9YDI

Dickerson dodecamer RNA duplex containing an A/G mismatch.

Summary for 9YDI

Entry DOI	10.2210/pdb9ydi/pdb
Descriptor	RNA 12-mer (2 entities in total)
Functional Keywords	dickerson dodecamer, rna oligonuleotide, a/g mismatch, rna
Biological source	synthetic construct
Total number of polymer chains	1
Total formula weight	3851.36
Authors	Harp, J.M.,Egli, M.E. (deposition date: 2025-09-22, release date: 2026-08-05)
Primary citation	Madaoui, M.,Kundu, J.,Datta, D.,Harp, J.M.,Egli, M.,Manoharan, M. A Postsynthetic Strategy for Oligonucleotides Containing 2-Fluoro-adenine and Isoguanine Nucleobases. Org.Lett., 28:9133-9138, 2026 Cited by PubMed Abstract: We describe a strategy for the synthesis of DNA, RNA and 2'--methyl (2'--Me) oligonucleotides containing 2-fluoro-adenine (A) and isoguanine (iG) nucleobases. To the best of our knowledge, this is the first nonenzymatic route for the synthesis of oligonucleotides containing 2-fluoro-adenine. We also describe the hydrolytic strategy for the conversion of 2-fluoro-adenine into isoguanine. Unlike 2,6-diaminopurine, 2-fluoro-adenine and isoguanine modifications are thermally destabilizing in the context of DNA, RNA, and 2'--methyl oligonucleotide duplexes. PubMed: 42455745 DOI: 10.1021/acs.orglett.6c01203 PDB entries with the same primary citation
Experimental method	X-RAY DIFFRACTION (1.03 Å)

Structure validation