4RIM

Native structure of intercalation-locked DNA tetraplex

Summary for 4RIM

• Entry DOI: 10.2210/pdb4rim/pdb
• Related: 4RIP
• Descriptor: DNA (5'-D(*AP*CP*TP*CP*GP*GP*AP*TP*GP*AP*T)-3') (1 entity in total)
• Functional Keywords: dna, homo-duplex, intercalation-locked dna tetraplex
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 3373.22

Authors

Tripathi, S.K.,Zhang, D.,Paukstelis, P. (deposition date: 2014-10-06, release date: 2015-02-11, Last modification date: 2024-02-28)

Primary citation

Tripathi, S.,Zhang, D.,Paukstelis, P.J.
An intercalation-locked parallel-stranded DNA tetraplex.
Nucleic Acids Res., 43:1937-1944, 2015

PubMed Abstract: DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson-Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(AC(Br)UCGGA(Br)UGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5'-most A-A base pairs between adjacent G-G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. (1)H-(1)H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures.

PubMed: 25628357
DOI: 10.1093/nar/gkv033

Experimental method

X-RAY DIFFRACTION (2.3 Å)