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PubMedDate not supplied

Nanostructures of complexes formed by calf thymus DNA interacting with cationic surfactants.

Synchrotron small-angle X-ray scattering was used to study the nanostructures of the complexes formed by calf thymus DNA interacting with cationic lipids (or surfactants) of didodecyldimethylammonium bromide (DDAB), cetyltrimethylammonium bromide (CTAB), and their mixture with a zwitterionic lipid of 1-palmitoyl-2-hydroxy-sn-glycero-3-phosphocholine (PHGPC). The effects of lipid/DNA ratios, DNA chain flexibility, lipid topology, and neutral lipid mixing on the nanostructures of DNA-lipid complexes were investigated. The complexes between double-stranded DNA (dsDNA) and double-tailed DDAB formed a bilayered lamellar structure, whereas the complexes between dsDNA and single-tailed CTAB preferred a structure of 2D hexagonal close packing of cylinders. With single stranded DNA (ssDNA) interacting with CTAB, the complexes showed a Pm3n cubic structure due to the different chain flexibility between dsDNA and ssDNA. The lipid molecules bound by rigid dsDNA like to form cylindrical micelles, whereas lipids bound to flexible ssDNA could form spherical or short cylindrical micelles. The addition of the neutral single-chained PHGPC lipids to the CTAB lipids could induce a structural transition of dsDNA-lipid complexes from a 2D hexagonal to a multi-bilayered lamellar structure. The parallel DNA strands were intercalated in the water layers of lamellar stacks of the mixed lipid bilayers. The DNA-DNA spacing depended on the ratios of charged lipid to neutral lipid, and charged lipid to DNA, respectively.

Animals↗
PubMed2005

Synthesis and spectral properties of DNA capped CdS nanoparticles in aqueous and non-aqueous media.

Synthesis of novel cadmium sulphide nanoparticles has been carried out in aqueous and non-aqueous media. DNA has been added during the synthesis of the nanoparticles, which results into cadmium-rich nanoparticles forming a stable complex with DNA. These particles exhibit strong fluorescence, spectral nature of which depends upon the medium in which the particles are synthesized. When interacted with proteins, fluorescence peak intensity of CdS nanoparticles increases considerably. It is possible that such CdS nanoparticles would be useful as a protein sensor.

Biosensing Techniques↗
PubMed2007

Nanopore sensor for fast label-free detection of short double-stranded DNAs.

Functionalizing surface enhanced the molecular sensing ability of a fabricated nanopore by increasing the translocation duration time for a short double-stranded DNA. The surface of nanopore was derivatized with gamma-aminopropyltriethoxysilane and the positively charged surface attracted DNA molecules when they were in the vicinity of nanopore. The translocation duration time of DNA increased due to the strong electrostatic interaction and it enabled us to detect a short double-stranded DNA (<1 kbp) that is under the size limit of a conventional solid state nanopore sensor. Both 539 and 910 bp double-stranded DNAs were analyzed with the surface functionalized nanopore and their translocation kinetics are presented in this work. The new feature of the surface modified nanopore that can detect short double-stranded DNA molecules could readily be applied for a rapid label-free diagnostic analysis in a Lab-On-a-Chip type DNA sensor.

Biosensing Techniques↗
PubMed2005

Design for DNA separation medium using bacterial cellulose fibrils.

In this paper, we present a novel DNA separation medium using bacterial cellulose fibrils. Bacterial cellulose has an intrinsic three-dimensional micrometer- to nanometer-scale network structure. Addition of this material to a low-concentration polymer solution (<5 cP) enables high-resolution electrophoretic separation of DNA, even for fragments of 10-100-bp or single-nucleotide polymorphism. The newly designed medium consists of a double mesh: a 10-nm flexible mesh derived from a conventional polymer medium containing 10-nm to 1-microm rigid pores made up of 10-microm bacterial cellulose fragments.

Acetobacter↗
PubMed2005

DNA-network-templated self-assembly of silver nanoparticles and their application in surface-enhanced Raman scattering.

A large-scale lambda-DNA network on a mica surface was successfully fabricated with a simple method. Silver nanoparticles capped with the cationic surfactant cetyltrimethylammonium bromide (CTAB) were self-assembled onto a two-dimensional DNA network template by electrostatic interaction and formed nanoporous silver films, which can be used as active surface-enhanced raman scattering (SERS) substrates. Two probe molecules, Rhodamine 6G (R6G) and 4-aminothiophenol (4-ATP), were studied on these substrates with very low concentrations, and great enhancement factors for R6G (0.21 x 10(10)-4.09 x 10(11)) and 4-ATP (approximately 1.70 x 10(5)) were observed. It was found that the enhancement ability was affected by the DNA concentration and the electrostatic absorption time of the CTAB-stabilized silver nanoparticles on the DNA strands. These SERS substrates formed by the self-assembly of silver nanoparticles on DNA network also show good stability and reproducibility in our experiments.

Aniline Compounds↗
PubMed2007

Molecular beam deposition of DNA nanometer films.

The development of novel photonic devices which incorporate biological materials is strongly tied to the development of thin film forming processes. Solution-based ("wet") processes when used with biomaterials in device fabrication suffer from dissolution of underlying layers, incompatibility with clean environment, inconsistent film properties, etc. We have investigated ultra-high-vacuum molecular beam deposition of surfactant-modified deoxyribonucleic acid (DNA). We have obtained effective deposition rates of approximately 0.1-1 A/s, enabling reproducible and controllable deposition of nanometer-scale films.

DNA↗
PubMed2026

Volumetric DNA microscopy for mapping spatial transcriptomes in three dimensions.

The architecture and function of biological systems are inherently three-dimensional, yet most existing spatial transcriptomic technologies remain restricted to thin tissue sections, limiting their capacity to resolve cellular organization and microenvironments within intact tissue volumes. To address this limitation, we developed volumetric DNA microscopy, a scalable, optics-free approach for spatial transcriptome profiling directly within intact biological specimens. The method encodes spatial information into DNA molecules that form a dense intermolecular network in situ, enabling the reconstruction of three-dimensional spatial relationships through short-read sequencing and computational analysis. Here we detail the complete workflow including in situ cDNA synthesis, spatial encoding through DNA nanoball formation, dual-scale proximity bridging between neighboring nanoballs and spatial reconstruction via geodesic spectral embedding. Sequencing libraries can be generated within 7-8 d by a competent graduate-level molecular biologist, followed by standardized downstream computational analysis. Because the workflow requires only routine molecular biology reagents and a benchtop sequencer, volumetric DNA microscopy provides a versatile platform for exploring genetic and morphological features in intact tissues.

Spatial Transcriptomics↗
PubMed2006

First blueprint, now bricks: DNA as construction material on the nanoscale.

For the most part DNA was considered Nature's instruction manual for life leading to the popular description 'blueprint of life'. However, DNA is now taking on a new aspect where it is finding use as a construction element for architecture on the nanoscale. This tutorial review addresses the importance of building ordered structures with DNA on the nanoscale, the underlying principles and approaches to build such scaffolds, the current limitations and the anticipated trajectory of the area. This is would be of interest to the chemical biology, supramolecular and bioengineering communities in particular.

DNA↗
PubMed2026

Multivalent cations stabilize DNA duplexes beyond charge neutralization.

Multivalent cations are abundant in cells and play essential roles in DNA duplex stability, genome packaging, and DNA-protein interactions. They can also condense DNA, making it challenging to determine their influence on DNA duplex stability. To overcome this challenge, we studied DNA unpeeling at equilibrium under high tension using magnetic tweezers, thereby preventing condensation. Experiments show that DNA duplex stability first increases and then decreases as cation concentration increases and the maximum DNA duplex stability increases with cation valence. The maximum free energy change of DNA was 3.33 k B T/bp for Na+ and increased to 3.98 k B T/bp for protamine, which is a small arginine-rich protein with a highly positive charge (&#x2248;21 for salmon sperm), corresponding to a relative increase of 19.5%. Consistently, all-atom molecular dynamics simulations show that higher-valent cations preferentially embed in the minor groove of DNA and clamp the minor groove, in contrast to the major-groove clamping reported for RNA, thereby stabilizing the helix more efficiently. These findings establish a single-molecule framework for quantifying DNA thermodynamics in complex ionic environments, which contributes to understanding ionic control of genome stability and to designing ion-tunable DNA-based nanostructures and delivery systems.

Journal Article↗
PubMed2001

Polymer-based gene delivery with low cytotoxicity by a unique balance of side-chain termini.

Protein expression after delivery of plasmid DNA to the cell nucleus depends on the processes of transcription and translation. Cytotoxic gene-delivery systems may compromise these processes and limit protein expression. This situation is perhaps most prevalent in current nonviral polycationic gene-delivery systems in which the polycationic nature of the delivery system can lead to cytotoxicity. To approach the problem of creating nontoxic but effective gene-delivery systems, we hypothesized that by optimizing the balance between polymer cationic density with endosomal escape moieties, effective gene transfer with low cytotoxicity could be created. As a model system, we synthesized a series of polymers whose side-chain termini varied with respect to the balance of cationic centers and endosomal escape moieties. Specifically, by polymer-analogous amidation we conjugated imidazole groups to the epsilon-amines of polylysine in varying mole ratios (73.5 mol % imidazole, 82.5 mol % imidazole, and 86.5 mol % imidazole). The primary epsilon-amine terminus of polylysine served as a model for the cationic centers, whereas the imidazole groups served as a model for the endosomal escape moieties. These polymers condensed plasmid DNA into nanostructures <150 nm and possessed little cytotoxicity in vitro. Transfection efficiency, as measured by luciferase protein expression, increased with increasing imidazole content of the polymers in a nonlinear relationship. The polymer with the highest imidazole content (86.5 mol %) mediated the highest protein expression, with levels equal to those mediated by polyethylenimine, but with little to no cytotoxicity.

Animals↗
PubMed2004

Translation of DNA signals into polymer assembly instructions.

We developed a DNA nanomechanical device that enables the positional synthesis of products whose sequences are determined by the state of the device. This machine emulates the translational capabilities of the ribosome. The device has been prototyped to make specific DNA sequences. The state of the device is established by the addition of DNA set strands. There is no transcriptional relationship between the set strands and the product strands. The device has potential applications that include designer polymer synthesis, encryption of information, and use as a variable-input device for DNA-based computation.

Base Sequence↗
PubMed2005

Bioconjugated nanoparticle for DNA protection from ultrasound damage.

To research whether poly-L-lysine-starch nanoparticle (PLL-StNP) could protect DNA from ultrasound damage or not, a series experiments were carried out: plasmid DNA-PLL-StNP complexes were treated with ultrasound for diverse times; the electrophoresis result proved that DNA bound to the complexes all the same. To investigate whether the conjugated DNA was completely protected or not, cDNA fragments bound to PLL-StNP were treated with ultrasound, and matched molecular beacons (MBs) were added. The cDNA-MB-PLL-StNP complexes exhibited dramatically increasing fluorescence, and had the same intensity as that of those MBs that were hybridized with free cDNA fragments. After being treated by ultrasound, the pIRGFP plasmid DNA-PLL-StNP complexes were transferred into COS-7 cells mediated by ultrasound. Green fluorescence protein expressed in most of the cells. Those results indicated that PLL-StNP could completely protect DNA from ultrasound damage. Furthermore, the DNA kept the same function as untreated one.

Biocompatible Materials↗
PubMed2006

Nucleic acids analysis with nano-Ag-Tb(III) by a resonance light scattering technique.

The nano-Ag-terbium(III)-mucleic acids system was observed by a resonance light scattering (RLS) technique for the first time, and the quantitative analysis of nucleic acids at nanogram levels was established. Studies showed that the RLS intensity of the nano-Ag-terbium(III) system can be obviously enhanced by nucleic acid, which was characterized by the RLS spectrum and the UV-Vis spectrum. In this system, the nanoparticles were only of a definite size and in a limited particle concentration region. Further research indicated that under the optimum conditions, the enhanced intensity of RLS is in proportion to the concentration of nucleic acids in the ranges of 7.0 x 10(-9) g ml(-1) to 8.0 x 10(-6) g ml(-1) for calf thymus DNA (ctDNA), 2.0 x 10(-8) g ml(-1) to 1.0 x 10(-6) g ml(-1) for fish sperm DNA (fsDNA) and 1.0 x 10(-9) g ml(-1) to 1.0 x 10(-7) g ml(-1) for yeast RNA (yRNA). The detection limits were 1.4 ng ml(-1) for ctDNA, 1.2 ng ml(-1) for fsDNA and 0.85 ng ml(-1) for yRNA, respectively. Synthetic and real samples were determined satisfactorily.

Calibration↗
PubMed2005

Generating highly ordered DNA nanostrand arrays.

Highly ordered arrays of stretched DNA molecules were generated over the millimeter scale by using a modified molecular combing method and soft lithography. Topological micropatterning on polydimethyl siloxane stamps was used to mediate the dynamic assembly of DNA molecules into arranged nonostrand arrays. These arrays consisted of either short nanostrands of several micrometers with fixed length and orientation or long nanostrands up to several hundred micrometers in length. The nanostrand arrays were transferred onto flat solid surfaces by contact printing, allowing for the creation of more complex patterns. This technique has potential applications for the construction of next-generation DNA chips and functional circuits of DNA-based 1D nanostructures.

DNA↗