posted on 2019-06-20, 00:00authored byMaged F. Serag, Aimaiti Aikeremu, Ryoko Tsukamoto, Hubert Piwoński, Maram Abadi, Noritada Kaji, Jason R. Dwyer, Yoshinobu Baba, Satoshi Habuchi
Histones
are basic protein monomers capable of interacting with
DNA, providing the mechanism of DNA compaction inside the cell nucleus.
The well-ordered assembly process of histone and DNA is a potential
candidate as the approach for building DNA–protein nanostructures.
Here, utilizing the sequence-independent histone–DNA interaction,
we present an approach to self-assemble histones and single-stranded
DNA (ssDNA) to form well-defined histone–DNA (sHD) nanoparticles
and their multidimensional cross-linked complexes (cHD). By using
various molecular biology and microscopy techniques, we elucidate
the structure of these complexes, and we show that they are formed
at carefully controlled conditions of temperature, ionic strength,
concentration, and incubation time. We also demonstrate using a set
of ssDNA molecular rulers and a geometric accommodation model that
the assembly of sHD and cHD particles proceeds with precise geometry
so that the number of ssDNA in these particles can be programmed by
the length of ssDNA. We further show that the formation of cHD amplifies
the effect of the length of ssDNA on the self-assembly, allowing for
distinguishing ssDNA of different lengths at single nucleotide resolution.
We envision that our geometry-directed approach of self-assembling
histone–DNA nanostructures and the fundamental insights can
serve as a structural platform to advance building precisely ordered
DNA–protein nanostructures.