8PWR

TINA-conjugated antiparallel DNA triplex

Replaces:  6QHI

Summary for 8PWR

• Entry DOI: 10.2210/pdb8pwr/pdb
• NMR Information: BMRB: 34836
• Descriptor: DNA (5'-D(*TP*CP*CP*TP*CP*CP*T)-3'), DNA (5'-D(*AP*GP*GP*AP*GP*GP*A)-3'), DNA (5'-D(*TP*GP*GP*TP*GP*(J32)P*GP*T)-3') (3 entities in total)
• Functional Keywords: triplex, tina, antiparallel, conjugate, dna
• Biological source: Homo sapiens; More
• Total number of polymer chains: 3
• Total formula weight: 6872.72

Authors

Garavis, M.,Edwards, P.J.B.,Serrano-Chacon, I.,Doluca, O.,Filichev, V.V.,Gonzalez, C. (deposition date: 2023-07-21, release date: 2024-01-17, Last modification date: 2024-03-27)

Primary citation

Garavis, M.,Edwards, P.J.B.,Serrano-Chacon, I.,Doluca, O.,Filichev, V.V.,Gonzalez, C.
Understanding intercalative modulation of G-rich sequence folding: solution structure of a TINA-conjugated antiparallel DNA triplex.
Nucleic Acids Res., 52:2686-2697, 2024

PubMed Abstract: We present here the high-resolution structure of an antiparallel DNA triplex in which a monomer of para-twisted intercalating nucleic acid (para-TINA: (R)-1-O-[4-(1-pyrenylethynyl)phenylmethyl]glycerol) is covalently inserted as a bulge in the third strand of the triplex. TINA is a potent modulator of the hybridization properties of DNA sequences with extremely useful properties when conjugated in G-rich oligonucleotides. The insertion of para-TINA between two guanines of the triplex imparts a high thermal stabilization (ΔTM = 9ºC) to the structure and enhances the quality of NMR spectra by increasing the chemical shift dispersion of proton signals near the TINA location. The structural determination reveals that TINA intercalates between two consecutive triads, causing only local distortions in the structure. The two aromatic moieties of TINA are nearly coplanar, with the phenyl ring intercalating between the flanking guanine bases in the sequence, and the pyrene moiety situated between the Watson-Crick base pair of the two first strands. The precise position of TINA within the triplex structure reveals key TINA-DNA interactions, which explains the high stabilization observed and will aid in the design of new and more efficient binders to DNA.

PubMed: 38281138
DOI: 10.1093/nar/gkae028

Experimental method

SOLUTION NMR