Elementary processes of DNA surface hybridization resolved by single-molecule kinetics: implication for macroscopic device performance

Harashima, Takanori; Hasegawa, Yoshihiko; Kaneko, Satoshi; Jono, Yuki; Fujii, Shintaro; Kiguchi, Manabu; Nishino, Tomoaki

doi:10.1039/d0sc04449k

Cited by 5 publications

(5 citation statements)

References 46 publications

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“…It is clear from Figure that the phosphorylation rapidly proceeds upon the injection of Akt1 and ATP in the first 5 min and reaches saturation. We can note the fluctuation after the saturation around 15–20 min, and one possible explanation of this behavior is the changes in the enzymatic activities caused by the microscopic environments, as we have previously revealed in the hybridization of a single DNA duplex …”

Section: Resultssupporting

confidence: 54%

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Unique Electrical Signature of Phosphate for Specific Single-Molecule Detection of Peptide Phosphorylation

et al. 2022

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Single-molecule measurements of biomaterials bring novel insights into cellular events. For almost all of these events, post-translational modifications (PTMs), which alter the properties of proteins through their chemical modifications, constitute essential regulatory mechanisms. However, suitable single-molecule methodology to study PTMs is very limited. Here we show single-molecule detection of peptide phosphorylation, an archetypal PTM, based on electrical measurements. We found that the phosphate group stably bridges a nanogap between metal electrodes and exhibited high electrical conductance, which enables specific single-molecule detection of peptide phosphorylation. The present methodology paves the way to single-molecule studies of PTMs, such as single-molecule kinetics for enzymatic modification of proteins as shown here.

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Section: Resultssupporting

confidence: 54%

“…We can note the fluctuation after the saturation around 15−20 min, and one possible explanation of this behavior is the changes in the enzymatic activities caused by the microscopic environments, as we have previously revealed in the hybridization of a single DNA duplex. 39…”

Section: ■ Results and Discussionmentioning

confidence: 99%

Unique Electrical Signature of Phosphate for Specific Single-Molecule Detection of Peptide Phosphorylation

et al. 2022

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“…The duplex formation between thiolate terminated single-stranded DNA and its complementary chain has been reported previously. 43 Most of the previous experimental and theoretical works consider localization of HOMO on the bases (namely on the guanine) and regard such HOMO as the charge transporting pathway (hole transport) in DNA. Therefore, we selected amino and thiolate as the anchoring groups since it is well known that they also promote CT through HOMO of the molecular wire.…”

Section: Resultsmentioning

confidence: 99%

Additive transport in DNA molecular circuits

et al. 2022

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“…Advances in single-molecule works include experiments inferring DNA hybridization kinetics through measuring real-time conductance during DNA hybridization to immobilized probes on the Au (111) ( 50 ) or graphene ( 51 ) sensor surface. Both findings support concentration-dependent DNA hybridization kinetics, and the latter can resolve single-base mismatches.…”

Section: Discussionmentioning

confidence: 99%

Displacement and dissociation of oligonucleotides during DNA hairpin closure under strain

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et al. 2022

Nucleic Acids Research

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The hybridization kinetic of an oligonucleotide to its template is a fundamental step in many biological processes such as replication arrest, CRISPR recognition, DNA sequencing, DNA origami, etc. Although single kinetic descriptions exist for special cases of this problem, there are no simple general prediction schemes. In this work, we have measured experimentally, with no fluorescent labelling, the displacement of an oligonucleotide from its substrate in two situations: one corresponding to oligonucleotide binding/unbinding on ssDNA and one in which the oligonucleotide is displaced by the refolding of a dsDNA fork. In this second situation, the fork is expelling the oligonucleotide thus significantly reducing its residence time. To account for our data in these two situations, we have constructed a mathematical model, based on the known nearest neighbour dinucleotide free energies, and provided a good estimate of the residence times of different oligonucleotides (DNA, RNA, LNA) of various lengths in different experimental conditions (force, temperature, buffer conditions, presence of mismatches, etc.). This study provides a foundation for the dynamics of oligonucleotide displacement, a process of importance in numerous biological and bioengineering contexts.

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Elementary processes of DNA surface hybridization resolved by single-molecule kinetics: implication for macroscopic device performance

Abstract: Hybridization of a single DNA molecule on a surface was investigated by electrical conductance measurements. The hybridization efficiency increases with increasing the DNA concentration, in contrast to preceding studies with ensemble studies.

Cited by 5 publications

References 46 publications

Unique Electrical Signature of Phosphate for Specific Single-Molecule Detection of Peptide Phosphorylation

Unique Electrical Signature of Phosphate for Specific Single-Molecule Detection of Peptide Phosphorylation

Additive transport in DNA molecular circuits

Displacement and dissociation of oligonucleotides during DNA hairpin closure under strain

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