Abstract

The mouse Ms6-hm microsatellite consists of a tandem array of the pentamer d(CAGGG)n. This microsatellite is extremely hypervariable, showing a germ line mutation rate of 2.5%/gamete. The mechanism responsible for this instability is not known. The ability to form intrastrand structures is a conserved feature of many hypervariable sequences, and it has been suggested that the formation of such structures might account for instability by affecting DNA replication, repair, or recombination. Here we show that this microsatellite is able to form intrastrand structures as well. Under physiological conditions, the Ms6-hm microsatellite forms a hairpin as well as two different unusual intrastrand tetraplexes. The hairpin forms in the absence of monovalent cation and contains G.A, G.C, and G.G base pairs in a 1:1:1 ratio. In the presence of K+, a tetraplex is formed in which the adenines are unpaired and extrahelical, and the cytosines are involved in C.C pairs. In Na+, a tetraplex forms that contains C.C+ pairs, with the adenines being intrahelical and hydrogen-bonded to guanines. Tetraplex formation in the presence of Na+ requires both cytosines and adenines and might reflect the altered internal dimensions of this tetraplex, perhaps resulting from the ability of the C.C+ pairs to become intercalated in this sequence context. Our demonstration of the stabilization of tetraplexes by hydrogen bonding between adenines and guanines expands the hydrogen-bonding possibilities for tetraplexes and suggests that the category of sequences with tetraplex-forming potential may be larger than previously appreciated.

Highlights

  • From the Section on Genomic Structure and Function, Laboratory of Molecular and Cellular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0830

  • The ability to form intrastrand structures is a conserved feature of many hypervariable sequences, and it has been suggested that the formation of such structures might account for instability by affecting DNA replication, repair, or recombination

  • Since the properties of the arrest sites are all consistent with tetraplex formation, our working hypothesis was that the structural basis of the blocks to DNA synthesis seen in this region was the formation of one or more intrastrand tetraplexes with unusual properties

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Summary

Introduction

From the Section on Genomic Structure and Function, Laboratory of Molecular and Cellular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0830. The mouse Ms6-hm microsatellite consists of a tandem array of the pentamer d(CAGGG)n. The mouse microsatellite locus Ms6-hm on chromosome 4 is an example of a highly unstable tandem array [2] This microsatellite, which contains repeats of the pentamer d(CAGGG), shows a high rate of both germ line and somatic mutations [3], with germ line mutation rates of 2.5%/gamete and the number of repeats ranging from 200 to. It has been suggested that instability might result from repeated strand slippage in the repeat tract during replication [8], and as such, these blocks might play a role in promoting this process These blocks do not form in the presence of cations such as Rbϩ, Csϩ, Liϩ, or NH4ϩ. The properties of the Ms6-hm microsatellite are consistent with intrastrand tetraplex formation

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