Human chromosomal centromere (AATGG)_n sequence forms stable structures with unusual base pairs

Abstract

Nine DNA sequences related to the purine strand of the human centromeric satellite (AATGG)~.(CCATr)n repeat have been studied by two-dimensional nuclear magnetic resonance spectroscopy. Earlier studies have suggested that the structure of (AATGG)n sequence has an equilibrium between the duplex form and a fold-hack form. Structural refinement of d(CAATGG) and its related sequences by an NOE-constrained simulated annealing procedure reveals that the duplex form incorporates dynamic type-I G-A base pairs. 1D exchangeable proton NMR data support this model. The reverse sequence motif (GGTAA) destabilizes the structure.

Structure of a C-rich strand fragment of the human centromeric satellite III: a pH-dependent intercalation topology

“…These structures may be stabilized differently in vivo than in vitro by intranuclear ligands, inter i-motif inter-actions (for instance, loop-loop interactions) and/ or by the effective concentration of the high number of d(CCATT) repeats. The fact that the complementary G-rich strand, once separated from its Crich counterpart, also adopts different kinds of structures (hairpin, stem-looped, duplex) in sol-ution (Jaishree & Wang, 1994;Castati et al, 1994;Chou et al, 1996) and that on this strand also a single nucleotide substitution has dramatic effect on the structure (Zhu et al, 1996), is consistent with this idea.…”

“…Like satellite a, satellite III could be part of the functional centromere (Grady et al, 1992;Therkelsen et al, 1997). It includes the tandem repeats (CCATT)n (AATGG)n. The G-rich strand can form several stemloop structures in vitro (Jaishree & Wang, 1994;Castati et al, 1994;Gupta et al, 1994;Chou et al;1996;Zhu et al, 1996).…”

GNA Trinucleotide Loop Sequences Producing Extraordinarily Stable DNA Minihairpins

“…Other d(GNA) fragments can be expected to behave as the d(GAA) fragment, and it is possible that these d(GNA) sequences act as nucleation sites for unusual structures important for biological function. An NMR study on a centromeric repeat, (AATGG) n [)(GGAAT) n ], shows that the repeat sequence can easily be folded into a hairpin structure consisting of a stem with some A-T and G-A base pairs and a GGA loop (Jaishree & Wang, 1994). Even in the genome or in plasmids, GNA sequences show unusual behavior.…”

Sheared purine·purine pairing in biology

“…Several attempts have been made to solve the structure of the putative TGGAA:TGGAA duplex. Jaishree & Wang (1994) used a C(AATGG) sequence as a model for the (AATGG) tandem repeat. Unfortunately, the extra 5 H -terminal C residue changed thè`r egister'' of the pairing and forced the (AATGG) sequence to adopt an entirely different duplex con®guration with terminal GC pairs and two isolated head-to-head G anti ÁA anti pairs separated by Watson-Crick pairs.…”