9YDJ

Dickerson dodecamer RNA duplex containing 2-F-6-aminopurine/U base pairing

This is a non-PDB format compatible entry.

Summary for 9YDJ

• Entry DOI: 10.2210/pdb9ydj/pdb
• Descriptor: RNA 12-mer, MAGNESIUM ION (3 entities in total)
• Functional Keywords: dickerson dodecamer, rna oligonucleotide, 2-f-6-aminopurine, rna
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 3935.95

Authors

Harp, J.M.,Egli, M. (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

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

Experimental method

X-RAY DIFFRACTION (1.3 Å)