Geometry-Based Self-Assembly of Histone-DNA Nanostructures at Single-Nucleotide Resolution

Maged F. Serag, Aimaiti Aikeremu, Ryoko Tsukamoto, Hubert Piwoński, Maram Abadi, Noritada Kaji, Jason R. Dwyer, Yoshinobu Baba, Satoshi Habuchi

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish
Pages (from-to)8155-8168
Number of pages14
JournalACS nano
Volume13
Issue number7
DOIs
Publication statusPublished - Jul 23 2019

Fingerprint

nucleotides
Nucleotides
Histones
Self assembly
self assembly
Single-Stranded DNA
Nanostructures
DNA
deoxyribonucleic acid
Geometry
geometry
Proteins
Molecular biology
proteins
Ionic strength
assembly
Microscopic examination
Compaction
Monomers
molecular biology

All Science Journal Classification (ASJC) codes

  • Materials Science(all)
  • Engineering(all)
  • Physics and Astronomy(all)

Cite this

Serag, M. F., Aikeremu, A., Tsukamoto, R., Piwoński, H., Abadi, M., Kaji, N., ... Habuchi, S. (2019). Geometry-Based Self-Assembly of Histone-DNA Nanostructures at Single-Nucleotide Resolution. ACS nano, 13(7), 8155-8168. https://doi.org/10.1021/acsnano.9b03259

Geometry-Based Self-Assembly of Histone-DNA Nanostructures at Single-Nucleotide Resolution. / Serag, Maged F.; Aikeremu, Aimaiti; Tsukamoto, Ryoko; Piwoński, Hubert; Abadi, Maram; Kaji, Noritada; Dwyer, Jason R.; Baba, Yoshinobu; Habuchi, Satoshi.

In: ACS nano, Vol. 13, No. 7, 23.07.2019, p. 8155-8168.

Research output: Contribution to journalArticle

Serag, MF, Aikeremu, A, Tsukamoto, R, Piwoński, H, Abadi, M, Kaji, N, Dwyer, JR, Baba, Y & Habuchi, S 2019, 'Geometry-Based Self-Assembly of Histone-DNA Nanostructures at Single-Nucleotide Resolution', ACS nano, vol. 13, no. 7, pp. 8155-8168. https://doi.org/10.1021/acsnano.9b03259
Serag, Maged F. ; Aikeremu, Aimaiti ; Tsukamoto, Ryoko ; Piwoński, Hubert ; Abadi, Maram ; Kaji, Noritada ; Dwyer, Jason R. ; Baba, Yoshinobu ; Habuchi, Satoshi. / Geometry-Based Self-Assembly of Histone-DNA Nanostructures at Single-Nucleotide Resolution. In: ACS nano. 2019 ; Vol. 13, No. 7. pp. 8155-8168.
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