8EPI

Engineering Crystals with Tunable Symmetries from 14- or 16-Base-Long DNA Strands

Summary for 8EPI

• Entry DOI: 10.2210/pdb8epi/pdb
• Descriptor: DNA (5'-D(P*CP*GP*TP*GP*GP*A)-3'), DNA (5'-D(*CP*GP*AP*CP*G)-3'), DNA (5'-D(P*TP*CP*CP*TP*A)-3') (3 entities in total)
• Functional Keywords: dna, four-fold rotational axis, left-handed, parallel
• Biological source: synthetic construct; More
• Total number of polymer chains: 3
• Total formula weight: 4809.27

Authors

Zhang, C.,Zhao, J.,Lu, B.,Sha, R.,Seeman, N.C.,Noinaj, N.,Mao, C. (deposition date: 2022-10-05, release date: 2023-03-08, Last modification date: 2024-04-03)

Primary citation

Zhang, C.,Zhao, J.,Lu, B.,Seeman, N.C.,Sha, R.,Noinaj, N.,Mao, C.
Engineering DNA Crystals toward Studying DNA-Guest Molecule Interactions.
J.Am.Chem.Soc., 145:4853-4859, 2023

PubMed Abstract: Sequence-selective recognition of DNA duplexes is important for a wide range of applications including regulating gene expression, drug development, and genome editing. Many small molecules can bind DNA duplexes with sequence selectivity. It remains as a challenge how to reliably and conveniently obtain the detailed structural information on DNA-molecule interactions because such information is critically needed for understanding the underlying rules of DNA-molecule interactions. If those rules were understood, we could design molecules to recognize DNA duplexes with a sequence preference and intervene in related biological processes, such as disease treatment. Here, we have demonstrated that DNA crystal engineering is a potential solution. A molecule-binding DNA sequence is engineered to self-assemble into highly ordered DNA crystals. An X-ray crystallographic study of molecule-DNA cocrystals reveals the structural details on how the molecule interacts with the DNA duplex. In this approach, the DNA will serve two functions: (1) being part of the molecule to be studied and (2) forming the crystal lattice. It is conceivable that this method will be a general method for studying drug/peptide-DNA interactions. The resulting DNA crystals may also find use as separation matrices, as hosts for catalysts, and as media for material storage.

PubMed: 36791277
DOI: 10.1021/jacs.3c00081

Experimental method

X-RAY DIFFRACTION (2.55 Å)