50 research outputs found
Structural Rigidity of Paranemic (PX) and Juxtapose (JX) DNA Nanostructures
Crossover motifs are integral components for designing DNA based
nanostructures and nanomechanical devices due to their enhanced rigidity
compared to the normal B-DNA. Although the structural rigidity of the double
helix B-DNA has been investigated extensively using both experimental and
theoretical tools, to date there is no quantitative information about
structural rigidity and the mechanical strength of parallel crossover DNA
motifs. We have used fully atomistic molecular dynamics simulations in explicit
solvent to get the force-extension curve of parallel DNA nanostructures to
characterize their mechanical rigidity. In the presence of mono-valent Na+
ions, we find that the stretch modulus (\gamma_1) of the paranemic crossover
(PX) and its topo-isomer JX DNA structure is significantly higher (~ 30%)
compared to normal B-DNA of the same sequence and length. However, this is in
contrast to the original expectation that these motifs are almost twice rigid
compared to the double-stranded B-DNA. When the DNA motif is surrounded by a
solvent with Mg2+ counterions, we find an enhanced rigidity compared to Na+
environment due to the electrostatic screening effects arising from the
divalent nature of Mg2+ ions. This is the first direct determination of the
mechanical strength of these crossover motifs which can be useful for the
design of suitable DNA for DNA based nanostructures and nanomechanical devices
with improved structural rigidity.Comment: 30 pages, 7 figure
The Flexibility of DNA Double Crossover Molecules
Double crossover molecules are DNA structures containing two Holliday junctions connected by two double helical arms. There are several types of double crossover molecules, differentiated by the relative orientations of their helix axes, parallel or antiparallel, and by the number of double helical half-turns (even or odd) between the two crossovers. They are found as intermediates in meiosis and they have been used extensively in structural DNA nanotechnology for the construction of one-dimensional and two-dimensional arrays and in a DNA nanomechanical device. Whereas the parallel double helical molecules are usually not well behaved, we have focused on the antiparallel molecules; antiparallel molecules with an even number of half-turns between crossovers (termed DAE molecules) produce a reporter strand when ligated, facilitating their characterization in a ligation cyclization assay. Hence, we have estimated the flexibility of antiparallel DNA double crossover molecules by means of ligation-closure experiments. We are able to show that these molecules are approximately twice as rigid as linear duplex DNA
DNA Cages with Icosahedral Symmetry in Bionanotechnology
Blueprints for polyhedral cages with icosahedral symmetry made of circular DNA molecules are provided. The basic rule is that every edge of the cage is met twice in opposite directions by the DNA strand(s), and vertex junctions are realized by a set of admissible junction types. As nanocontainers for cargo storage and delivery, the icosidodecahedral cages are of special interest because they have the largest volume per surface ratio of all cages discussed here
DNA Nanotechnology for Nucleic Acid Analysis: DX Motif-Based Sensor
[Image: see text] A sensor that fluoresces in the presence of specific nucleic acids was designed and characterized. The sensor uses a molecular beacon probe and three adaptor strands to form five-stranded associate, a DX-tile, with a specific analyte. The new sensor can be used as a highly selective and affordable tool for real-time analysis of DNA and RNA