2MRZ

Dimeric structure of the Human A-box

Summary for 2MRZ

• Entry DOI: 10.2210/pdb2mrz/pdb
• NMR Information: BMRB: 25099
• Descriptor: DNA (5'-D(P*TP*CP*CP*TP*TP*TP*TP*CP*CP*A)-3') (1 entity in total)
• Functional Keywords: i-motif, centromere, self-recognition, dna
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 5891.88

Authors

Garavis, M.,Escaja, N.,Gabelica, V.,Villasante, A.,Gonzalez, C. (deposition date: 2014-07-18, release date: 2015-06-03, Last modification date: 2024-05-01)

Primary citation

Garavis, M.,Escaja, N.,Gabelica, V.,Villasante, A.,Gonzalez, C.
Centromeric Alpha-Satellite DNA Adopts Dimeric i-Motif Structures Capped by AT Hoogsteen Base Pairs.
Chemistry, 21:9816-9824, 2015

PubMed Abstract: Human centromeric alpha-satellite DNA is composed of tandem arrays of two types of 171 bp monomers; type A and type B. The differences between these types are concentrated in a 17 bp region of the monomer called the A/B box. Here, we have determined the solution structure of the C-rich strand of the two main variants of the human alpha-satellite A box. We show that, under acidic conditions, the C-rich strands of two A boxes self-recognize and form a head-to-tail dimeric i-motif stabilized by four intercalated hemi-protonated C:C(+) base pairs. Interestingly, the stack of C:C(+) base pairs is capped by T:T and Hoogsteen A:T base pairs. The two main variants of the A box adopt a similar three-dimensional structure, although the residues involved in the formation of the i-motif core are different in each case. Together with previous studies showing that the B box (known as the CENP-B box) also forms dimeric i-motif structures, our finding of this non-canonical structure in the A box shows that centromeric alpha satellites in all human chromosomes are able to form i-motifs, which consequently raises the possibility that these structures may play a role in the structural organization of the centromere.

PubMed: 26013031
DOI: 10.1002/chem.201500448

Experimental method

SOLUTION NMR