Interaction of Carbon Dots with Nucleic Acids Is Driven by Their Surface Charge
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F26%3A00644870" target="_blank" >RIV/68081707:_____/26:00644870 - isvavai.cz</a>
Result on the web
<a href="https://pubs.acs.org/doi/10.1021/acs.jcim.5c02242?src=getftr&utm_source=clarivate&getft_integrator=clarivate" target="_blank" >https://pubs.acs.org/doi/10.1021/acs.jcim.5c02242?src=getftr&utm_source=clarivate&getft_integrator=clarivate</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/acs.jcim.5c02242" target="_blank" >10.1021/acs.jcim.5c02242</a>
Alternative languages
Result language
angličtina
Original language name
Interaction of Carbon Dots with Nucleic Acids Is Driven by Their Surface Charge
Original language description
Carbon dots (CDs) are nanoscale carbon materials with tunable optical properties, low toxicity, and modular functionalization, making them a promising material for biomedical applications. For safe and efficient applications in theranostics, it is essential to assess how CDs interact with biomolecules. Here, we focus on the effect of CDs on the structure and function of nucleic acids (NAs), relevant to NA structural stability, chromatin organization, and gene regulation. We performed more than 150 mu s of atomistic molecular dynamics simulations, encompassing a diverse set of NA structures, from canonical DNA and RNA helices through noncanonical motifs such as tetraloops and G-quadruplexes, up to nucleosomes. We simulated their interactions with graphitic CDs with two sizes and distinct surface chemistries: neutral hydrophobic (CD0), negatively charged (CD-), and positively charged (CD+). We identified multiple nonspecific interaction modes including stacking to bases, CH-pi contacts, and electrostatic interactions with the NA backbone. All CD types formed contacts with NAs, but only CD+ remained tightly bound and is therefore relevant for NA-related applications. The CD nonspecific binding did not compromise the global NA architecture, and we did not observe any intercalation or base-pair disruption. In the nucleosome, CD+ adsorb to DNA and occasionally bridge adjacent DNA gyres, that may alter local chromatin dynamics. In summary, the surface charge and particle size emerged as the key determinants of NA-CD interactions, providing atomistic guidance for the rational design of CDs optimized for theranostic applications.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10401 - Organic chemistry
Result continuities
Project
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Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2026
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Journal of Chemical Information and Modeling
ISSN
1549-9596
e-ISSN
1549-960X
Volume of the periodical
66
Issue of the periodical within the volume
1
Country of publishing house
US - UNITED STATES
Number of pages
14
Pages from-to
591-604
UT code for WoS article
001643676500001
EID of the result in the Scopus database
2-s2.0-105027247015