3 research outputs found
Heteroepitaxial Streptavidin Nanocrystals Reveal Critical Role of Proton “Fingers” and Subsurface Atoms in Determining Adsorbed Protein Orientation
Characterization of noncovalent interactions between nanometer-sized structures, such as proteins, and solid surfaces is a subject of intense interest of late owing to the rapid development of numerous solid materials for medical and technological applications. Yet the rational design of these surfaces to promote the adsorption of specific nanoscale complexes is hindered by a lack of an understanding of the noncovalent interactions between nanostructures and solid surfaces. Here we take advantage of the unexpected observation of two-dimensional nanocrystals of streptavidin on muscovite mica to provide details of the streptavidin–mica interface. Analysis of atomic force microscopic images together with structural modeling identifies six positively charged residues whose terminal amine locations match the positions of the single atom-sized anionic cavities in the basal mica surface to within 1 Å. Moreover, we find that the streptavidin crystallites are oriented only along a single direction on this surface and not in either of three different directions as they must be if the protein interacted solely with the 3-fold symmetric basal surface atoms. Hence, this broken symmetry indicates that the terminal amine protons must also interact directly with the subsurface hydroxide atoms that line the bottom of these anionic cavities and generate only a single axis of symmetry. Thus, in total, these results reveal that subsurface atoms can have a significant influence on protein adsorption and orientation and identify the insertion of proton “fingers” as a means by which proteins may generally interact with solid surfaces
Super-resolution Imaging of Individual Human Subchromosomal Regions <i>in Situ</i> Reveals Nanoscopic Building Blocks of Higher-Order Structure
It is widely recognized
that the higher-order spatial organization
of the genome, beyond the nucleosome, plays an important role in many
biological processes. However, to date, direct information on even
such fundamental structural details as the typical sizes and DNA content
of these higher-order structures <i>in situ</i> is poorly
characterized. Here, we examine the nanoscopic DNA organization within
human nuclei using super-resolution direct stochastic optical reconstruction
microscopy (dSTORM) imaging and 5-ethynyl-2′-deoxyuridine click
chemistry, studying single fully labeled chromosomes within an otherwise
unlabeled nuclei to improve the attainable resolution. We find that,
regardless of nuclear position, individual subchromosomal regions
consist of three different levels of DNA compaction: (i) dispersed
chromatin; (ii) nanodomains of sizes ranging tens of nanometers containing
a few kilobases (kb) of DNA; and (iii) clusters of nanodomains. Interestingly,
the sizes and DNA content of the nanodomains are approximately the
same at the nuclear periphery, nucleolar proximity, and nuclear interior,
suggesting that these nanodomains share a roughly common higher-order
architecture. Overall, these results suggest that DNA compaction within
the eukaryote nucleus occurs <i>via</i> the condensation
of DNA into few-kb nanodomains of approximately similar structure,
with further compaction occurring <i>via</i> the clustering
of nanodomains
Molecular Threading and Tunable Molecular Recognition on DNA Origami Nanostructures
The
DNA origami technology holds great promise for the assembly
of nanoscopic technological devices and studies of biochemical reactions
at the single-molecule level. For these, it is essential to establish
well controlled attachment of functional materials to predefined sites
on the DNA origami nanostructures for reliable measurements and versatile
applications. However, the two-sided nature of the origami scaffold
has shown limitations in this regard. We hypothesized that holes of
the commonly used two-dimensional DNA origami designs are large enough
for the passage of single-stranded (ss)-DNA. Sufficiently long ssDNA
initially located on one side of the origami should thus be able to
“thread” to the other side through the holes in the
origami sheet. By using an origami sheet attached with patterned biotinylated
ssDNA spacers and monitoring streptavidin binding with atomic force
microscopic (AFM) imaging, we provide unambiguous evidence that the
biotin ligands positioned on one side have indeed threaded through
to the other side. Our finding reveals a previously overlooked critical
design feature that should provide new interpretations to previous
experiments and new opportunities for the construction of origami
structures with new functional capabilities