Reversible assembly of protein-DNA nanostructures triggered by mediated electron transfer

Vogt, Stephan; Wenderhold-Reeb, Sabine; Nöll, Gilbert

doi:10.1016/j.electacta.2017.02.075

Cited by 5 publications

(5 citation statements)

References 35 publications

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“…As in each pocket up to two flavin ligands can be incorporated, dodecin is able to bind up to 12 flavins in total. , Dodecin binds not only native but also artificial flavins, as well as flavin–DNA ligands with high affinity, and therefore dodecin can be reconstituted on top of flavin-terminated DNA monolayers. Apododecin binds flavin ligands only with high affinity when they are oxidized, whereas flavin reduction induces the dissociation of the holoprotein complex. ,,, Based on these unusual redox properties we have shown that dodecin layers formed on top of flavin-terminated DNA monolayers can be disassembled (via flavin reduction) and reassembled in a reversible manner. This requires that dehybridization of the dsDNA does not occur within the time scale of the experiment.…”

Section: Introductionmentioning

confidence: 94%

“…Apododecin binds flavin ligands only with high affinity when they are oxidized, whereas flavin reduction induces the dissociation of the holoprotein complex. 12,13,26,27 Based on these unusual redox properties we have shown that dodecin layers formed on top of flavinterminated DNA monolayers can be disassembled (via flavin reduction) and reassembled in a reversible manner. This Scheme 1 a a Stable dodecin monolayers can be formed on top of a flavin-terminated dsDNA layer with a relative flavin surface coverage of 100% (left hand side).…”

Section: ■ Introductionmentioning

confidence: 98%

“…On the other hand double-stranded DNA (dsDNA) monolayers at surfaces turned out to be sufficiently stable to allow the formation of durable protein–DNA nanostructures. For instance, we have shown that stable protein–DNA nanostructures can be formed by reconstitution of the multiligand binding flavoprotein dodecin at flavin-terminated DNA monolayers. ,, Dodecin is a dodecameric flavoprotein with a diameter of 6–7 nm that comprises six flavin binding pockets. As in each pocket up to two flavin ligands can be incorporated, dodecin is able to bind up to 12 flavins in total. , Dodecin binds not only native but also artificial flavins, as well as flavin–DNA ligands with high affinity, and therefore dodecin can be reconstituted on top of flavin-terminated DNA monolayers.…”

Section: Introductionmentioning

confidence: 99%

“…For instance, we have shown that stable protein−DNA nanostructures can be formed by reconstitution of the multiligand binding flavoprotein dodecin at flavin-terminated DNA monolayers. 12,13,26 Dodecin is a dodecameric flavoprotein with a diameter of 6−7 nm that comprises six flavin binding pockets. As in each pocket up to two flavin ligands can be incorporated, dodecin is able to bind up to 12 flavins in total.…”

Section: ■ Introductionmentioning

confidence: 99%

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Langmuir Analysis of the Binding Affinity and Kinetics for Surface Tethered Duplex DNA and a Ligand–Apoprotein Complex

Vogt

Nöll

2018

Langmuir

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In this work, the hybridization and dehybridization of ssDNA with 20 bases at gold coated sensor surfaces modified with complementary 20 bases capture probe ssDNA was investigated at 18 °C by quartz crystal microbalance measurements with dissipation monitoring (QCM-D). A sequence of 20 base pairs with a melting temperature of about 64 °C was chosen, since in many biosensor studies the target molecules are DNA or RNA oligomers of similar length. It turned out that at the applied experimental conditions the DNA hybridization was irreversible, and therefore the hybridization and dehybridization process could not be described by the Langmuir model of adsorption. Nevertheless, quantitative dehybridization could be achieved by rinsing the sensor surface thoroughly with pure water. When in contrast the hybridization of a target with only 10 bases complementary to the outermost 10 bases of the 20 bases capture probe was studied, binding and unbinding were reversible, and the hybridization/dehybridization process could be satisfactorily described by the Langmuir model. For the 10 base pair sequence, the melting temperature was about 36 °C. Apparently, for Langmuir behavior, it is important that the experiments are applied at a temperature sufficiently close to the melting temperature of the sequence under investigation to ensure that at least traces of the target molecules are unhybridized (i.e., there needs to be an equilibrium between hybridized and dehybridized target molecules). To validate the reliability of our experimental approach we also studied the reconstitution and disassembly of the flavoprotein dodecin at flavin-terminated DNA monolayers, as according to previous studies it is assumed that the apododecin-flavin system can be well described by the Langmuir model. As a result, this assumption could be verified. Using three different approaches, K values were obtained that differ not more than by a factor of 4.

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Section: Introductionmentioning

confidence: 94%

Section: ■ Introductionmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Langmuir Analysis of the Binding Affinity and Kinetics for Surface Tethered Duplex DNA and a Ligand–Apoprotein Complex

Vogt

Nöll

2018

Langmuir

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“…The dodecameric dodecin appears to be an ideal model compound for NMR diffusion studies because of its high symmetry giving stronger NMR signals than asymmetric compounds. Furthermore, it is known from previous studies that dodecin does not show non‐specific binding to DNA , In addition dodecin comprises a high stability also at elevated temperatures.…”

Section: Resultsmentioning

confidence: 99%

Diffusion‐Ordered NMR Spectroscopy of Guest Molecules in DNA Hydrogels and Related Matrices

et al. 2018

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Diffusion‐ordered NMR spectroscopy was used to monitor the diffusion of guest molecules in DNA hydrogels and related DNA matrices. As guest molecule the highly symmetric hollow‐spherical flavoprotein dodecin was studied. Thermoresponsive hydrogels were formed by self‐assembly via hybridization of linear double‐stranded DNA building blocks of 30 base pairs equipped with sticky ends, i. e. additional overhangs of 15 bases on both ends, which were complementary to each other. This resulted in hydrogels, in which dodecin was freely diffusing. When in contrast self‐assembly was performed with rather short building blocks (9 base pairs + sticky ends of 6 bases), the diffusion of the guest molecule was hampered, but as hybridization was reversible within the timescale of the experiment, the resulting DNA matrix did not behave as a true gel. Apparently true DNA hydrogels with small mesh size can be obtained only, when self‐assembly of short DNA building blocks via hybridization is combined with enzymatic ligation leading to a covalently linked network. In that case, the minimum achievable mesh size should be limited by the diameter of the ligase. While DNA hydrogels are an ideal matrix to host rather large molecules or even living cells, it is a challenge to design pristine DNA hydrogels with mesh sizes sufficiently small to capture guest molecules such as drugs or enzymes in the size of only a few nm.

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Combining plasmonic and electrochemical biosensing methods

Hemmerová,

Homola

2024

Biosensors and Bioelectronics

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Reversible assembly of protein-DNA nanostructures triggered by mediated electron transfer

Cited by 5 publications

References 35 publications

Langmuir Analysis of the Binding Affinity and Kinetics for Surface Tethered Duplex DNA and a Ligand–Apoprotein Complex

Langmuir Analysis of the Binding Affinity and Kinetics for Surface Tethered Duplex DNA and a Ligand–Apoprotein Complex

Diffusion‐Ordered NMR Spectroscopy of Guest Molecules in DNA Hydrogels and Related Matrices

Combining plasmonic and electrochemical biosensing methods

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