biostudies-literatureChen Jthe National Key R&D Program of Chinathe National Research Programs from the Ministry of Science and Technology of Chinathe National Nature Science Foundation of Chinathe China Postdoctoral Science Foundationthe National Key R&D Program of Chinathe National Nature Science Founation of Chinae2312596121https://www.ebi.ac.uk/biostudies/studies/S-EPMC10945798biostudies-literatureUnknown121(11)Self-assembled DNA crystals offer a precise chemical platform at the ångström-scale for DNA nanotechnology, holding enormous potential in material separation, catalysis, and DNA data storage. However, accurately controlling the crystallization kinetics of such DNA crystals remains challenging. Herein, we found that atomic-level 5-methylcytosine (5mC) modification can regulate the crystallization kinetics of DNA crystal by tuning the hybridization rates of DNA motifs. We discovered that by manipulating the axial and combination of 5mC modification on the sticky ends of DNA tensegrity triangle motifs, we can obtain a series of DNA crystals with controllable morphological features. Through DNA-PAINT and FRET-labeled DNA strand displacement experiments, we elucidate that atomic-level 5mC modification enhances the affinity constant of DNA hybridization at both the single-molecule and macroscopic scales. This enhancement can be harnessed for kinetic-driven control of the preferential growth direction of DNA crystals. The 5mC modification strategy can overcome the limitations of DNA sequence design imposed by limited nucleobase numbers in various DNA hybridization reactions. This strategy provides a new avenue for the manipulation of DNA crystal structure, valuable for the advancement of DNA and biomacromolecular crystallography.Proceedings of the National Academy of Sciences of the United States of AmericaProgramming crystallization kinetics of self-assembled DNA crystals with 5-methylcytosine modification.PMC109457982022YFF07100002022YFF12018012021M7021062022M72271092056117 21934007T2188102 2199113422122406Liu XChen JXie XLv HWang FLi QShi JDai ZJin ZTang YFan CfalseProgramming crystallization kinetics of self-assembled DNA crystals with 5-methylcytosine modification.Self-assembled DNA crystals offer a precise chemical platform at the ångström-scale for DNA nanotechnology, holding enormous potential in material separation, catalysis, and DNA data storage. However, accurately controlling the crystallization kinetics of such DNA crystals remains challenging. Herein, we found that atomic-level 5-methylcytosine (5mC) modification can regulate the crystallization kinetics of DNA crystal by tuning the hybridization rates of DNA motifs. We discovered that by manipulating the axial and combination of 5mC modification on the sticky ends of DNA tensegrity triangle motifs, we can obtain a series of DNA crystals with controllable morphological features. Through DNA-PAINT and FRET-labeled DNA strand displacement experiments, we elucidate that atomic-level 5mC modification enhances the affinity constant of DNA hybridization at both the single-molecule and macroscopic scales. This enhancement can be harnessed for kinetic-driven control of the preferential growth direction of DNA crystals. The 5mC modification strategy can overcome the limitations of DNA sequence design imposed by limited nucleobase numbers in various DNA hybridization reactions. This strategy provides a new avenue for the manipulation of DNA crystal structure, valuable for the advancement of DNA and biomacromolecular crystallography.2024-01-01T00:00:00Z2024 Mar2025-04-26T03:38:38.37Z2025-04-06T10:48:55.85ZS-EPMC109457983843755510.1073/pnas.2312596121