Structural properties of DNA oligomers containing (GACX)_n and (GAXC)_n tandem repeats

Abstract

The antisense DNA sequence of mature mouse micro RNA, miR341, includes three repeats of the tetranucleotide (GACC). The -GAC- repeat is known to form a parallel duplex, in acidic environments. The thermal melting profile of miR341 DNA, at pH 4, 5, and 6 indicates the formation of a very stable structure, which loses its stability when pH is increased. Thus, the addition of a cytosine at the 3' end of the (GAC) motif preserves the molecule's potential to fold into an unusual structure at low pH. The effect of modifying the nucleotide composition of the GACC sequence on the secondary structures formed by oligomers containing seven tandem repeats of the altered motifs was examined here. UV melting profiles were determined, as a function of pH, for 28-mers of the two series (GAXC)(7) and (GACX)(7) (X= A/C/T/G)(.) The sequence (GACC)(7) was found to be extremely sensitive to pH variations, with a stable structure formed at pH 5 (T(m) ≥ 60°C). NMR spectroscopy established that the low pH structure is not B-DNA. (GACA)(7) and (GACT)(7) also formed stable structures at low pH but the addition of guanine at the 3'end, as seen in the (GACG) series resulted in the loss of this property. Introducing a break in the 5'-GAC-3' motif, explored in the (GAXC) series, also inhibits formation of stable structures under acidic conditions.