7QA9

10bp DNA/DNA duplex

Summary for 7QA9

• Entry DOI: 10.2210/pdb7qa9/pdb
• NMR Information: BMRB: 34679
• Descriptor: DNA (5'-D(*CP*CP*AP*TP*TP*AP*TP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*AP*TP*AP*AP*TP*GP*G)-3') (2 entities in total)
• Functional Keywords: duplex, 10bp, dna
• Biological source: Octodon degus; More
• Total number of polymer chains: 2
• Total formula weight: 6088.03

Authors

Li, Q.,Trajkovski, M.,Fan, C.,Chen, J.,Zhou, Y.,Lu, K.,Li, H.,Su, X.,Xi, Z.,Plavec, J.,Zhou, C. (deposition date: 2021-11-16, release date: 2022-11-16, Last modification date: 2024-06-19)

Primary citation

Li, Q.,Trajkovski, M.,Fan, C.,Chen, J.,Zhou, Y.,Lu, K.,Li, H.,Su, X.,Xi, Z.,Plavec, J.,Zhou, C.
4'-SCF 3 -Labeling Constitutes a Sensitive 19 F NMR Probe for Characterization of Interactions in the Minor Groove of DNA.
Angew.Chem.Int.Ed.Engl., 61:e202201848-e202201848, 2022

PubMed Abstract: Fluorinated nucleotides are invaluable for F NMR studies of nucleic acid structure and function. Here, we synthesized 4'-SCF -thymidine (T ) and incorporated it into DNA by means of solid-phase DNA synthesis. NMR studies showed that the 4'-SCF group exhibited a flexible orientation in the minor groove of DNA duplexes and was well accommodated by various higher order DNA structures. The three magnetically equivalent fluorine atoms in 4'-SCF -DNA constitute an isolated spin system, offering high F NMR sensitivity and excellent resolution of the positioning of T within various secondary and tertiary DNA structures. The high structural adaptability and high sensitivity of T make it a valuable F NMR probe for quantitatively distinguishing diverse DNA structures with single-nucleotide resolution and for monitoring the dynamics of interactions in the minor groove of double-stranded DNA.

PubMed: 36163470
DOI: 10.1002/anie.202201848

Experimental method

SOLUTION NMR