Rational Design of Highly Responsive pH Sensors Based on DNA i-Motif

Abstract

Availability of strategies for molecular biosensing over a finely adjustable dynamic range is essential for understanding and controlling vital biological processes. Herein we report design principles of highly responsive pH sensors based on a DNA i-motif where both response sensitivity and transition midpoint can be tuned with high precision over the physiologically relevant pH interval. The tuning is accomplished via rational manipulations of an i-motif structure as well as incorporation of allosteric control elements. This strategy delivers molecular sensing systems with a transition midpoint tunable with 0.1 pH units precision and with a total response range as narrow as 0.2 pH units which can be adjusted to a variety of outputs (e.g., fluorescent readout). The potential of the presented approach is not limited by pH sensing but may extend toward manipulation of other quadruplex based structures or the development of ultraresponsive elements for artificial molecular machines and signaling systems.

Pyrene functionalized molecular beacon with pH-sensitive i-motif in a loop

“…4 obtained for separate solutions method. Moreover, our results demonstrated that the manipulation of an i-motif composition can lead to the development of pH sensors with a specifically defined transition midpoint (precision of 0.1 pH units) and a good response resolution (0.2 pH units or better), which agrees with the results for FRET pH sensor based on similar design platform recently reported by Nesterov et al [27]. It is worth mention that we performed preliminary experiments [28] to check if the pHSO_A sensor could sense pH change in a living cell.…”

Multistimuli‐responsive White Luminescent Fluids Using Hybrid Lanthanide Metal–Coordinate Complex Probes

“…[ 19 ] Molecular pH sensors that function over a broad pH range are particularly useful but challenging to design and as a result most function under either predominantly acidic or basic conditions. [ 20 ] We observed broad spectrum pH sensitivity of material (1) between pH 4 and pH 10 the solutions emit variations of white light with the strongest intensity at neutral pH; (2) a switch from blue to cyan emission is observed for solutions at pH < 4; (3) blue emitting solutions are formed at pH > 10 ( Figure 4 and Figure S9, Supporting Information). At pH 3 and below, all emission bands are dramatically reduced, indicative of general dissociation of metal-ligand bonds due to protonation of the pyridyl coordination site (pKa [H2Tpy]2+ = 3.57, pKa [HTpy]+ = 4.54).…”

Controlling Hybridization Chain Reactions with pH

“…These include sequence-dependency limitations (only C-rich sequences with a certain consecutive content of cytosines can form i-motif), structural constraints (formation of the complete tertiary structure is required in order to allow a pH-control), and a limited and quite narrow pH dynamic range (this usually spans not more than 2 orders of magnitude). 52,53 In response to the above limitations the use of triplexforming domains as an additional tool to control reactions in DNA-based nanotechnology can provide several advantages. For example, although homopurine sequences are needed to form triplex structures, the sequence-dependent limitations of our approach are far less strict than those related to the use of imotifs.…”