNA, especially those with poly-thymidine (T) sequences, can significantly inhibit its oxidase activity. On the contrary, Tph-BT showed weak peroxidase activity, and the presence of ssDNA, particularly poly-cytosine (C) sequences, can remarkably enhance the peroxidase activity. The influence of base type, base length, and other factors on the activities of two enzymes is also studied, and the results reveal that the adsorption of ssDNA on the surface of Tph-BT prevented intersystem crossing (ISC) and energy transfer processes to reduce 1 O2 generation, while the electrostatic interaction between ssDNA and TMB enhanced Tph-BT's affinity for TMB to facilitate the electron transfer from TMB to • OH. This study investigates multitype mimetic enzyme activities of nonmetallic D-A conjugated COFs and demonstrates their feasibility of regulation by ssDNA.

Promotion of DNA Adsorption onto Microplastics by Transition Metal Ions

Microplastics can adsorb and spread a variety of pollutants in the ecosystem posing a threat to human health. One of the common pollution sources of environmental waters is metal ions, which not only adsorb on microplastics but can also promote the adsorption of other invasive species such as environmental DNA. Recently, we showed that environmentally abundant metal ions (Na+, Mg2+ and Ca2+) can promote the adsorption of single-stranded DNA (ssDNA) onto microplastics. Herein, we investigated the effect of transition metal ions including Zn2+ and Mn2+ and compared them with Mg2+ for promoting DNA adsorption. To better mimic environmental DNA, we also used a salmon sperm double-stranded DNA (dsDNA) (~2000 bp). For both ssDNA and dsDNA, the transition metals induced a higher adsorption capacity compared to Mg2+, and that correlated with the higher binding affinity of transition metals to DNA. Although metal-mediated interactions were vital for ssDNA adsorption, the dsDNA adsorbed on the microplastics even in the absence of metal ions, likely due to the abundance of binding sites of the 100-times longer dsDNA. Finally, desorption studies revealed that hydrophobic interactions were responsible for dsDNA adsorption in the absence of metal ions.

Utilization of DNA and 2D metal oxide interaction for an optical biosensor.

The efficient monitoring and early detection of viruses may provide essential information about diseases. In this work, we have highlighted the interaction between DNA and a two-dimensional (2D) metal oxide for developing biosensors for further detection of viral infections. Spectroscopic measurements have been used to probe the efficient interactions between single-stranded DNA (ssDNA) and the 2D metal oxide and make them ideal candidates for detecting viral infections. We have also used fully atomistic molecular dynamics (MD) simulation to give a microscopic understanding of the experimentally observed ssDNA-metal oxide interaction. The adsorption of ssDNA on the inorganic surface was found to be driven by favourable enthalpy change, and 5'-guanine was identified as the interacting nucleotide base. Additionally, the in silico assessment of the conformational changes of the ssDNA chain during the adsorption process was also performed in a quantitative manner. Finally, we comment on the practical implications of these developments for sensing that could help design advanced systems for preventing virus-related pandemics.

Understanding Oligonucleotide Hybridization and the Role of Anchoring on the Single-Walled Carbon Nanotube Corona Phase for Viral Sensing Applications

Semiconducting single-walled carbon nanotubes (SWCNTs) with tailored corona phases (CPs), or surface-adsorbed molecules, have emerged as a promising interface for sensing applications. The adsorption of an analyte can be specifically transduced as a modulation of their band-gap near-infrared (nIR) photoluminescence (PL). One such CP ideal for this purpose is single-stranded DNA (ssDNA), where subsequent sequence-dependent hybridization can result in PL emission wavelength shifts. Due to ssDNA adsorption to the SWCNT surface, the resultant noncanonical hybridization and its effect on SWCNT photophysical properties are not well understood. In this work, we study 20- and 21-mer DNA and RNA hybridization on the complementary ssDNA-SWCNT CP in the context of nucleic acid sensing for SARS-CoV-2 sequences as model analytes. We found that the van’t Hoff transition enthalpy of hybridization on SWCNT CP was −11.9 kJ mol–1, much lower than that of hybridization in solution (−707 kJ mol–1). We used SWCNT solvatochromism to calculate the solvent-exposed surface area to indicate successful hybridization. We found that having a 30-mer anchor region in addition to the complementary region significantly improved PL response sensitivity and selectivity, with a (GT)15 anchor preferred for RNA targets. Coincubation of ssDNA-SWCNTs with an analyte at 37 °C resulted in faster hybridization kinetics without sacrificing specificity. Other methods aimed to improve CP rearrangement kinetics such as bath sonication and surfactant additions were ineffective. We also determined that the target sequence choice is important as secondary structure formation in the target is negatively correlated with hybridization. Best-performing CPs showed detection limits of 11 and 13 nM for DNA and RNA targets, respectively. Finally, we simulated sensing conditions using the saliva environment, showing sensor compatibility in biofluids. In total, this work elucidates key design features and processing to enable sequence-specific hybridization on ssDNA-SWCNT CPs.

A fluorescent aptasensor for the detection of Aflatoxin B1 by graphene oxide mediated quenching and release of fluorescence

Aflatoxin B1 contamination in food and agro commodities has been major concern of global food safety and trade industry. There is an urgent need to develop sensitive and on-site detection methods for aflatoxins mainly, AFB1 monitoring. In the present study, a fluorophore (Alexa Fluor 488) based aptamer biosensor was devised in combination with graphene oxide (GO) for the detection of Aflatoxin B1 (AFB1). The optimized diagnostic procedure consisted of a fluorescent modified aptamer (Ax-AFLA5) as detection probe and GO mediated quenching of the same; to the quenched system AFB1 was added resulting in subsequent release of fluorescence. The principle of GO based adsorption of ssDNA and successive desorption in the presence of target mycotoxin was utilised in development of the bioassay. In presence of target mycotoxin, the GO adsorbed ssDNA attained a structural conformation resulting in desorption and subsequent release of fluorescence. Assay parameters such as concentration of fluorescent probe, GO and incubation time were evaluated and optimized. The optical signal thus generated could determine presence of AFB1 in the given sample. Selectivity of the method with other mycotoxins was evaluated. The linear range of AFB1 from 0.2–200 ppb was assessed. Visible green fluorescence release was observed at 20 ppb under UV transilluminator and the detection limit of the developed assay was interpreted as 20 ppb of AFB1. The suitability of the assay for AFB1 quantification in groundnut and natural samples was also evaluated. Thus, the developed assay can be a field deployable, reliable and rapid alternative tool for onsite screening method of aflatoxins and other mycotoxins at field level.

Probing the adsorption behavior and free energy landscape of single-stranded DNA oligonucleotides on single-layer MoS2 with molecular dynamics

Interfacing single-stranded DNA (ssDNA) with 2D transition metal dichalcogenides are important for numerous technological advancements. However, the molecular mechanism of this process, including the nature of intermolecular association and conformational details of the self-assembled hybrids is still not well understood. Here, atomistic molecular dynamics simulation is employed to study the distinct adsorption behavior of ssDNA on a single-layer MoS2 in aqueous environment. The ssDNA sequences [T10, G10, A10, C10, U10, (GT)5, and (AC)5] are chosen on the basis that short ssDNA segments can undergo a spontaneous conformational change upon adsorption and allow efficient sampling of the conformational landscape. Differences in hybridization is attributed to the inherent molecular recognition ability of the bases. While the binding appears to be primarily driven by energetically favorable van der Waals π-stacking interactions, equilibrium structures are modulated by the ssDNA conformational changes. The poly-purines demonstrate two concurrently competing π-stacking interactions: nucleobase–nucleobase (intramolecular) and nucleobase–MoS2 (intermolecular). The poly-pyrimidines, on the other hand, reveal enhanced π-stacking interactions, thereby maximizing the number of contacts. The results provide new molecular-level understanding of ssDNA adsorption on the MoS2 surface and facilitate future studies in design of functional DNA/MoS2 structure-based platforms for DNA sequencing, biosensing (optical, electrochemical, and electronic), and drug delivery.

Fabrication of graphene nanoplatelets embedded “partition cartridge” for efficient separation of target-bound ssDNA during SELEX

Graphene oxide (GO)-a carbon allotrope is widely used in aptamer generation process called SELEX (systematic evolution of ligands by exponential enrichment) and efficiently adsorbs non-target specific ssDNA onto its surface during the partitioning step of SELEX. The amount of GO required to adsorb ssDNA is high that imposes new challenges. Here, we have demonstrated graphene nanoplatelets (GrNP) that can be exploited with less material for efficient partitioning. Further, we have compared the non-target specific ssDNA adsorption on graphene oxide (GO), and graphene nanoplatelets (GrNP) and fabricated the “partitioning cartridge” for efficient separation of target (Monocrotophos and Endosulfan) bound-ssDNA from unbound ssDNA (non-target specific). To fabricate the partitioning cartridge, the spin column was utilized from common molecular biology lab waste. The fabricated “partition cartridge” alienated the target bound ssDNA efficiently and used further for polymerase chain reaction successfully. The fabricated partitioning cartridge is easy to fabricate, cost effective and recycles the plastic waste thus the environment friendly approach.

Ratiometric fluorescent sensor based on 2D MOF nanosheets modified by DNA for sensitive detection of Hg2+

Mercury is highly toxic and can accumulate throughout the food cycle, leading to water contamination and foodstuffs pollution. Therefore, increasing attention has been paid to explore effective detection of Hg2+. Here, we report a sensitive Hg2+ sensor based on single-stranded DNA (ssDNA) modified two-dimensional (2D) MOF nanosheets by a ratiometric fluorescent method. The chosen 2D MOF nanosheets possess intrinsic peroxidase-like catalytic ability, ssDNA adsorption and fluorescence quenching. We demonstrate that the adsorption of ssDNA can significantly improve the peroxidase mimetic activity of 2D MOF nanosheets, enhancing the fluorescence of substrate Amplex Red. Taking advantages of the favorable characteristics above, we fabricate an efficient Hg2+ sensor. In the presence of Hg2+, the ssDNA is released from 2D MOF nanosheets, which results in a decreasing of peroxidase mimetic activity of 2D MOF nanosheets and a fluorescence enhancement of attached fluorophore. A linear relationship between ratiometric fluorescence of substrate and fluorophore and Hg2+ concentrations is obtained. The detection limit is 5 nM, which is much lower than the maximal contamination level in drinking water (30 nM) by Word Health Organization. These findings show 2D MOF based ratiometric fluorescent sensor is a convenient and efficient strategy to detect Hg2+.

Oxidation degree dependent adsorption of ssDNA onto graphene-based surface* *Project supported by the National Natural Science Foundation of China (Grant Nos. 11305237 and 11974366), the Fundamental Research Funds for the Central Universities, China, the Natural Science Foundation of Shanghai, China (Grant No. 19ZR1463200), and the Key Research Program of Chinese Academy of Sciences (Grant No. QYZDJ-SSW-SLH053).

DNA/GO composite plays a significant role in the research field of biotechnology and nanotechnology, and attracts a great deal of interest. However, it is still unclear how the oxidation degree of the graphene-based surface affects the adsorption process of single-strand DNA (ssDNA). In this paper, based on the molecular dynamics simulations, we find that ssDNA molecule is absorbed on the GO surface in the most stable state with the oxidation degree around 15%. The microscopic mechanism is attributed to the van Der Walls and the electrostatic interactions between the ssDNA molecule and the graphene-based surface, which is accompanied with the π–π stacking and hydrogen bond formation. The number of π–π stacking between ssDNA and GO reaches the maximum value when the oxidation degree is around 15% among all the GO surfaces. Our simulation results also reveal the coexistence of stretched and curved configurations as well as the adsorption orientation of ssDNA on the GO surface. Furthermore, it is found that the absorbed ssDNA molecules are more likely to move on the graphene-based surface of low oxidation degree, especially on pristine graphene. Our work provides the physics picture of ssDNA’s physisorption dynamics onto graphene-based surface and it is helpful in designing DNA/GO nanomaterials.

Label-free detection of exosomes based on ssDNA-modulated oxidase-mimicking activity of CuCo2O4 nanorods

A label-free method for exosome detection was proposed. It is based on the target-responsive controllability of oxidase-like activity of Cu/Co bimetallic metal-organic frameworks (CuCo2O4 nanorods). In the absence of exosomes, the oxidase-like activity was inhibited due to the adsorption of CD63 aptamer onto nanorods’ surface. In the presence of exosomes, CD63 aptamer was disassembled from CuCo2O4 nanorods by virtue of CD63 aptamer-exosome recognition, which resulted in the recovery of oxidase-like activity. The activity inhibition is attributed to the fact that the ssDNA adsorption hindered the electron transfer between CuCo2O4 nanorods and colorimetric substrates. Under optimal conditions, a sensitive colorimetric method for detecting exosomes was established over a range of 5.6 × 104 to 8.9 × 105 particles μL−1 with a detection limit of 4.5 × 103 particles μL−1. The method was further applied in distinguishing healthy people and breast cancer patients by testing exosomes in the serum samples and showed satisfying differentiation ability.

Colorimetric oligonucleotide-based sensor for ultra-low Hg2+ in contaminated environmental medium: Convenience, sensitivity and mechanism

A colorimetric sensor for detection of Hg2+ is developed via graphene oxide/gold nanoparticles (GO/AuNPs) nanocomposite as peroxidase mimic. In the absence of Hg2+, the adsorption of ss-DNA on GO/AuNPs resulted in the decrease of peroxidase-like activity of GO/AuNPs, which catalyzed the oxidation of 3, 3, 5, 5-tetramethylbenzidine (TMB) to be very light blue. In the presence of Hg2+, the oligonucleotides of T-Hg2+-T conformation formed by thymine-Hg(II)-thymine interaction could not be adsorbed or bonded on GO/AuNPs, and the GO/AuNPs resumed their original high activity of peroxidase mimic and catalyzed the oxidation of TMB into distinct blue product. Under optimized conditions, the absorbance value at the wavelength of 655 nm (A655) was linearly related with the concentration of Hg2+ in the range between 5.2 × 10−9 M and 1.2 × 10−7 M with a detection limit of 3.8 × 10−10 M. By visual observation with the naked eye, Hg2+ as low as 3.3 × 10−7 M could cause color change in solution. The specific T-Hg2+-T binding made it easy to selectively detect Hg2+. The results show that the colorimetric assay offers great potential for the detection of Hg2+ in real samples.

Polymeric microcarrier for diagnostic assays and gene delivery systems

The interaction of deoxyribonucleic acid (DNA) with polymeric nano- and microcarriers has attracted significant attention in the studies on DNA diagnostic assays, DNA isolation and particularly gene delivery and cancer therapy agents. Therefore, in this study, plain poly(glycerol dimethacrylate) (poly(GDMA)) and poly(dimethylaminoethyl methacrylate)-grafted poly(GDMA) microgel particles were synthesized for high single-stranded DNA (ssDNA) adsorption and desorption capacity. Temperature- and pH-sensitive uniform poly(GDMA) particles were synthesized through a two-stage procedure. A GDMA dispersion polymerization procedure was used in the first stage of the study to obtain microgel particles with approximately 900 nm size. The surface-initiated atom transfer radical polymerization procedure, a living-polymerization technique of 2-dimethylaminoethyl methacrylate (DMAEM), was used in the second stage of the study to obtain polycationic molecular brushes on microgel particles. The resulting temperature- and pH-responsive microgels were used as a sorbent for ssDNA adsorption. Compared with commonly used sorbents, reasonably high ssDNA adsorptions were achieved with the proposed sorbent. The adsorbed ssDNA was desorbed from the sorbent at a high yield. The adsorption and desorption behaviors make poly(DMAEM)-grafted poly(GDMA) microgel particles a promising carrier/sorbent for ssDNA.

Characterizing the Interactions of DNA Oligomers with Graphene Field-Effect Transistors

Introduction: Graphene field-effect transistors (G-FETs) constitute an emerging platform for biosensing applications. Indeed, graphene is an ideal material for the detection of biomolecules: every atom of its monolayer structure is in contact with its environment, resulting in an electrical conductivity that is highly responsive to local electrostatic fluctuations from adjacent molecules. For genomic applications, most detection methods use DNA probe sequences bound to the graphene surface, in order to capture a specific target DNA sequence and detect the corresponding change in the electrical response of the sensor1 - 2. However, the effect of interactions between DNA and graphene on the electrical conductance is still not fully understood. Here, we investigate specifically the adsorption of short DNA oligomers on graphene field-effect transistors, in order to model and control the effect of such interactions in biosensing applications with G-FETs. Methods and Results: First, we fabricated G-FET sensors as follow3: Using photolithography techniques, an array of source and drain electrodes were patterned in gold on a Si wafer with a SiO2 insulator layer, as well as a common on-chip gate electrode in platinum. High-quality monolayer CVD-grown graphene was transferred onto the substrate and then etched to create 6 x 4 µm ribbons between each source-drain pair. Transfer curves (Isd vs. Vg) performed in saline buffer solution revealed a conductance minimum at the charge neutrality point of the graphene. Devices were then exposed to solutions of DNA, consisting in 22-single-stranded nucleotides (ssDNA) or double-stranded nucleotides (dsDNA) DNA oligomers diluted in 0,01X PBS buffer. Selected G-FET devices were exposed to different ssDNA concentrations during 15 min, followed by washing steps with 0,01X PBS. Electrical curves were recorded before, during and after each DNA exposure. In this presentation, we will present results showing that ssDNA exposure causes a left-shift of the charge neutrality point above a concentration threshold, and that this shift is proportional to ssDNA concentration. In addition, non-covalent adsorption of ssDNA on graphene appears to be reversible upon washing. Finally, we will discuss differences between the adsorption of dsDNA and ssDNA. Conclusion and Relevance: Our results suggest that unspecific DNA adsorption on graphene can lead to a G-FET response, which needs to be modeled, compensated and /or passivated in biosensing experiments, especially in order to achieve low detection limits for target sequences in complex biological media.

Graphene Quantum Dot Oxidation Governs Noncovalent Biopolymer Adsorption

Graphene quantum dots (GQDs) are an allotrope of carbon with a planar surface amenable to functionalization and nanoscale dimensions that confer photoluminescence. Collectively, these properties render GQDs an advantageous platform for nanobiotechnology applications, including optical biosensing and delivery. Towards this end, noncovalent functionalization offers a route to reversibly modify and preserve the pristine GQD substrate, however, a clear paradigm has yet to be realized. Herein, we demonstrate the feasibility of noncovalent polymer adsorption to GQD surfaces, with a specific focus on single-stranded DNA (ssDNA). We study how GQD oxidation level affects the propensity for polymer adsorption by synthesizing and characterizing four types of GQD substrates ranging ~60-fold in oxidation level, then investigating noncovalent polymer association to these substrates. Adsorption of ssDNA quenches intrinsic GQD fluorescence by 31.5% for low-oxidation GQDs and enables aqueous dispersion of otherwise insoluble no-oxidation GQDs. ssDNA-GQD complexation is confirmed by atomic force microscopy, by inducing ssDNA desorption, and with molecular dynamics simulations. ssDNA is determined to adsorb strongly to no-oxidation GQDs, weakly to low-oxidation GQDs, and not at all for heavily oxidized GQDs. Finally, we reveal the generality of the adsorption platform and assess how the GQD system is tunable by modifying polymer sequence and type.

A SIMPLE MODEL OF DNA ADSORPTION ON CARBON NANOTUBE

One of the major interaction mechanisms between carbon nanotubes (CNT) and DNA is $ \pi \mbox{-} \pi $ stacking, which is a van der Waals type of interaction. Attraction between the polycyclic aromatic surface elements of CNTs and the aromatic nucleotides of DNA leads to reversible adsorption (physisorption) between them. We propose to describe the ssDNA adsorption on CNT using zipper model and address the connection between the thermodynamics of adsorption and the flexibility of ssDNA.

Molecular Dynamics Simulations of DNA Adsorption on Graphene Oxide and Reduced Graphene Oxide-PEG-NH2 in the Presence of Mg2+ and Cl− ions

Graphene and its functionalised derivatives are transforming the development of biosensors that are capable of detecting nucleic acid hybridization. Using a Molecular Dynamics (MD) approach, we explored single-stranded or double-stranded deoxyribose nucleic acid (ssDNA or dsDNA) adsorption on two graphenic species: graphene oxide (GO) and reduced graphene oxide functionalized with aminated polyethylene glycol (rGO-PEG-NH2). Innovatively, we included chloride (Cl−) and magnesium (Mg2+) ions that influenced both the ssDNA and dsDNA adsorption on GO and rGO-PEG-NH2 surfaces. Unlike Cl−, divalent Mg2+ ions formed bridges between the GO surface and DNA molecules, promoting adsorption through electrostatic interactions. For rGO-PEG-NH2, the Mg2+ ions were repulsed from the graphenic surface. The subsequent ssDNA adsorption, mainly influenced by electrostatic forces and hydrogen bonds, could be supported by π–π stacking interactions that were absent in the case of dsDNA. We provide a novel insight for guiding biosensor development.

Length feature of ssDNA adsorption onto graphene oxide with both large unoxidized and oxidized regions.

DNA/GO functional structures have been widely used in biosensors, biomedicine and materials science. However, most studies about DNA/GO functional structures do not take into account the coexistence of both large unoxidized and oxidized regions on GO sheets. This special local structure provides the boundary region, which is the junction area between unoxidized and oxidized regions, and exhibits a special amphiphilic property of the GO sheets. Here based on molecular dynamics simulations, our results predict that the adsorption efficiency of long strand ssDNA molecules adsorbed on GO is 43%. Further analysis has shown that the ssDNA adsorption behaviors on the GO surface are more likely to start in the boundary region, even for 20 mer ssDNA molecules. Looking into the adsorption dynamic process we can see that the hydrogen bonds between ssDNA and GO are very active and easily broken and formed, especially for the boundary region of the GO surface, resulting in easy capture and adsorption of the ssDNA molecules on this region. The result provides insightful understanding of the adsorption behavior of ssDNA molecules on this amphiphilic GO surface and is helpful in the design of DNA/GO functional structure-based biosensors.

Kaplanmış Manyetik Kürelere DNA Adsorpsiyonu: Fiziksel ve Kimyasal Adsorpsiyonun Karşılaştırılması

Based on their unique properties various iron magnetic nanoparticles have proved to be excellent nanomaterials for applications in separation and concentration process. Immobilization of deoxyribonucleic acid (DNA) molecules on the magnetic beads are acutely important and have potential uses in many techniques such as DNA extraction, concentration, biosensors, microarrays and next generation sequencing. In this study the adsorption of single stranded DNA (ssDNA) via poly-l-lysine coated iron oxide magnetic beads was performed under varying conditions of poly-l-lysine amount, initial DNA concentration, ionic strength, bonding type and length of DNA. The adsorption process was examined via Langmuir and Freundlich isotherm models. The ionic interaction between negatively charged DNA and positively charged surface of magnetic beads showed multilayer adsorption with Freundlich adsorption isotherm, covalent bonding between modified DNA and surface by crosslinking provided higher adsorption efficiency with Langmuir adsorption isotherm. Both adsorption methods provided magnetic beads with favorable adsorption of ssDNA.