Abstract
We report here the three-dimensional structure of an i-motif/duplex junction, determined by NMR methods at neutral pH. By including a minor groove tetrad at one side of the C:C+ stack of a monomeric i-motif, and a stem/loop hairpin at the other side, we have designed stable DNA constructs in which i-DNA and B-DNA regions coexist in a wide range of experimental conditions. This study demonstrates that i- and B-DNA are structurally compatible, giving rise to a distinctive fold with peculiar groove shapes. The effect of different residues at the i-motif/duplex interface has been explored. We also show that these constructs can be adapted to sequences of biological relevance, like that found in the promoter region of the KRAS oncogene.
Highlights
We report here the three-dimensional structure of an i-motif/duplex junction, determined by NMR methods at neutral pH
Very little is known about the structure of i-motif/duplex junctions (IDJs), they are probably as common as those involving G-quadruplexes.[10]
The importance of these interactions is reflected by the fact that consensus sequences based on their capability to form favorable C:C+/minor groove tetrads (MGTs) interactions have been found to be prevalent in the human genome, occurring preferentially near regulatory regions
Summary
We report here the three-dimensional structure of an i-motif/duplex junction, determined by NMR methods at neutral pH. The effects of cytosine tract length and connecting loops have been widely studied in the past few years.[11] Capping interactions at the sides of the C:C+ stack play important roles in i-motif stability.[12] In particular, minor groove tetrads (MGTs) have been found to be excellent capping elements, able to stabilize i-motifs at neutral conditions.[7] MGTs result from the association of Watson− Crick or G:T base-pairs through their minor groove side.
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