Mechanochemical Sensing: A Biomimetic Sensing Strategy

Shrestha, Prakash; Mandal, Shankar; Mao, Hanbin

doi:10.1002/cphc.201500080

Cited by 7 publications

(7 citation statements)

References 78 publications

(34 reference statements)

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“…To address this issue, we have pioneered single-molecule mechanochemical sensing (SMMS) , in which mechanochemical coupling has been exploited to directly connect molecular recognition and signal transduction units. Mechanochemical coupling occurs when individual macromolecules change their conformation upon ligand binding.…”

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confidence: 99%

Mechanochemical Sensing of Single and Few Hg(II) Ions Using Polyvalent Principles

et al. 2016

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Sensitivity of biosensors is set by the dissociation constant (K) between analytes and probes. Although potent amplification steps can be accommodated between analyte recognition and signal transduction in a sensor to improve the sensitivity 4-6 orders of magnitude below K, they compromise temporal resolution. Here, we demonstrated mechanochemical sensing that broke the K limit by 9 orders of magnitude for Hg detection without amplifications. Analogous to trawl fishing, we introduced multiple Hg binding units (thymine (T)-T pairs) in a molecular trawl made of two poly-T strands. Inspired by dipsticks to gauge content levels, mechanical information (force/extension) of a DNA hairpin dipstick was used to measure the single or few Hg ions bound to the molecular trawl, which was levitated by two optically trapped particles. The multivalent binding and single-molecule sensitivity allowed us to detect unprecedented 1 fM Hg ions in 20 min in field samples treated by simple filtrations.

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confidence: 99%

Mechanochemical Sensing of Single and Few Hg(II) Ions Using Polyvalent Principles

et al. 2016

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“…The DNA constructs for single-molecule mechanochemical sensing (SMMS) were prepared as described in the previous report . The sensing element was contained inside the DNA hairpin (see DNA sequences in Table S1) sandwiched between two long dsDNA handles .…”

Section: Methodsmentioning

confidence: 99%

“…Recently, we pioneered a new strategy, mechanochemical sensing, , to probe individual molecules in solution. This method uses a single-molecule mechanophore to transduce binding events into mechanical signals.…”

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confidence: 99%

Single-Molecule Mechanochemical pH Sensing Revealing the Proximity Effect of Hydroniums Generated by an Alkaline Phosphatase

et al. 2018

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Due to the fast diffusion, small molecules such as hydronium ions (HO) are expected to be homogeneously distributed, even close to the site-of-origin. Given the importance of HO in numerous processes, it is surprising that HO concentration ([HO]) has yet to be profiled near its generation site with nanometer resolution. Here, we innovated a single-molecule method to probe [HO] in nanometer proximity of individual alkaline phosphatases. We designed a mechanophore with cytosine (C)-C mismatch pairs in a DNA hairpin. Binding of HO to these C-C pairs changes mechanical properties, such as stability and transition distance, of the mechanophore. These changes are recorded in optical tweezers and analyzed in a multivariate fashion to reduce the stochastic noise of individual mechanophores. With this method, we found [HO] increases in the nanometer vicinity of an active alkaline phosphatase, which supports that the proximity effect is the cause for increased rates in cascade enzymatic reactions.

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“…Mechanical signals in mechanochemical sensing have shown these promising potentials and proved their complementarity to the optical and electrochemical signals. 14 Mechanochemical sensing uses mechanochemistry principles to detect chemical analytes. Mechanochemistry is an emerging discipline that investigates chemical processes from mechanical perspectives.…”

Section: Introductionmentioning

confidence: 99%

Single-Molecule Mechanochemical Sensing

Tahir

Mao

2022

Acc. Chem. Res.

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Conspectus Single-molecule mechanochemical sensing (SMMS) is a novel biosensing technique using mechanical force as a signal transduction mechanism. In the mechanochemical sensing, the chemical binding of an analyte molecule to a sensing template is converted to mechanical signals, such as tensile force, of the template. Since mechanical force can be conveniently monitored by single-molecule tools, such as optical tweezers, magnetic tweezers, or Atomic Force Microscopy, mechanochemical sensing is often carried out at the single molecule level. In traditional format of ensemble sensing, sensitivity can be achieved via chemical or electrical amplifications, which are materials intensive and time-consuming. To address these problems, in 2011, we used the principle of mechanochemical coupling in a single molecular template to detect single nucleotide polymorphism (SNP) in DNA fragments. The single-molecule sensitivity in such SMMS strategy allows to removing complex amplification steps, drastically conserving materials and increasing temporal resolution in the sensing. By placing many probing units throughout a single-molecule sensing template, SMMS can have orders of magnitude better efficiency in the materials usage (i.e., high Atom Economy) with respect to the ensemble biosensing. The SMMS sensing probes also enable topochemical arrangement of different sensing units. By placing these units in a spatiotemporally addressable fashion, single-molecule topochemical sensors have been demonstrated in our lab to detect an expandable set of microRNA targets. Because of the stochastic behavior of single-molecule binding, however, it is challenging for the SMMS to accurately report analyte concentrations in a fixed time window. While multivariate analysis has been shown to rectify background noise due to stochastic nature of single-molecule probes, a template containing an array of sensing units has shown ensemble average behaviors to address the same problem. In this so-called ensemble single-molecule sensing, collective mechanical transitions of many sensing units occur in the SMMS sensing probes, which allows accurate quantification of analytes. For the SMMS to function as a viable sensing approach readily adopted by biosensing communities, the future of the SMMS technique relies on the reduction in the complexity and cost of instrumentation to report mechanical signals. In this account, we first explain the mechanism and main features of the SMMS. We then specify basic elements employed in SMMS. Using DNA as an exemplary SMMS template, we further summarize different types of SMMS which present multiplexing capability and increased throughput. Finally, recent efforts to develop simple and affordable high throughput methods for force generation and measurement are discussed in this Account for potential usage in the mechanochemical sensing.

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Mechanochemical Sensing: A Biomimetic Sensing Strategy

Cited by 7 publications

References 78 publications

Mechanochemical Sensing of Single and Few Hg(II) Ions Using Polyvalent Principles

Mechanochemical Sensing of Single and Few Hg(II) Ions Using Polyvalent Principles

Single-Molecule Mechanochemical pH Sensing Revealing the Proximity Effect of Hydroniums Generated by an Alkaline Phosphatase

Single-Molecule Mechanochemical Sensing

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