Unusual Structures of the Tandem Repetitive DNA Sequences Located at Human Centromeres

The presence of the highly conserved repetitive DNA sequence d(AATGG)_n·d(CCATT)_n in human centromeres argues for a special role for this sequence in recognition, most probably through the formation of an unusual structure during mitosis. Quantitative one- and two-dimensional nuclear magnetic resonance (1D/2D NMR) spectroscopic studies reveal that the Watson-Crick duplex d(AATGG)_n· d(CCATT)_n adopts the usual B-DNA conformation as illustrated by taking d(AATGG)₃·d(CCATT)₃ as an example, whereas the d(CCATT)_n strand is essentially a random coil. In contrast, the d(AATGG)_n strand adopts an unusual stem-loop motif for repeat lengths n = 2, 3, 4, and 6. In addition to normal Watson-Crick A·T pairs, the stem-loop structures are stabilized by mismatched A·G and G·G pairs in the stem and G-G-A stacking in the loop. Stem-loop structures of d(AATGG)_n are independently verified by gel electrophoresis and nuclease digestion studies and were also previously shown to be as stable as the corresponding Watson-Crick duplex d(AATGG)_n·d(CCATT)_n [Grady et al. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 1695–1699]. Therefore, the sequence d(AATGG)_n can, indeed, nucleate a stem-loop structure at little free energy cost, and if, during mitosis, it is located on the chromosome surface, it can provide specific recognition sites for kinetochore function.