Silver Nanoclusters Serve as Fluorescent Rivets Linking Hoogsteen Triplex DNA and Hairpin-Loop DNA Structures

Riddhi Nagda, Sooyeon Park, Il Lae Jung, Keonwook Nam, Hari Chandana Yadavalli, Young Min Kim, Kyungjik Yang, Jooyoun Kang, Peter Waaben Thulstrup, Morten Jannik Bjerrum, Minhaeng Cho, Tae Hwan Kim, Young Hoon Roh, Pratik Shah, Seong Wook Yang

Research output: Contribution to journalArticlepeer-review

Abstract

Greater understanding of the mutual influence between DNA and the associated nanomaterial on the properties of each other can provide alternative strategies for designing and developing DNA nanomachines. DNA secondary structures are essential for encapsulating highly emissive silver nanoclusters (DNA/AgNCs). Likewise, AgNCs stabilize secondary DNA structures, such as hairpin DNA, duplex DNA, and parallel-motif DNA triplex. In this study, we found that the fluorescence of AgNCs encapsulated within a Hoogsteen triplex DNA structure can be turned on and off in response to pH changes. We also show that AgNCs can act as nanoscale rivets, linking two functionally distinctive DNA nanostructures. For instance, we found that a Hoogsteen triplex DNA structure with a seven-cytosine loop encapsulates red fluorescent AgNCs. The red fluorescence faded under alkaline conditions, whereas the fluorescence was restored in a near-neutral environment. Hairpin DNA and random DNA structures did not exhibit this pH-dependent AgNCs fluorescence. A fluorescence lifetime measurement and a small-angle X-ray scattering analysis showed that the triplex DNA-encapsulated AgNCs were photophysically convertible between bright and dark states. An in-gel electrophoresis analysis indicated that bright and dark convertibility depended on the AgNCs-riveted dimerization of the triplex DNAs. Moreover, we found that AgNCs rivet the triplex DNA and hairpin DNA to form a heterodimer, emitting orange fluorescence. Our findings suggest that AgNCs between two cytosine-rich loops can be used as nanorivets in designing noncanonical DNA origami beyond Watson-Crick base pairing.

Original languageEnglish
Pages (from-to)13211-13222
Number of pages12
JournalACS nano
Volume16
Issue number8
DOIs
Publication statusPublished - 2022 Aug 23

Keywords

  • Head-to-head dimerization
  • Hoogsteen triplex DNA
  • Nanorivets
  • Silver nanoclusters
  • and Noncanonical DNA origami

ASJC Scopus subject areas

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

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