3 research outputs found
Structurally Ordered Nanowire Formation from Co-Assembly of DNA Origami and Collagen-Mimetic Peptides
We describe the co-assembly of two
different building units: collagen-mimetic
peptides and DNA origami. Two peptides <b>CP</b><sup><b>++</b></sup> and <b>sCP</b><sup><b>++</b></sup> are designed
with a sequence comprising a central block (Pro-Hyp-Gly) and two positively
charged domains (Pro-Arg-Gly) at both N- and C-termini. Co-assembly
of peptides and DNA origami two-layer (<b>TL</b>) nanosheets
affords the formation of one-dimensional nanowires with repeating
periodicity of ∼10 nm. Structural analyses suggest a face-to-face
stacking of DNA nanosheets with peptides aligned perpendicularly to
the sheet surfaces. We demonstrate the potential of selective peptide-DNA
association between face-to-face and edge-to-edge packing by tailoring
the size of DNA nanostructures. This study presents an attractive
strategy to create hybrid biomolecular assemblies from peptide- and
DNA-based building blocks that takes advantage of the intrinsic chemical
and physical properties of the respective components to encode structural
and, potentially, functional complexity within readily accessible
biomimetic materials
Site-Specific Surface Functionalization of Gold Nanorods Using DNA Origami Clamps
Precise control over surface functionalities
of nanomaterials offers
great opportunities for fabricating complex functional nanoarchitectures
but still remains challenging. In this work, we successfully developed
a novel strategy to modify a gold nanorod (AuNR) with specific surface
recognition sites using a DNA origami clamp. AuNRs were encapsulated
by the DNA origami through hybridization of single-stranded DNA on
the AuNRs and complementary capture strands inside the clamp. Another
set of capture strands on the outside of the clamp create the specific
recognition sites on the AuNR surface. By means of this strategy,
AuNRs were site-specifically modified with gold nanoparticles at the
top, middle, and bottom of the surface, respectively, to construct
a series of well-defined heterostructures with controlled “chemical
valence”. Our study greatly expands the utility of DNA origami
as a tool for building complex nanoarchitectures and represents a
new approach for precise tailoring of nanomaterial surfaces
Martini 3 Coarse-Grained Force Field for Carbohydrates
The Martini 3 force
field is a full reparametrization of the Martini
coarse-grained model for biomolecular simulations. Due to the improved
interaction balance, it allows for a more accurate description of
condensed phase systems. In the present work, we develop a consistent
strategy to parametrize carbohydrate molecules accurately within the
framework of Martini 3. In particular, we develop a canonical mapping
scheme which decomposes arbitrarily large carbohydrates into a limited
number of fragments. Bead types for these fragments have been assigned
by matching physicochemical properties of mono- and disaccharides.
In addition, guidelines for assigning bonds, angles, and dihedrals
were developed. These guidelines enable a more accurate description
of carbohydrate conformations than in the Martini 2 force field. We
show that models obtained with this approach are able to accurately
reproduce osmotic pressures of carbohydrate water solutions. Furthermore,
we provide evidence that the model differentiates correctly the solubility
of the polyglucoses dextran (water-soluble) and cellulose (water insoluble
but soluble in ionic liquids). Finally, we demonstrate that the new
building blocks can be applied to glycolipids. We show they are able
to reproduce membrane properties and induce binding of peripheral
membrane proteins. These test cases demonstrate the validity and transferability
of our approach