Selecting Molecular Recognition. What Can Existing Aptamers Tell Us about Their Inherent Recognition Capabilities and Modes of Interaction?

Zhang, Qian; Landgraf, Ralf

doi:10.3390/ph5050493

Cited by 16 publications

(5 citation statements)

References 99 publications

(106 reference statements)

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“…Aptamers are small nucleic acid sequences that selectively bind to target molecules, and can be seen as a nucleic acid analogue of antibodies [ 88 , 89 ]. Kuga et al [ 90 ] investigated a method to attach aptamers to diamond.…”

Section: Biolabelsmentioning

confidence: 99%

Improving surface and defect center chemistry of fluorescent nanodiamonds for imaging purposes—a review

2015

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Diamonds are widely used for jewelry owing to their superior optical properties accounting for their fascinating beauty. Beyond the sparkle, diamond is highly investigated in materials science for its remarkable properties. Recently, fluorescent defects in diamond, particularly the negatively charged nitrogen-vacancy (NV-) center, have gained much attention: The NV- center emits stable, nonbleaching fluorescence, and thus could be utilized in biolabeling, as a light source, or as a Förster resonance energy transfer donor. Even more remarkable are its spin properties: with the fluorescence intensity of the NV- center reacting to the presence of small magnetic fields, it can be utilized as a sensor for magnetic fields as small as the field of a single electron spin. However, a reproducible defect and surface and defect chemistry are crucial to all applications. In this article we review methods for using nanodiamonds for different imaging purposes. The article covers (1) dispersion of particles, (2) surface cleaning, (3) particle size selection and reduction, (4) defect properties, and (5) functionalization and attachment to nanostructures, e.g., scanning probe microscopy tips.Graphical AbstractWe review how diamond surface and defect chemistry can be optimized for different (bio) applications

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Section: Biolabelsmentioning

confidence: 99%

Improving surface and defect center chemistry of fluorescent nanodiamonds for imaging purposes—a review

2015

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“… 11 , 33 Similarly, largely hydrophobic molecules have proven to be suboptimal targets, as aptamers are generally hydrophilic and have limited options to interact with such molecules unless modified nucleotides are introduced into their sequence. 34 , 35 …”

Section: Target Types and Selex Variantsmentioning

confidence: 99%

“…Positive charges, on the other hand, can increase the strength of interactions but may also exacerbate unspecific binding 11,33 . Similarly, largely hydrophobic molecules have proven to be suboptimal targets, as aptamers are generally hydrophilic and have limited options to interact with such molecules unless modified nucleotides are introduced into their sequence 34,35 …”

Section: Target Types and Selex Variantsmentioning

confidence: 99%

SELEX: Critical factors and optimization strategies for successful aptamer selection

Kohlberger

Gadermaier

2021

Biotech and App Biochem

162

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Within the last decade, the application range of aptamers in biochemistry and medicine has expanded rapidly. More than just a replacement for antibodies, these intrinsically structured RNA-or DNA-oligonucleotides show great potential for utilization in diagnostics, specific drug delivery, and treatment of certain medical conditions. However, what is analyzed less frequently is the process of aptamer identification known as systematic evolution of ligands by exponential enrichment (SELEX) and the functional mechanisms that lie at its core. SELEX involves numerous singular processes, each of which contributes to the success or failure of aptamer generation. In this review, critical steps during aptamer selection are discussed in-depth, and specific problems are presented along with potential solutions. The discussed aspects include the size and molecule type of the selected target, the nature and stringency of the selection process, the amplification step with its possible PCR bias, the efficient regeneration of RNA or single-stranded DNA, and the different sequencing procedures and screening assays currently available. Finally, useful quality control steps and their role within SELEX are presented. By understanding the mechanisms through which aptamer selection is influenced, the design of more efficient SELEX procedures leading to a higher success rate in aptamer identification is enabled.

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“…Two of the major problems pointed out so far are the lack of associated safety data, a central concern of regulatory authorities for approval of new therapies; [ 184 ] and the lack of a clear roadmap toward large‐scale good manufacturing practices grade synthesis and purification, which are required for clinical trials. [ 185 ] However, with the approval of Macugen by the FDA in 2004, as well as several aptamers having reached phase II clinical trials, this situation might be reaching a turning point. [ 171 ] Some inherent physicochemical characteristics of aptamers have also been mentioned as limitations that should be kept in mind.…”

Section: Solid‐phase Presentationmentioning

confidence: 99%

Biomaterials for Sequestration of Growth Factors and Modulation of Cell Behavior

Teixeira

Domingues

Shevchuk

et al. 2020

Adv Funct Materials

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Growth factors (GFs) are proteins secreted by cells that regulate a variety of biological processes. Although they have long been proposed as potent therapeutic agents, their administration in a soluble form has proven costly and ineffective due to their short half-lives in biological environments. Biomaterial-based approaches are increasingly sought as alternatives to improve the efficacy or, ideally, replace the need for exogenous administration of GFs in regenerative medicine strategies. The means by which these systems evolve from biomaterials for conventional controlled release of GFs to the recent extracellular matrix (ECM)-inspired approaches for sequestering these labile molecules and regulating their spatiotemporal activity and presentation are reviewed. Focus is placed on biomaterials functionalized either with ECM components, which show promiscuous GF binding, or with targeted GF ligands (antibodies, aptamers, or peptides). The potential of synthetic platforms with abiotic affinity as cost-effective alternatives to the current biological ligands is also discussed. Overall, the various GF sequestering systems developed so far have remarkably improved the activity of GFs at reduced doses and, in some cases, completely avoided the need for their exogenous administration to guide cell fates. These bioinspired concepts thus enable the rational exploration of the full therapeutic potential of GFs in regenerative medicine.

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Selecting Molecular Recognition. What Can Existing Aptamers Tell Us about Their Inherent Recognition Capabilities and Modes of Interaction?

Cited by 16 publications

References 99 publications

Improving surface and defect center chemistry of fluorescent nanodiamonds for imaging purposes—a review

Improving surface and defect center chemistry of fluorescent nanodiamonds for imaging purposes—a review

SELEX: Critical factors and optimization strategies for successful aptamer selection

Biomaterials for Sequestration of Growth Factors and Modulation of Cell Behavior

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