pH-Dependent Capping Interactions Induce Large-Scale Structural Transitions in i-Motifs

Abstract

We study here a DNA oligonucleotide having the ability to form two different i-motif structures whose relative stability depends on pH and temperature. The major species at neutral pH is stabilized by two C:C+ base pairs capped by two minor groove G:C:G:C tetrads. The high pH and thermal stability of this structure are mainly due to the favorable effect of the minor groove tetrads on their adjacent positively charged C:C+ base pairs. At pH 5, we observe a more elongated i-motif structure consisting of four C:C+ base pairs capped by two G:T:G:T tetrads. Molecular dynamics calculations show that the conformational transition between the two structures is driven by the protonation state of key cytosines. In spite of large conformational differences, the transition between the acidic and neutral structures can occur without unfolding of the i-motif. These results represent the first case of a conformational switch between two different i-motif structures and illustrate the dramatic pH-dependent plasticity of this fascinating DNA motif.

Crystal Structure of an i‐Motif from the HRAS Oncogene Promoter

“…The C−C + capping interactions observed in iHRAS is similar to those seen in other iM structures [28, 29, 32, 39–41] . For example, the iM core formed by CCG triplet repeats (PDB ID 4PZQ) is flanked by one G−G base pair at each end [39] .…”

“…The CÀ C + capping interactions observed in iHRAS is similar to those seen in other iM structures. [28,29,32,[39][40][41] For example, the iM core formed by CCG triplet repeats (PDB ID 4PZQ) is flanked by one GÀ G base pair at each end. [39] As is the case for iHRAS, that structure displays a large propeller twist (23°and 39°) and a large buckle angle (16°a nd 27°) for the two GÀ G base pairs as well as large helical twists for the CÀ G steps (56°and 53°).…”

A Bright and Ionizable Cytosine Mimic for i-Motif Structures

“…Previous studies of the human telomeric repeat sequence containing end-labeled FRET probes also revealed an approximate 0.4 pH unit shift between the pH T value for collapse of the oligonucleotide into a compact form by FRET (pH T = 6.2) as compared to CD analyses of the same samples (pH T = 5.8) . Together these results can be rationalized by recent NMR studies showing the formation of partially folded i -motif structures containing C + :C base pairs at pH values above those needed for complete acid-mediated folding of the structure …”

“…44 Together these results can be rationalized by recent NMR studies showing the formation of partially folded i-motif structures containing C + :C base pairs at pH values above those needed for complete acidmediated folding of the structure. 45 To evaluate the ability of ts C to report structural changes involving hemiprotonated ts C + :C base pairs in real-time, toehold-mediated strand-displacement and/or hybridization reactions were conducted at pH = 5.0 (Figure 4). 29,46 After adding 1.2 equiv of complement (strand #1) to an im-DNA at pH = 5.0, a ds-DNA was generated according to fluorescence decreases at 485 and 555 nm (Figure 4A).…”

Rapid and Highly Efficient Separation of i-Motif DNA Species by CE-UV and Multivariate Curve Resolution

“…Circular dichroism (CD) and ultraviolet (UV) absorption spectroscopies are used to monitor unfolding induced by temperature changes . Whereas these techniques provide a whole view of the unfolding process, nuclear magnetic resonance (NMR) allows a local view of the changes accompanying these conformational processes . Complementary information may be obtained from separation techniques such as size exclusion chromatography (SEC) or polyacrylamide gel electrophoresis (PAGE).…”