1YBN

Solution structure of the 3'E topology of the i-motif tetramer of d(CCCCAA)

Summary for 1YBN

• Entry DOI: 10.2210/pdb1ybn/pdb
• Related: 1YBL 1YBR 294D
• Descriptor: 5'-D(*CP*CP*CP*CP*AP*A)-3' (1 entity in total)
• Functional Keywords: dna; i-motif; hemiprotonated cytidine; tetrahymena; telomer, dna
• Biological source: synthetic construct
• Total number of polymer chains: 4
• Total formula weight: 6952.73

Authors

Esmaili, N.,Leroy, J.-L. (deposition date: 2004-12-21, release date: 2005-01-11, Last modification date: 2024-05-01)

Primary citation

Esmaili, N.,Leroy, J.-L.
i-motif solution structure and dynamics of the d(AACCCC) and d(CCCCAA) tetrahymena telomeric repeats
Nucleic Acids Res., 33:213-224, 2005

PubMed Abstract: Using NMR methods, we have resolved the i-motif structures formed by d(AACCCC) and by d(CCCCAA), two versions of the DNA sequence repeated in the telomeric regions of the C-rich strand of tetrahymena chromosomes. Both oligonucleotides form fully symmetrical i-motif tetramers built by intercalation of two hemiprotonated duplexes containing four C*C+ pairs. The structures are extremely stable. In the tetramer of d(AACCCC), the outermost C*C+ pairs are formed by the cytidines of the 5' ends of the cytidine tracts. A2 forms an A2*A2 (H6trans-N7) pair stacked to C3*C3+ and cross-strand stacked to A1. At 0 degrees C, the lifetimes of the hemiprotonated pairs range from 1 ms for the outermost pair to approximately 1 h for the innermost pairs. The tetramer of d(CCCCAA) adopts two distinct intercalation topologies in slow conformational exchange. One, whose outermost C*C+ pairs are built by the cytidines of the 5' end and the other by those of the 3' end. In both topologies, the adenosine bases are fairly well stacked to the adjacent C*C+ pairs. They are not paired but form symmetrical pseudo-pairs with their H6cis amino proton and N1 nitrogen pointing towards each other.

PubMed: 15647504
DOI: 10.1093/nar/gki160

Experimental method

SOLUTION NMR