Gold nanoparticle aggregation-based highly sensitive DNA detection using atomic force microscopy

The potential ability of atomic force microscopy (AFM) as a quantitative bioanalysis tool is demonstrated by using gold nanoparticles as a size enhancer in a DNA hybridization reaction. Two sets of probe DNA were functionalized on gold nanoparticles and sandwich hybridization occurred between two probe DNAs and target DNA, resulting in aggregation of the nanoparticles. At high concentrations of target DNA in the range from 100 nM to 10 μM, the aggregation of gold nanoparticles was determined by monitoring the color change with UV-vis spectroscopy. The absorption spectra broadened after the exposure of DNA–gold nanoparticles to target DNA and a new absorption band at wavelengths >600 nm was observed. However, no differences were observed in the absorption spectra of the gold nanoparticles at low concentrations of target DNA (10 pM to 10 nM) due to insufficient aggregation. AFM was used as a biosensing tool over this range of target DNA concentrations in order to monitor the aggregation of gold nanoparticles and to quantify the concentration of target DNA. Based on the AFM images, we successfully evaluated particle number and size at low concentrations of target DNA. The calibration curve obtained when mean particle aggregate diameter was plotted against concentration of target DNA showed good linearity over the range 10 pM to 10 nM, the working range for quantitative target DNA analysis. This AFM-based DNA detection technique was three orders of magnitude more sensitive than a DNA detection method based on UV-vis spectroscopy.     

CdTe纳米荧光探针的合成及其与DNA的相互作用

以巯基丙酸(RSH)为稳定剂,采用水相法合成了功能性CdTe纳米晶,并通过X射线衍射(XRD)和透射电镜(TEM)对其粒度和形貌进行表征。建立了一种以水溶性CdTe量子点作为荧光探针测定DNA的方法,当DNA浓度为0.2~40μmol.dm-3时,荧光强度与DNA浓度呈良好的线性关系,检测限为80nmol.dm-3,11次重复测定含有5.6μmol.dm-3的小牛胸ctDNA得到的相对标准偏差为3.4%。考察了CdTe量子点浓度、pH值、温度及作用时间等因素对DNA荧光强度的影响。研究发现CdTe纳米粒子与DNA之间存在强烈的相互作用,量子点的荧光猝灭与DNA浓度呈线性关系;作用机理研究表明,CdTe纳米粒子与DNA之间存在静电相互作用,且DNA对CdTe纳米粒子的猝灭为动态猝灭过程。     

Morphology and properties of globular polymeric materials in the solid state: A composite material of DNA with a cationic surfactant

The aim of the present study was to control entanglements in order to regulate the properties of polymeric solids. Initially, fabrication of polymeric solids with few entanglements was attempted. Films of the DNA–cationic surfactant, cetyltrimethylammonium bromide (CTAB) (DNA–CTA), were cast from ethanol solution at room temperature. Morphological examination of DNA–CTA complex films using atomic force microscopy (AFM) revealed that these films were constructed by particle‐like substances. Geometrical analysis of AFM images showed that the particle‐like substances were the aggregates of several DNA–CTA globules. Mechanical characterization suggested that there were fewer entanglements than with normal plastic films. Small angle X‐ray scattering experiments during annealing indicated that molecular motions were highly excited in the surface region of each particle. In conclusion, a globular polymeric film with fewer entanglements was fabricated. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 730–738     

Chromatographic behavior of IgM:DNA complexes

This study documents the presence of stable complexes between monoclonal IgM and genomic DNA in freshly harvested mammalian cell culture supernatants. 75% of the complex population elutes from size exclusion chromatography with the same retention volume as IgM. DNA comprises 24% of the complex mass, corresponding to an average of 347 base pairs per IgM molecule, distributed among fragments smaller than about 115 base pairs. Electrostatic interactions appear to provide most of the binding energy, with secondary stabilization by hydrogen bonding and metal affinity. DNA-dominant complexes are unretained by bioaffinity chromatography, while IgM-dominant complexes are retained and coelute with IgM. DNA-dominant complexes are repelled from cation exchangers, while IgM-dominant complexes are retained and partially dissociated. Partially dissociated forms elute in order of decreasing DNA content. The same pattern is observed with hydrophobic interaction chromatography. All complex compositions bind to anion exchangers and elute in order of increasing DNA content. A porous particle anion exchanger was unable to dissociate DNA from IgM. Monolithic anion exchangers, offering up to 15-fold higher charge density, achieved nearly complete complex dissociation. The charge-dense monolith surface appears to outcompete IgM for the DNA. Monoliths also exhibit more than double the IgM dynamic binding capacity of the porous particle anion exchanger, apparently due to better surface accessibility and more efficient mass transfer.     

Rapid Non‐Crosslinking Aggregation of DNA‐Functionalized Gold Nanorods and Nanotriangles for Colorimetric Single‐Nucleotide Discrimination

Gold nanoparticles modified with DNA duplexes are rapidly and spontaneously aggregated at high ionic strength. In contrast, this aggregation is greatly suppressed when the DNA duplex has a single‐base mismatch or a single‐nucleotide overhang located at the outermost surface of the particle. These colloidal features emerge irrespective of the size and composition of the particle core; however, the effects of the shape remain unexplored. Using gold nanorods and nanotriangles (nanoplatelets), we show herein that both remarkable rapidity in colloidal aggregation and extreme susceptibility to DNA structural perturbations are preserved, regardless of the shape and aspect ratio of the core. It is also demonstrated that the DNA‐modified gold nanorods and nanotriangles are applicable to naked‐eye detection of a single‐base difference in a gene model. The current study corroborates the generality of the unique colloidal properties of DNA‐functionalized nanoparticles, and thus enhances the feasibility of their practical use.     

DNA diffusion in aqueous solution in presence of suspended particles

Although nanoparticles, which are comparable in size to polymer chains, are widely used as fillers to polymer matrices for developing functional and high performance materials, the dynamics of polymers constrained between solid particles has not been well elucidated. In this study, dynamics of individual polymer under such condition was investigated with fluorescent microscopy using DNA solutions as model systems. For individual T4 and λ DNA molecules in aqueous suspensions of spherical polystyrene particles with diameter of 1 μm, it was found that (i) the radius of gyration of DNA is independent of the particle volume fraction, ?_p, (ii) DNA diffusion is not sensitive to ?_p up to a certain critical ?_p where the average distance between particle surfaces is close to DNA size, and (iii) the DNA diffusion becomes slower at higher ?_p. The diffusion coefficient of DNA was larger, by a factor of 2, in the suspensions at intermediate ?_p than in the corresponding confined geometry (channel/slit between fixed walls), whereas this difference asymptotically vanished with increasing ?_p. This result suggested that the DNA diffusion in the suspensions with intermediate ?_p is accelerated by the particle motion. In fact, the diffusion coefficient measured for DNA in the suspensions was semiquantitatively described by the Rouse constraint‐release model considering the matrix effect on the probe chain diffusion. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 1103–1111, 2009     

DNA gel particles: An overview

A general understanding of interactions between DNA and oppositely charged compounds forms the basis for developing novel DNA-based materials, including gel particles. The association strength, which is altered by varying the chemical structure of the cationic cosolute, determines the spatial homogeneity of the gelation process, creating DNA reservoir devices and DNA matrix devices that can be designed to release either single- (ssDNA) or double-stranded (dsDNA) DNA. This review covers recent developments on the topic of DNA gel particles formed in water–water emulsion-type interfaces. The degree of DNA entrapment, particle morphology, swelling/dissolution behavior and DNA release responses are discussed as functions of the nature of the cationic agent used. On the basis of designing DNA gel particles for therapeutic purposes, recent studies on the determination of the surface hydrophobicity and the hemolytic and the cytotoxic assessments of the obtained DNA gel particles have been also reported.     

应用纳米磁性球电化学检测特定序列DNA

采用分散聚合法制备纳米磁性羧基球,利用化学偶联法将末端修饰氨基的寡聚核苷酸固定在纳米磁性球表面,制成新型核酸探针,该探针可特异性结合目标单链寡聚核苷酸.在磁场作用下,将纳米磁珠与本体溶液分离并富集在电极表面,以中性红为嵌合指示剂,用示差脉冲伏安法测定杂交结果.经过条件优化,本法测定DNA的浓度线性范围为1.0×10^-6～5.0×10^-9mol/L,检出限为8.6×10^-10mol/L.     

可改变DNA构象的非离子糖基表面活性剂

通过Zeta电位及粒径分析考察发现随着体系中辛基葡萄糖多苷表面活性剂质量 农度的增加，DNA分子在溶液中的构趋于缩拢。通过DNA-C_8APG复合物的UV吸收及 CD谱图进一步考察了DNA二级结构变化。随后的扫描电子显微镜（SEM）照片也证实 DNA分子在水溶液中的构象缩拢。通过表面张力UV图谱分析，推测非离子糖基表面 活性剂与DNA分子复合物结合的可能结构是表面活性剂与DNA之间的疏水作用及 多羟基的糖类的亲水头基结构与DNA带负电的核酸磷酸骨架以氢健的方式结合。     

An Exonuclease III‐Powered,On‐Particle Stochastic DNA Walker

DNA‐based machines have attracted rapidly growing interest owing to their potential in drug delivery, biocomputing, and diagnostic applications. Herein, we report a type of exonuclease III (Exo III)‐powered stochastic DNA walker that can autonomously move on a spherical nucleic acid (SNA)‐based 3D track. The motion is propelled by unidirectional Exo III digestion of hybridized DNA tracks in a burnt‐bridge mechanism. The operation of this Exo III‐propelled DNA walker was monitored in real time and at the single‐particle resolution using total internal reflection fluorescence microscopy (TIRF). We further interrogated the morphological effect of the 3D track on the nuclease activity, which suggested that the performance of the DNA walker was critically dependent upon the DNA density and the track conformation. Finally, we demonstrated potential bioanalytical applications of this SNA‐based stochastic DNA walker by exploiting movement‐triggered cascade signal amplification.     

Chromatin and Nucleosome Organizations and DNA Replication of Nucleus Reassembled in vitro Using Purified Exogenous DNA and Xenopus Egg Extracts

It has been demonstrated in the last ten years that the nuclear reassembly may occur in the cell-free systems from frog egg extracts added with exogenous naked DNA. However, there remains an open question : is the cell-free reassembled nucleus structurally similar to the nucleus in the intact cell ? That is, does the cell-free reassembled nucleus contain nucleosomes and chromatin? For this issue, we have designed experiments for identifying the internal structures of the cell-free reassembled nucleus. These experiments show that the nucleus reassembled in vitro also contains chromatin which is composed of typical 10 nm nucleosome fibers of "beads-on-a-string", 30 nm filaments and the next higher-order structures. The digestion experiment with the enzyme micrococcal nuclease has demonstrated that the DNA in the nucleosome of the reconstituted chromatin is about 200 base pairs (bp) in length, of which 165 bp may be in the nucleosome particle, and 35 bp may be in the linker between two particles. Prolongin     

Molecularly Regulated Reversible DNA Polymerization

Natural polymers are synthesized and decomposed under physiological conditions. However, it is challenging to develop synthetic polymers whose formation and reversibility can be both controlled under physiological conditions. Here we show that both linear and branched DNA polymers can be synthesized via molecular hybridization in aqueous solutions, on the particle surface, and in the extracellular matrix (ECM) without the involvement of any harsh conditions. More importantly, these polymers can be effectively reversed to dissociate under the control of molecular triggers. Since nucleic acids can be conjugated with various molecules or materials, we anticipate that molecularly regulated reversible DNA polymerization holds potential for broad biological and biomedical applications.     

Optimized DNA hybridization detection on nanocolloidal particles by dielectrophoresis

Oligonucleotides of varying surface coverage are functionalized onto the surface of 100 nm silica particles and the corresponding hybridization reaction with target ssDNA is studied using dielectrophoresis (DEP). The measured DEP cross‐over frequency (cof) is found to be sensitive to the oligonucleotide surface conformation. Zeta potential and particle size measurements suggest that at low oligo surface concentrations, non‐specific binding of oligo to the particle surface prevents efficient hybridization. At high surface coverage, steric hindrance due to the fully stretched, tightly packed oligo conformation prevents diffusion of DNA molecules to the particle surface. The optimum surface coverage exists at intermediate coverage where the particle is found to be the least electrically conductive, and hence exhibits the lowest measured cof. A simple DEP cof measurement hence allows one to determine the optimal oligo surface coverage for increased hybridization efficiency and detection sensitivity.     

超声合成Fe3O4@SiO2复合纳米磁性粒子用于质粒DNA的提纯

用超声合成了Fe3O4@SiO2复合纳米磁性粒子, 并用于质粒DNA的提取. 用透射电镜(TEM)、红外光谱(FT-IR)、震动样品磁场计(VSM)、X光电子能谱仪(XPS)等方法对合成的复合磁性粒子的表面形貌、结构、磁性质等进行了表征, 合成的复合磁微粒粒径分布均匀, 在15～20 nm, 磁响应性好. 用该复合磁微粒提取DNA的纯度能达到A260/A280＝ 1.8±0.1, 琼脂糖电泳证明质粒DNA结构基本没有被破坏, 主要为超螺旋结构, 能满足PCR等后续分子生物学操作的要求.     

INVESTIGATION OF POLYDL-LACTIDE-b-POLY（ETHYLENE GLYCOL）-b-POLYDL-LACTIDE MICROSPHERES CONTAINING PLASMID DNA

PolyDL-lactide (PDLLA) and the block copolymer, polyDL-lactide-b-poly(ethylene glycol)-b-polyDL-lactide (PELA) were used as the microsphere matrix to encapsulate plasmid DNA. The PDLLA, PELA, pBR322-1oaded PDLLA and pBR322-1oaded PELA microspheres were prepared by solvent extraction method based on the formation of multiple w1/o/w2 emulsion. The microspheres were characterized by surface morphology, mean particle size, particle size distribution and loading efficiency. The integrity of DNA molecules after being extracted from microspheres was determined by agarose gel electrophoresis. The result suggested that plasmid DNA molecules could retain their integrity after being encapsulated by PELA. The PELA microspheres could prevent plasmid DNA from being digested by DNase. The in vitro degradation and release profiles of plasmid DNA-loaded microspheres were measured in pH - 7.4 buffer solution at 37℃. The in vitro degradation profiles of the microspheres were evaluated by the deterioration in microspheres surface morphology, the molecular weight reduction of polymer, the mass loss of microspheres, the changes of pH values of degradation medium, and the changes of particle size. The in vitro release profiles of the microspheres were assessed by measurement of the amount of DNA presented in the release medium at determined intervals. The release profiles were correlation with the degradation profiles. The release of plasmid DNA from PELA microspheres showed a similar biphasic trend, that is, an initial burst release was followed by a slow, but sustained release.     

Binary self-assembly of highly symmetric DNA nanocages via sticky-end engineering

Discrete and symmetric three-dimensional(3D)DNA nanocages have been revoked as excellent candidates for various applications,such as guest component encapsulation and organization(e.g.dye molecules,proteins,inorganic nanoparticles,etc.)to construct new materials and devices.To date,a large variety of DNA nanocages has been synthesized through assembling small individual DNA motifs into predesigned structures in a bottom-up fashion.Most of them rely on the assembly using multiple copies of single type of motifs and a few sophisticated nanostructures have been engineered by co-assembling multi-types of DNA tiles simultaneously.However,the availability of complex DNA nanocages is still limited.Herein,we demonstrate that highly symmetric DNA nanocages consisted of binary DNA point-star motifs can be easily assembled by deliberately engineering the sticky-end interaction between the component building blocks.As such,DNA nanocages with new geometries,including elongated tetrahedron(E-TET),rhombic dodecahedron(R-DOD),and rhombic triacontahedron(R-TRI)are successfully synthesized.Moreover,their design principle,assembly process,and structural features are revealed by polyacryalmide gel electrophoresis(PAGE),atomic force microscope(AFM)imaging,and cryogenic transmission electron microscope imaging(cryo-TEM)associated with single particle reconstruction.     

Mineralogical composition of the meteorite El Pozo (Mexico): a Raman, infrared and XRD study

Narrowly distributed cationic poly (methyl methacrylate-co-diacetone acrylamide) (P(MMA-DAAM)) nanoparticles were successfully prepared by microemulsion polymerization. Photon correlation spectrometer (PCS) measurement and transmission electron microscope (TEM) observation revealed that z-average particle size of P(MMA-DAAM) is ∼27.5 nm. It was found that these cationic nanoparticles interact with DNA through electrostatic interaction to form P(MMA-DAAM)–DNA complex, which significantly enhances the resonance light scattering (RLS) signal. Therefore, a novel method using this polymer nanoparticle as a new probe for the detection of DNA by RLS technique is developed in this paper. The results showed this method is very convenient, sensitive, and reproducible.     

Single‐Particle Tracking and Modulation of Cell Entry Pathways of a Tetrahedral DNA Nanostructure in Live Cells

DNA is typically impermeable to the plasma membrane due to its polyanionic nature. Interestingly, several different DNA nanostructures can be readily taken up by cells in the absence of transfection agents, which suggests new opportunities for constructing intelligent cargo delivery systems from these biocompatible, nonviral DNA nanocarriers. However, the underlying mechanism of entry of the DNA nanostructures into the cells remains unknown. Herein, we investigated the endocytotic internalization and subsequent transport of tetrahedral DNA nanostructures (TDNs) by mammalian cells through single‐particle tracking. We found that the TDNs were rapidly internalized by a caveolin‐dependent pathway. After endocytosis, the TDNs were transported to the lysosomes in a highly ordered, microtubule‐dependent manner. Although the TDNs retained their structural integrity within cells over long time periods, their localization in the lysosomes precludes their use as effective delivery agents. To modulate the cellular fate of the TDNs, we functionalized them with nuclear localization signals that directed their escape from the lysosomes and entry into the cellular nuclei. This study improves our understanding of the entry into cells and transport pathways of DNA nanostructures, and the results can be used as a basis for designing DNA‐nanostructure‐based drug delivery nanocarriers for targeted therapy.     

Extended Langmuir approach to analyze the telomeric sequence using a biochromatographic concept

Immobilization of single-stranded DNA (ssDNA) on chromatographic support, i.e. copolymerized particles of styrene and glycidyl methacrylate via formation of amino groups with either N-methyl-1,3-propanediamine (stationary phase 1) or hexamethylenediamine (stationary phase 2) is a promise method to separate sequence specific DNA. However, the low ligand density of nonporous particles led to nonspecific interaction of the complementary oligonucleotide DNA in the sample with the stationary phase (1 or 2). In this paper, the binding process of telomere (tel; TTAGGG) to the complementary ssDNA immobilized (AATCCC) on the two chromatographic supports was studied for the first time using extended Langmuir equation. It appeared that the nonspecific adsorption of the tel due to electrostatic interaction between the polynucleotide sample (tel) and the residual amino groups on the particle surface via amination with hexamethylenediamine (stationary phase 2) was significant and could be reduced by using a high salt (NaCl) concentration in the bulk solvent. In contrast, the nonspecific adsorption of tel was neglected in the column using DNA-immobilized particles via amination with N-methyl-1,3-propanediamine (stationary phase 1). Thus, the affinity chromatography prepared via amination by N-methyl-1,3-propanediamine was more effective for analysis of sequence-specific DNA than the one prepared via amination by hexamethylenediamine.Moreover, for the two stationary phases, increasing NaCl concentration in the bulk solvent enhanced the hybridization between tel and the complementary immobilized oligonucleotide.     

Dissolving Hydroxyolite: A DNA Molecule into Its Hydroxyapatite Mold

In spite of the clinical importance of hydroxyapatite (HAp), the mechanism that controls its dissolution in acidic environments remains unclear. Knowledge of such a process is highly desirable to provide better understanding of different pathologies, as for example osteoporosis, and of the HAp potential as vehicle for gene delivery to replace damaged DNA. In this work, the mechanism of dissolution in acid conditions of HAp nanoparticles encapsulating double‐stranded DNA has been investigated at the atomistic level using computer simulations. For this purpose, four consecutive (multi‐step) molecular dynamics simulations, involving different temperatures and proton transfer processes, have been carried out. Results are consistent with a polynuclear decalcification mechanism in which proton transfer processes, from the surface to the internal regions of the particle, play a crucial role. In addition, the DNA remains protected by the mineral mold and transferred proton from both temperature and chemicals. These results, which indicate that biomineralization imparts very effective protection to DNA, also have important implications in other biomedical fields, as for example in the design of artificial bones or in the fight against osteoporosis by promoting the fixation of Ca²⁺ ions.