한빛사 논문
Pratik Shah1,†, Riddhi Nagda1,†, Il Lae Jung2,†, Yong Joo Bhang3, Sang-Woo Jeon4, Chang Seop Lee1, Changwoo Do5, Keonwook Nam7, Young Min Kim7, Sooyeon Park1, Young Hoon Roh7,*, Peter Waaben Thulstrup6,*, Morten Jannik Bjerrum6,*, Tae-Hwan Kim4,*, Seong Wook Yang1,8,*
1Department of Systems Biology, Institute of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
2Department of Radiation Biology, Environmental Radiation Research Group, Korea Atomic Energy Research Institute, Daejeon 34057, Korea
3Seoulin Bioscience Co. Ltd., 4F. #A, KOREA BIO PARK, 700, Daewangpangyo-ro, Bundang-gu, Seongnam-si 13488, Gyeonggi-do, Korea
4Department of Quantum System Engineering, Jeonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju, 54896, Korea
5Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831, United States
6Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen 2100, Denmark
7Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea.
8UNIK Center for Synthetic Biology, University of Copenhagen, Thorvaldsensvej 40, 2000 Frederiksberg, Copenhagen, Denmark
*Corresponding authors
†Equal contribution
Abstract
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.
KEYWORDS:DNA nanotechnology, silver nanoclusters, DNA assembly, noncanonical DNA structure, metal-mediated structure, biomaterial, DNA nanodevice
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