Functional Assembly of Aptamer Binding Sites by Single-Molecule Cut-and-Paste

Strackharn, Mathias; Ståhl, S.; Puchner, Elias M.; Gaub, Hermann E.

doi:10.1021/nl300422y

Cited by 18 publications

(16 citation statements)

References 20 publications

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“…5. This technique should be applicable to the fabrication of miniaturized patterns using RNA aptamers (Strackharn et al, 2012). The flexibility of TC-mIP allows the printing of any pattern of molecules with dimensions of mm order and thus TC-mIP can be applied for the solution-processed printing of biosensors and bioelectronics.…”

Section: Printing Of Arbitrary Patternmentioning

confidence: 99%

Temperature-controlled microintaglio printing for high-resolution micropatterning of RNA molecules

Kobayashi

Biyani

Ueno

et al. 2015

Biosensors and Bioelectronics

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We have developed an advanced microintaglio printing method for fabricating fine and high-density micropatterns and applied it to the microarraying of RNA molecules. The microintaglio printing of RNA reported here is based on the hybridization of RNA with immobilized complementary DNA probes. The hybridization was controlled by switching the RNA conformation via the temperature, and an RNA microarray with a diameter of 1.5 µm and a density of 40,000 spots/mm(2) with high contrast was successfully fabricated. Specifically, no size effects were observed in the uniformity of patterned signals over a range of microarray feature sizes spanning one order of magnitude. Additionally, we have developed a microintaglio printing method for transcribed RNA microarrays on demand using DNA-immobilized magnetic beads. The beads were arrayed on wells fabricated on a printing mold and the wells were filled with in vitro transcription reagent and sealed with a DNA-immobilized glass substrate. Subsequently, RNA was in situ synthesized using the bead-immobilized DNA as a template and printed onto the substrate via hybridization. Since the microintaglio printing of RNA using DNA-immobilized beads enables the fabrication of a microarray of spots composed of multiple RNA sequences, it will be possible to screen or analyze RNA functions using an RNA microarray fabricated by temperature-controlled microintaglio printing (TC-µIP).

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Section: Printing Of Arbitrary Patternmentioning

confidence: 99%

Temperature-controlled microintaglio printing for high-resolution micropatterning of RNA molecules

Kobayashi

Biyani

Ueno

et al. 2015

Biosensors and Bioelectronics

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“…The insert shows the structural formula of the attached MG fluorophore. (B) and (C) are reproduced with permission from [113], 2012 American Chemical Society.…”

Section: Introductionmentioning

confidence: 99%

“…When the functionalized AFM tip was approached to a monolayer of biotin immobilized on mica via APTES functionalization, irradiation triggered the release of the proteins from the tip in a photolytic reaction of the crosslinker [111]. The recently developed so-called single molecule cut-and-paste approach surface-assembles a pattern of nanoparticles [112] or organic fluorophores [113] one-by-one and with high precision (Figure 9). Briefly, the approach employs an AFM tip coated with short single stranded DNA oligomers, which picks up DNA strands from a substrate surface and delivers them at a desired surface destination.…”

Section: Introductionmentioning

confidence: 99%

“…The surface bound DNA strands finally carry binding sites for the selective attachment of the particle of choice, either being terminated with a biotin moiety for biotin-streptavidin sandwich binding to the surface or via formation of aptamer recognition sequences. The assembled fluorophores could further be directly visualized using a combined fluorescence and AFM system [113]. Such combinatory set-ups have increasingly found use in the direct quality assessment of AFM assembly processes; for instance, Martin Guthold and colleagues have used the AFM to transport fluorescent particles while following their position by fluorescence microscopy [3].…”

Section: Introductionmentioning

confidence: 99%

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Investigating bioconjugation by atomic force microscopy

et al. 2013

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Nanotechnological applications increasingly exploit the selectivity and processivity of biological molecules. Integration of biomolecules such as proteins or DNA into nano-systems typically requires their conjugation to surfaces, for example of carbon-nanotubes or fluorescent quantum dots. The bioconjugated nanostructures exploit the unique strengths of both their biological and nanoparticle components and are used in diverse, future oriented research areas ranging from nanoelectronics to biosensing and nanomedicine. Atomic force microscopy imaging provides valuable, direct insight for the evaluation of different conjugation approaches at the level of the individual molecules. Recent technical advances have enabled high speed imaging by AFM supporting time resolutions sufficient to follow conformational changes of intricately assembled nanostructures in solution. In addition, integration of AFM with different spectroscopic and imaging approaches provides an enhanced level of information on the investigated sample. Furthermore, the AFM itself can serve as an active tool for the assembly of nanostructures based on bioconjugation. AFM is hence a major workhorse in nanotechnology; it is a powerful tool for the structural investigation of bioconjugation and bioconjugation-induced effects as well as the simultaneous active assembly and analysis of bioconjugation-based nanostructures.

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“…For example, hybrid DNA–RNA molecules were specifically arranged and immobilized on a surface via complementary oligonucleotides. The resulting duplexes formed aptamers that stabilized the structure of a target dye molecule, enabling it to produce a fluorescent signal upon binding the SMC&P‐arranged constructs . Proteins have also been integrated into SMC&P, including constructs containing modified green fluorescent protein (GFP) with different surface‐immobilization strategies and a protein‐based handle for the cantilever .…”

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confidence: 99%

Strep -Tag II and Monovalent Strep -Tactin as Novel Handles in Single-Molecule Cut-and-Paste

et al. 2017

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Directed spatial assembly of single molecules on a surface presents an opportunity to precisely control the positioning, density, and geometry of molecules of interest within an ensemble. In contrast to bulk averaging, this enables detection and analysis of individual behavior within such a designed ensemble. The atomic force microscopy (AFM)‐based technique of single‐molecule cut‐and‐paste (SMC&P) facilitates the arrangement of a variety of biomolecules on a surface through different handling strategies. This technique requires cantilever‐ and surface‐handles that simultaneously adhere to a prerequisite rupture force hierarchy, and also do not cross‐interact with each other or the transported molecules. As the molecules of interest diversify, so too must the handling methods to accommodate their unique characteristics. Here, it is demonstrated that a previously developed monovalent variant of Strep‐Tactin and its corresponding Strep‐Tag II peptide ligand comprise a viable cantilever handling complex for SMC&P. Ultimately, this expansion to the SMC&P toolbox increases the system's versatility for new molecules of interest yet to be studied.

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Functional Assembly of Aptamer Binding Sites by Single-Molecule Cut-and-Paste

Cited by 18 publications

References 20 publications

Temperature-controlled microintaglio printing for high-resolution micropatterning of RNA molecules

Temperature-controlled microintaglio printing for high-resolution micropatterning of RNA molecules

Investigating bioconjugation by atomic force microscopy

Strep -Tag II and Monovalent Strep -Tactin as Novel Handles in Single-Molecule Cut-and-Paste

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