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

Mandal, Shankar; Sangeetha, S.; Shrestha, Prakash; Mao, Hanbin

doi:10.1021/acs.analchem.6b01899

Cited by 8 publications

(9 citation statements)

References 42 publications

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“…In addition, the proximity effect in the dual recognition can reduce the entropic penalty due to the formation of the bound complex. Similar effect has been observed in the polyvalent binding that has significantly increased binding affinity relative to the monomeric recognitions (19,20).…”

Section: Introductionsupporting

confidence: 75%

Submolecular dissection reveals strong and specific binding of polyamide–pyridostatin conjugates to human telomere interface

Mandal

Kawamoto

Yue

et al. 2019

Nucleic Acids Research

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To modulate biological functions, G-quadruplexes in genome are often non-specifically targeted by small molecules. Here, specificity is increased by targeting both G-quadruplex and its flanking duplex DNA in a naturally occurring dsDNA–ssDNA telomere interface using polyamide (PA) and pyridostatin (PDS) conjugates (PA-PDS). We innovated a single-molecule assay in which dissociation constant ( K d ) of the conjugate can be separately evaluated from the binding of either PA or PDS. We found K d of 0.8 nM for PA-PDS, which is much lower than PDS ( K d ∼ 450 nM) or PA ( K d ∼ 35 nM). Functional assays further indicated that the PA-PDS conjugate stopped the replication of a DNA polymerase more efficiently than PA or PDS. Our results not only established a new method to dissect multivalent binding into actions of individual monovalent components, they also demonstrated a strong and specific G-quadruplex targeting strategy by conjugating highly specific duplex-binding molecules with potent quadruplex ligands.

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Section: Introductionsupporting

confidence: 75%

Submolecular dissection reveals strong and specific binding of polyamide–pyridostatin conjugates to human telomere interface

Mandal

Kawamoto

Yue

et al. 2019

Nucleic Acids Research

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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%

“…The DNA constructs for single-molecule mechanochemical sensing (SMMS) 19 were prepared as described in the previous report. 21 The sensing element was contained inside the DNA hairpin (see DNA sequences in Table S1) sandwiched between two long dsDNA handles. 22 Briefly, the digoxigenin labeled 2690 bp dsDNA handle was prepared by digesting pEGFP (Clontech, Mountain View, CA) plasmid with SacI (NEB) and EagI (NEB).…”

mentioning

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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“…Screened by in vitro selection method, SELEX, 27 these secondary structures are also involved in DNA aptamers to bind analytes with nanomolar K d , achieving high specificities. 34 1 fM (20 min) 1 fM−100 pM Hg(II) fast detection complicated preparation materials inefficiency Poly(T) repeats 40 3 pM (20 min) 3 pM−10 μM Melamine fast detection multistep preparation (RCA) high-throughput material efficiency DNA origami 3 10 pM (10 min) 10 pM−50 nM PDGF fast detection low/medium throughput multiplexing material inefficiency Multiple DNA hairpins 43 1 fM (20 min) high signal-to-noise ratios. Most of the SMMS use force and extension as reporting signals.…”

Section: Single-molecule Probes For Chemical Bindingmentioning

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

Cited by 8 publications

References 42 publications

Submolecular dissection reveals strong and specific binding of polyamide–pyridostatin conjugates to human telomere interface

Submolecular dissection reveals strong and specific binding of polyamide–pyridostatin conjugates to human telomere interface

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

Single-Molecule Mechanochemical Sensing

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