Entropy-Based Rational Modulation of the pK_a of a Synthetic pH-Dependent Nanoswitch

Abstract

The rational regulation of the pK a of an ionizable group in a synthetic device could be achieved by controlling the entropy of the linker connecting the hydrogen bond forming domains. We demonstrate this by designing a set of pH-responsive synthetic DNA-based nanoswitches that share the same hydrogen bond forming domains but differ in the length of the linker. The observed acidic constant (pK a) of these pH-dependent nanoswitches is linearly dependent on the entropic cost associated with loop formation and is gradually shifted to more basic pH values when the length of the linker domain is reduced. Through mathematical modeling and thermodynamic characterization we demonstrate that the modulation of the observed pK a is due to a purely entropic contribution. This approach represents a very versatile strategy to rationally modulate the pK a of synthetic devices in a highly predictable and accurate way.

Triggered Dimerization and Trimerization of DNA Tetrahedra for Multiplexed miRNA Detection and Imaging of Cancer Cells

“…The information encoded in the base sequences of nucleic acids provides a rich “toolbox” to construct DNA switches; [ 1 ] DNA machines; [ 2–4 ] switchable DNA structures, [ 5,6 ] such as origami systems; and signal‐triggered binding [ 7,8 ] and catalytic [ 9,10 ] functions of nucleic acids (such as aptamers or DNAzymes). Different triggers to switch the functions of nucleic acids were reported, including the formation and dissociation of G‐quadruplex with K + ‐ions/crown ether, [ 11,12 ] the pH‐induced formation and dissociation of i‐motif [ 13–15 ] or triplex structures, [ 16–20 ] the light‐induced stabilization/destabilization of duplex nucleic acids by means of photoisomerizable trans / cis ‐azobenzene intercalators, [ 21,22 ] and the stabilization/destabilization of duplex nucleic acids by fuel/anti‐fuel strand displacement processes. [ 23,24 ] The advances in DNA nanotechnology [ 25–27 ] introduced a variety of nanostructures for electrochemical [ 28,29 ] and optical sensing, [ 30–32 ] and particularly for multiplexed sensing platforms [ 33–37 ] for the detection of genes, aptamer–ligand complexes, and microRNAs (miRNAs).…”

Folding‐upon‐Repair DNA Nanoswitches for Monitoring the Activity of DNA Repair Enzymes

“…Upon hMGMT incubation, the enzymatic demethylation of O 6 -MeG in the triplex nanoswitches restores their ability to form atriplex structure.This is particularly clear for 2-Me triplex nanoswitch that shows aF RET signal (1.9 AE 0.1) after hMGMT incubation that is within the error of the control non-methylated nanoswitch (2.1 AE 0.1) (Figure 4d). Of note,the folding dynamics of these switches are extremely rapid (K folding and K unfolding = 10 s À1 and 2s À1 ,r espectively) [36] and thus the rate-determining step in these measurements is given by the enzyme-catalyzed reaction. We found out that with hMGMT asaturation of signal is observed after 15 minutes of enzymatic reaction (Figure S15).…”

Reconstructing the Free Energy Profiles Describing the Switching Mechanism of a pH-Dependent DNA Nanodevice from ABMD Simulations

“…The tetraprotic systems share the same structural features but contain four protonation centers in the TETRA5, TETRA15 and TETRA25 nanoswitches (Figure S1B-D of Supplementary Materials, respectively). The sequences used for the model building are identical to those reported in the experimental work [29], and are displayed here:…”

“…In the last few years, we demonstrated the importance of Molecular Dynamics (MD) simulations coupled to experiments in describing and predicting the atomistic behavior of DNA nanoswitches [26,27] integrated into complex nanostructures [28]. Recently, it was experimentally shown that the pH-responsive behavior of a nucleic acid nanoswitch, which can form an intramolecular triplex structure through hydrogen bonds (Hoogsteen interactions) between a hairpin double helix (DH) and a single-strand triplex-forming oligo (TFO) with two protonation centers, strongly depends on the length of the linker connecting the two domains (Figure 1A) [29]. Furthermore, it has also been demonstrated that the linker-dependent modulation can be dissipated by the introduction of four protonation centers in the single stranded triplex-forming portion [29].…”

“…Recently, it was experimentally shown that the pH-responsive behavior of a nucleic acid nanoswitch, which can form an intramolecular triplex structure through hydrogen bonds (Hoogsteen interactions) between a hairpin double helix (DH) and a single-strand triplex-forming oligo (TFO) with two protonation centers, strongly depends on the length of the linker connecting the two domains (Figure 1A) [29]. Furthermore, it has also been demonstrated that the linker-dependent modulation can be dissipated by the introduction of four protonation centers in the single stranded triplex-forming portion [29]. In this work, we apply Adaptively Biased Molecular Dynamics (ABMD) simulations to describe the effect of varying the length of the linker from 5 to 25 bases in regulating the pH-dependent conformational unbinding of the TFO from the DH, simulating three diprotic and three tetraprotic DNA nanoswitches.…”