Noncanonical Head-to-Head Hairpin DNA Dimerization Is Essential for the Synthesis of Orange Emissive Silver Nanoclusters

Pratik Shah, Riddhi Nagda, Il Lae Jung, Yong Joo Bhang, Sang Woo Jeon, Chang Seop Lee, Changwoo Do, Keonwook Nam, Young Min Kim, Sooyeon Park, Young Hoon Roh, Peter Waaben Thulstrup, Morten Jannik Bjerrum, Tae Hwan Kim, Seong Wook Yang

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28 Citations (Scopus)


DNA secondary structures, such as dimers and hairpins, are important for the synthesis of DNA template-embedded silver nanoclusters (DNA/AgNCs). However, the arrangement of AgNCs within a given DNA template and how the AgNC influences the secondary structure of the DNA template are still unclear. Here, we introduce a noncanonical head-to-head hairpin DNA nanostructure that is driven by orange-emissive AgNCs. Through detailed in-gel analysis, sugar backbone switching, inductively coupled plasma mass spectrometry, small-angle X-ray scattering, and small angle neutron scattering, we show that the orange-emissive AgNCs mediate cytosine-Ag-cytosine bridging between two six-cytosine loop (6C-loop) hairpin DNA templates. Unlike green, red, or far-red emissive AgNCs, which are embedded inside a hairpin and duplex DNA template, the orange-emissive AgNCs are localized on the interface between the two 6C-loop hairpin DNA templates, thereby linking them. Moreover, we found that deoxyribose in the backbone of the 6C-loop at the third and fourth cytosines is crucial for the formation of the orange-emissive AgNCs and the head-to-head hairpin DNA structure. Taken together, we suggest that the specific wavelength of AgNCs fluorescence is determined by the mutual interaction between the secondary or tertiary structures of DNA- and AgNC-mediated intermolecular DNA cross-linking.

Original languageEnglish
Pages (from-to)8697-8706
Number of pages10
JournalACS Nano
Issue number7
Publication statusPublished - 2020 Jul 28

Bibliographical note

Funding Information:
This work was supported by the Korea Research Fellowship Program funded by the Ministry of Science and ICT (NRF-2017H1D3A1A01014182, NRF-2017M2A2A6A04093177), the Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea (Grant No. HI16C1118), by a grant from the Basic Science Research Program through the National Research Foundation (NRF) (Grant No. 2018R1A6A1A03025607, NRF-2018R1D1A1B07051125) funded by the Ministry of Education, Republic of Korea, by Brain Korea 21 (BK21) PLUS program, by the Yonsei University Research Fund of 2017-22-0046 and Novo-Nordisk Foundation Grant No. NNF16OC0021832.

Publisher Copyright:
© 2020 American Chemical Society.

All Science Journal Classification (ASJC) codes

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


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