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At least 55 records · Page 3Linked to original sources
PubMed2005

Three-helix bundle DNA tiles self-assemble into 2D lattice or 1D templates for silver nanowires.

We present a DNA nanostructure, the three-helix bundle (3HB), which consists of three double helical DNA domains connected by six immobile crossover junctions such that the helix axes are not coplanar. The 3HB motif presents a triangular cross-section with one helix lying in the groove formed by the other two. By differential programming of sticky-ends, 3HB tiles can be arrayed in two distinct lattice conformations: one-dimensional filaments and two-dimensional lattices. Filaments and lattices have been visualized by high-resolution, tapping mode atomic force microscopy (AFM) under buffer. Their dimensions are shown to be in excellent agreement with designed structures. We also demonstrate an electroless chemical deposition for fabricating metallic nanowires templated on self-assembled filaments. The metallized nanowires have diameters down to 20 nm and display Ohmic current-voltage characteristic.

DNA↗
PubMed2005

A modular approach to DNA-programmed self-assembly of macromolecular nanostructures.

DNA-programmed organic reactions are new and powerful tools for assembling chemical compounds into predetermined complex structures and a brief review of their use is given. This approach is particular efficient for the selection and covalent coupling of multiple components. DNA-templated synthesis is used for polymerization of PNA tetramers and for copying of the connectivity information in DNA. Direct DNA-programmed multicomponent coupling of custom designed organic modules is described. The macromolecular structures obtained are highly conjugated potentially conducting nanoscaffolds. Some future developments in this area are discussed.

DNA↗
PubMed2000

Self-assembled nanostructures based on DNA: towards the development of nanobiotechnology.

DNA is a promising construction material for the supramolecular 'bottom-up' engineering of artificial nanostructured devices. The use of DNA for the selective positioning of macromolecular components, the fabrication of nanostructured DNA scaffolds, as well as the DNA-templated synthesis of nanometer-sized and mesoscopic complexes, consisting of inorganic and bioorganic compounds, are exciting areas of current research.

Animals↗
PubMed2001

Peptide nucleic acid-assisted topological labeling of duplex dna.

Peptide nucleic acids (PNAs) are a family of synthetic polyamide mimics of nucleic acids that offer a variety of applications. Pyrimidine bis-PNAs can be used for rational design of novel interlocked DNA nanostructures, earring labels, representing locked pseudorotaxanes or locked catenanes. These structures are created through DNA ligase-mediated catenation of duplex DNA with a circularized oligonucleotide tag at a designated DNA site. The assembly is performed via formation of the PD-loop consisting of a pair of bis-PNA openers and the probe oligonucleotide. The openers locally expose one of the two strands of duplex DNA for hybridizing the probe, whose termini are complementary to the displaced DNA strand. After hybridization, they are in juxtaposition and can subsequently be linked by DNA ligase. As a result, a true topological link forms at a precise position on the DNA double helix yielding locked, earring-like label. DNA topological labeling can be done both in solution and, for longer templates, within the agarose gel plug. Accordingly, highly localized DNA detection with rolling circle amplification of hybridization signal and effective micromanipulations with DNA duplexes become possible through precise spatial positioning of various ligands on the DNA scaffold.

DNA↗
PubMed2006

Interaction of tin(II) and arsenic(III) with DNA at the nanostructure film modified electrodes.

Biosensors based on DNA and DNA-carbon nanotubes film immobilized at the surface of a screen-printed carbon electrode were used for simple in vitro tests of chemical toxicity. The damage to DNA caused by tin(II) and arsenic(III) compounds as components of specific reaction media was evaluated by means of an electrochemical DNA marker, [Co(phen)3](3+), as the portion of original dsDNA which survives an incubation of the biosensor in the cleavage medium. The results were confirmed by the electrically heated electrode and by the measurement of the DNA guanine moiety signal.

Arsenic↗
PubMed2006

Architecture with GIDEON, a program for design in structural DNA nanotechnology.

We present geometry based design strategies for DNA nanostructures. The strategies have been implemented with GIDEON-a graphical integrated development environment for oligonucleotides. GIDEON has a highly flexible graphical user interface that facilitates the development of simple yet precise models, and the evaluation of strains therein. Models are built on a simple model of undistorted B-DNA double-helical domains. Simple point and click manipulations of the model allow the minimization of strain in the phosphate-backbone linkages between these domains and the identification of any steric clashes that might occur as a result. Detailed analysis of 3D triangles yields clear predictions of the strains associated with triangles of different sizes. We have carried out experiments that confirm that 3D triangles form well only when their geometrical strain is less than 4% deviation from the estimated relaxed structure. Thus geometry-based techniques alone, without detailed energetic considerations, can be used to explain certain general trends in DNA structure formation. We have used GIDEON to build detailed models of double crossover and triple crossover molecules, evaluating the non-planarity associated with base tilt and junction misalignments. Computer modeling using a graphical user interface overcomes the limited precision of physical models for larger systems, and the limited interaction rate associated with earlier, command-line driven software.

Base Sequence↗
PubMed2003

Parallel molecular computations of pairwise exclusive-or (XOR) using DNA "string tile" self-assembly.

Self-assembling DNA nanostructures are an efficient means of executing parallel molecular computations. However, previous experimental demonstrations of computations by DNA tile self-assembly only allowed for one set of distinct input to be processed at a time. Here, we report the multibit, parallel computation of pairwise exclusive-or (XOR) using DNA "string tile" self-assembly. A set of DNA tiles encoding the truth table for the XOR logical operation was constructed. Parallel tile self-assembly and ligation led to the formation of reporter DNA strands which encoded both the input and the output of the computations. These reporter strands provided a molecular look-up table containing all possible pairwise XOR calculations up to a certain input size. The computation was readout by sequencing the cloned reporter strands. This is the first experimental demonstration of a parallel computation by DNA tile self-assembly in which a large number of distinct input were simultaneously processed.

DNA↗
PubMed2006

Single-chain antibodies against DNA aptamers for use as adapter molecules on DNA tile arrays in nanoscale materials organization.

Complex DNA nanostructures have been developed as structural components for the construction of nanoscale objects. Recent advances have enabled self-assembly of organized DNA nanolattices and their use in patterning functional bio-macromolecules and other nanomaterials. Adapter molecules that bind specifically to both DNA lattices and nanomaterials would be useful components in a molecular construction kit for patterned nanodevices. Herein we describe the selection from phage display libraries of single-chain antibodies (scFv) for binding to a specific DNA aptamer and their development as adapter molecules for nanoscale construction. We demonstrate the decoration of various DNA tile structures with aptamers and show binding of the selected single-chain antibody as well as the self-assembly of mixed DNA-protein biomolecular lattices.

Antibodies↗
PubMed2004

An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots.

Given a nucleic acid sequence, a recent algorithm allows the calculation of the partition function over secondary structure space including a class of physically relevant pseudoknots. Here, we present a method for computing base-pairing probabilities starting from the output of this partition function algorithm. The approach relies on the calculation of recursion probabilities that are computed by backtracking through the partition function algorithm, applying a particular transformation at each step. This transformation is applicable to any partition function algorithm that follows the same basic dynamic programming paradigm. Base-pairing probabilities are useful for analyzing the equilibrium ensemble properties of natural and engineered nucleic acids, as demonstrated for a human telomerase RNA and a synthetic DNA nanostructure.

Algorithms↗
PubMed2025

Single-Molecule Nanopore Detection of Non-Canonical Thymine-Melamine Hydrogen Bonding Base Pair in DNA Abasic Site.

The binding of small molecules to DNA may represent a mutagenic process capable of inducing genomic structural alterations and functional impairment. Melamine (MA), a toxic small molecule, exhibits a hydrogen-bonding interface structurally analogous to adenine, enabling to form non-canonical thymine-melamine (T-MA) base pairs like Watson-Crick pairing. This property allows MA to program DNA nanostructure formation. Given MA's documented biological consequences, such as kidney disease, reproductive toxicity, and central nervous system dysfunction, sensitive detection of MA-DNA interactions has become critically important. However, such subtle structural changes remain challenging to identify because of the paucity of effective detection approaches in a high-resolution manner. To overcome this limitation, nanopore measurement is employed to identify T-MA hydrogen bonding base pairing in DNA. Results demonstrate that nanopore enables unambiguous identification of T-MA hydrogen bonding via mechanically unzipping thymine-melamine-thymine (T-MA-T) triplets in DNA structures. The approach achieves single-base-pair resolution, as evidenced by nucleotide substitutions flanking the abasic site in complex DNA structures. In addition, nanopore-based kinetic analysis reveals an enhanced intramolecular stability in MA-binding DNA compared to those consisting of complete canonical DNA pairs. This research establishes a powerful platform for high-resolution interrogation of DNA-small molecule interactions and quantitative biophysical characterization of mutagenic modifications at the nanoscale.

Single Molecule Imaging↗
PubMed2004

Ligase-mediated construction of branched DNA strands: a novel DNA joining activity catalyzed by T4 DNA ligase.

Branched nucleic acid strands exist as intermediates in certain biological reactions, and bifurcating DNA also presents interesting opportunities in biotechnological applications. We describe here how T4 DNA ligase can be used for efficient construction of DNA molecules having one 5' end but two distinct 3' ends that extend from the 2' and 3' carbons, respectively, of an internal nucleotide. The nature of the reaction products is investigated, and optimal reaction conditions are reported for the construction of branched oligonucleotides. We discuss the utility of these branched DNA nanostructures for gene detection.

Adenosine Triphosphate↗
PubMed2006

Direct and random routing of a molecular motor protein at a DNA junction.

With the aim of investigating how motor proteins negotiate DNA nanostructures, we produced test circuits based on recombination intermediates in which 1D translocation across a Holliday junction (HJ) could be assessed by subsequent triplex displacement signals on each DNA arm. Using the EcoR124I restriction-modification enzyme, a 3'-5' double-strand DNA (dsDNA) translocase, we could show that the motor will tend to follow its translocated strand across a junction. Nonetheless, as the frequency of junction bypass events increases, the motor will occasionally jump tracks.

DNA, Cruciform↗
PubMed2006

DNA-templated nickel nanostructures and protein assemblies.

We report a straightforward method for the fabrication of DNA-templated nickel nanostructures on surfaces. These nickel nanomaterials have potential to be applied as nanowires, as templated catalyst lines, as nanoscale magnetic domains, or in directed protein localization. Indeed, we show here that histidine-tagged phosducin-like protein (His-PhLP) binds with high selectivity to both Ni2+-treated surface DNA and DNA-templated nickel metal to create linear protein assemblies on surfaces. The association of His-PhLP with DNA-templated nickel ions or metal is reversible under appropriate rinsing conditions. Nanoscale DNA-templated protein assemblies might be useful in the construction of high-density protein lines for proteomic analysis, for example. Importantly, these nanofabrication procedures are not limited to linear DNA and can be applied readily to other self-assembled DNA topologies.

DNA↗
PubMedDate not supplied

DNA hybridization in nanostructural molecular assemblies enables detection of gene mutations without a fluorescent probe.

We have developed a simple single nucleotide polymorphisms (SNPs) analysis utilizing DNA hybridization in nanostructural molecular assemblies. The novel technique enables the detection of a single-base mismatch in a DNA sequence without a fluorescent probe. This report describes for the first time that DNA hybridization occurs in the nanostructural molecular assemblies (termed reverse micelles) formed in an organic medium. The restricted nanospace in the reverse micelles amplifies the differences in the hybridization rate between mismatched and perfectly matched DNA probes. For a model system, we hybridized a 20-mer based on the p53 gene sequence to 20-mer complementary oligonucleotides with various types of mismatches. Without any DNA labeling or electrochemical apparatus, we successfully detected the various oligonucleotide mismatches by simply measuring the UV absorbance at 260 nm.

DNA Mutational Analysis↗
PubMed2004

Assembly of an antiparallel homo-adenine DNA duplex by small-molecule binding.

Molecules that reversibly bind DNA and trigger the formation of non-Watson-Crick secondary structures would be useful in the design of dynamic DNA nanostructures and as potential leads for new therapeutic agents. We demonstrate that coralyne, a small crescent-shaped molecule, promotes the formation of a duplex secondary structure from homo-adenine oligonucleotides. AFM studies reveal that the staggered alignment of homo-adenine oligonucleotides upon coralyne binding produces polymers of micrometers in length, but only 2 nm in height. A DNA duplex was also studied that contained eight A.A mismatches between two flanking 7-bp Watson-Crick helices. CD spectra confirm that the multiple A.A mismatches of this duplex bind coralyne in manner similar to that of homo-adenine oligonucleotides. Furthermore, the melting temperature of this hybrid duplex increases by 13 degrees C upon coralyne binding. These observations illustrate that the helical structure of the homo-adenine-coralyne duplex is compatible with the B-form DNA helix.

Adenine↗
PubMedDate not supplied

[Mechanisms of interaction between DNA and chemical analogues of microbial anabiosis autoinducers].

The alkylhydroxybenzene (AHB) autoregulatory factors d1 (fd1) of microorganisms have been found to directly interact with highly polymeric DNA. This circumstance results in changes, related to alterations in the topology of this macromolecule, in DNA physicochemical properties. The physicochemical properties of DNA in the presence of chemical analogues of microbial AHBs (methylresorcinol; hexylresorcinol; and 2-(4-hydroxyphenyl)ethane-1-ol, also known as tyrosol) were investigated using adsorption spectrophotometry, fluorometry, heat denaturation, viscosimetry, and electrophoresis in agarose gel. A number of concordant effects pointing to DNA-AHB interactions were revealed that manifesed themselves in the hypochromic properties of the resulting complexes, an increase in their melting temperature and viscosity, a decrease in their electrophoretic mobility, and a change in the fluorescent properties of AHBs upon complexation with DNA. Such alterations were particularly significant in the presence of hexylresorcinol, which possessed the maximum alkyl radical length among the fd1 analogues tested. Using atomic force microscopy, we visualized the micelle-like DNA nanostructures forming in the presence of AHBs. The results obtained provided the basis for developing a hypothetical model of the interaction between the biopolymer macromolecule and low-molecular-weight AHBs that takes into account the differences in the hydrophobicity of individual AHB homologues functioning as ligands. In terms of our model, we discuss AHB involvement in the stabilization of DNA and alteration of its topology, i.e., in the process related to intragenomic rearrangements, which account for the intrapopulational variability of bacteria, including dissociation processes.

Animals↗
PubMed2003

DNA-templated self-assembly of protein arrays and highly conductive nanowires.

A DNA nanostructure consisting of four four-arm junctions oriented with a square aspect ratio was designed and constructed. Programmable self-assembly of 4 x 4 tiles resulted in two distinct lattice morphologies: uniform-width nanoribbons and two-dimensional nanogrids, which both display periodic square cavities. Periodic protein arrays were achieved by templated self-assembly of streptavidin onto the DNA nanogrids containing biotinylated oligonucleotides. On the basis of a two-step metallization procedure, the 4 x 4 nanoribbons acted as an excellent scaffold for the production of highly conductive, uniform-width, silver nanowires.

Biotinylation↗
PubMed2006

Nanostructured layers from DNA, DNA:AU, DNA:C60 clusters.

The idea is requisite to coat DNA, DNA:Au, DNA:C60 clusters from water solution, which can be magnetic and electrical active in biosensor systems and to detect their functional properties by microwave techniques (). Our research has been focused on the application of I-V characteristics and surface microwave resonator methods to recognise and predict these molecular interactions based on primary structure and associated physic-chemical properties. In results we have actually shown that these molecular cluster layers on Si and Al2O3 substrates can conduct, switch electric current and respond on power of microwave (additives Au, C60, determine the conductivity of layers). We also aim to apply these Si and Al2O3 ships for Biochip.

Biosensing Techniques↗