1X26

Solution structure of the AA-mismatch DNA complexed with naphthyridine-azaquinolone

Summary for 1X26

• Entry DOI: 10.2210/pdb1x26/pdb
• Descriptor: 5'-D(*CP*TP*AP*AP*CP*AP*GP*AP*AP*TP*G)-3', 5'-D(*CP*AP*TP*TP*CP*AP*GP*TP*TP*AP*G)-3', N~3~-{3-[(7-METHYL-1,8-NAPHTHYRIDIN-2-YL)AMINO]-3-OXOPROPYL}-N~1~-[(7-OXO-7,8-DIHYDRO-1,8-NAPHTHYRIDIN-2-YL)METHYL]-BET A-ALANINAMIDE (3 entities in total)
• Functional Keywords: dna, aa mismatch, drug
• Total number of polymer chains: 2
• Total formula weight: 7633.45

Authors

Nakatani, K.,Hagihara, S.,Goto, Y.,Kobori, A.,Hagihara, M.,Hayashi, G.,Kyo, M.,Nomura, M.,Mishima, M.,Kojima, C. (deposition date: 2005-04-20, release date: 2006-04-04, Last modification date: 2024-05-29)

Primary citation

Nakatani, K.,Hagihara, S.,Goto, Y.,Kobori, A.,Hagihara, M.,Hayashi, G.,Kyo, M.,Nomura, M.,Mishima, M.,Kojima, C.
Small-molecule ligand induces nucleotide flipping in (CAG)n trinucleotide repeats
Nat.Chem.Biol., 1:39-43, 2005

PubMed Abstract: DNA trinucleotide repeats, particularly CXG, are common within the human genome. However, expansion of trinucleotide repeats is associated with a number of disorders, including Huntington disease, spinobulbar muscular atrophy and spinocerebellar ataxia. In these cases, the repeat length is known to correlate with decreased age of onset and disease severity. Repeat expansion of (CAG)n, (CTG)n and (CGG)n trinucleotides may be related to the increased stability of alternative DNA hairpin structures consisting of CXG-CXG triads with X-X mismatches. Small-molecule ligands that selectively bound to CAG repeats could provide an important probe for determining repeat length and an important tool for investigating the in vivo repeat extension mechanism. Here we report that napthyridine-azaquinolone (NA, 1) is a ligand for CAG repeats and can be used as a diagnostic tool for determining repeat length. We show by NMR spectroscopy that binding of NA to CAG repeats induces the extrusion of a cytidine nucleotide from the DNA helix.

PubMed: 16407992
DOI: 10.1038/nchembio708

Experimental method

SOLUTION NMR