A Proton‐Fuelled DNA Nanomachine

Abstract

The molecular-recognition properties of DNA are sufficiently well understood to enable the self-assembly of defined structures and devices on the nanometer scale. [1, 2] DNA machines based on a competing hybridization mechanism have been reported.[2] These nanomachines are fuelled by complementary oligonucleotides and accumulate doublestranded DNA waste products that poison the system. Herein we report a novel molecular machine driven by a distinct mechanism that is fast and relatively clean. It is based on a four-stranded DNA structure, called the i-motif, that can be formed from sequences containing stretches of cytosine (C) residues. [3][4][5][6][7] In this structure protonated C forms a noncanonical base pair with an unprotonated C (i.e., a CDC + base pair), and these base pairs interdigitate to form a quadruple helix that is stable under slightly acidic conditions. [3][4][5][6][7] A pH titration of the formation of the i-motif folded structure shows a sharp transition around pH 6.5; [4,5] thus, the design of a DNA nanomachine driven by pH changes is enabled.As illustrated in Figure 1, our system comprises a 21mer single-stranded oligonucleotide X containing four stretches of CCC. The second component is a 17 mer DNA strand Y, whose sequence is complementary to X with the exception of two bases. The two mismatches are necessary to stop strand Y folding into a G-quadruplex, a four-stranded structure that results from stacked tetrads of hydrogen-bonded guanine residues, [8] and to moderate the melting point of the double helix formed (see Supporting Information). At acidic pH (pH 5.0) strand X folds into the closed i-motif structure. [3,4,7] In this closed state, complementary strand Y adopts a floppy random-coil conformation. When the pH value is raised to 8.0, strand X unfolds and is captured by hybridization to Y with formation of an extended duplex structure (the open state). Interconversion of the closed and open states of the machine is thus mediated by alternating addition of H + and OH À .To visualize the open and closed states of this machine, a doubly labeled version of X (i.e., X*) was synthesized with a rhodamine green fluorophore at the 5' end and a dabcyl quencher at the 3' end. When the 5' and 3' ends of strand X* are nearby, the fluorescence of rhodamine green is quenched by dabcyl, whereas rhodamine green fluorescence is strong when it is held away from the dabcyl moiety. [7,9] Rhodamine green was chosen since its fluorescence yield is insensitive to pH value in the range pH 4.0-9.0; [10] therefore, the fluorescence of this system depends only on whether the machine is open or closed. [2,7] Fluorescence quenching was also exploited as an internal indicator for titrating the required amount of H + or OH À to switch between the open and closed states. In the fully extended, open state (pH 8.0), when rhodamine green is excited at 504 nm strong emission is observed at 534 nm; when closed by lowering the pH to 5.0, the fluorescence emission is reduced to 16 % (Figure 2 a).The structures associated ...

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