基礎講座 電気泳動(Electrophoresis)

Metal ions are essential to many chemical, biological, and environmental processes. In the past two decades, many DNA-based metal sensors have emerged. While the main biological role of DNA is to store genetic information, its chemical structure is ideal for metal binding via both the phosphate backbone and nucleobases. DNA is highly stable, cost-effective, easy to modify, and amenable to combinatorial selection. Two main classes of functional DNA were developed for metal sensing: aptamers and DNAzymes. While a few metal binding aptamers are known, it is generally quite difficult to isolate such aptamers. On the other hand, DNAzymes are powerful tools for metal sensing since they are selected based on catalytic activity, thus bypassing the need for metal immobilization. In the last five years, a new surge of development has been made on isolating new metal-sensing DNA sequences. To date, many important metals can be selectively detected by DNA often down to the low parts-per-billion level. Herein, each me...

Metal Sensing by DNA

Aptamers are nucleic acid molecules that mimic antibodies by folding into complex 3D shapes that bind to specific targets. Although some aptamers exist naturally as the ligand-binding elements of riboswitches, most are generated in vitro and can be tailored for a specific target. Relative to antibodies, aptamers benefit from their ease of generation, low production cost, low batch-to-batch variability, reversible folding properties and low immunogenicity. However, the true value of aptamers lies in the simplicity by which these molecules can be engineered into sensors, actuators and other devices that are often central to emerging technologies. This Review examines changing trends in aptamer technology by analysing the first quarter century of aptamer data that is available in the scientific literature (1990–2015). We highlight specific examples that showcase the use of aptamers in key applications, discuss challenges that have impeded the success of aptamers in practical applications, provide suggestions for choosing chemical modifications that can lead to enhanced activity or stability, and propose standards for the characterization of aptamers in the scientific literature. Aptamers are nucleic acid molecules that can be evolved to bind to specific molecular targets and have found applications in technologies such as sensors and actuators. This Review provides a critical analysis of the first 25 years of aptamer research.

Analysis of aptamer discovery and technology

Current approaches in SELEX: An update to aptamer selection technology.

Aptamers are short, single-stranded DNA, RNA, or synthetic XNA molecules that can be developed with high affinity and specificity to interact with any desired targets. They have been widely used in facilitating discoveries in basic research, ensuring food safety and monitoring the environment. Furthermore, aptamers play promising roles as clinical diagnostics and therapeutic agents. This review provides update on the recent advances in this rapidly progressing field of research with particular emphasis on generation of aptamers and their applications in biosensing, biotechnology and medicine. The limitations and future directions of aptamers in target specific delivery and real-time detection are also discussed.

Recent Advances in Aptamer Discovery and Applications.

Artificially expanded genetic information systems (AEGISs) are unnatural forms of DNA that increase the number of independently replicating nucleotide building blocks To do this, AEGIS pairs are joined by different arrangements of hydrogen bond donor and acceptor groups, all while retaining their Watson–Crick geometries We report here a unique case where AEGIS DNA has been used to execute a systematic evolution of ligands by exponential enrichment (SELEX) experiment This AEGIS–SELEX was designed to create AEGIS oligonucleotides that bind to a line of breast cancer cells AEGIS–SELEX delivered an AEGIS aptamer (ZAP-2012) built from six different kinds of nucleotides (the standard G, A, C, and T, and the AEGIS nonstandard P and Z nucleotides, the last having a nitro functionality not found in standard DNA) ZAP-2012 has a dissociation constant of 30 nM against these cells The affinity is diminished or lost when Z or P (or both) is replaced by standard nucleotides and compares well with affinities of standard GACT aptamers selected against cell lines using standard SELEX The success of AEGIS–SELEX relies on various innovations, including (i) the ability to synthesize GACTZP libraries, (ii) polymerases that PCR amplify GACTZP DNA with little loss of the AEGIS nonstandard nucleotides, and (iii) technologies to deep sequence GACTZP DNA survivors These results take the next step toward expanding the power and utility of SELEX and offer an AEGIS–SELEX that could possibly generate receptors, ligands, and catalysts having sequence diversities nearer to that displayed by proteins

https://www.pnas.org/content/pnas/111/4/1449.full.pdf

In vitro selection with artificial expanded genetic information systems

In this paper, we describe the elucidation of the target of an aptamer against ovarian cancer previously obtained by cell-SELEX (SELEX = systematic evolution of ligands by exponential enrichment). The target’s identity, stress-induced phosphoprotein 1 (STIP1), was determined by mass spectrometry and validated by flow cytometry, using siRNA silencing and protein blotting. Initial oncologic studies show that the aptamer inhibits cell invasion, indicating that STIP1, which is currently under investigation as a potential biomarker for ovarian cancer, plays a critical role in this process. These results serve as an excellent example of how protein target identification of aptamers obtained by cell-SELEX can serve as a means to identify promising biomarker candidates and can promote the development of aptamers as a new drug class to block important oncological processes.

Identification of Cell Membrane Protein Stress-Induced Phosphoprotein 1 as a Potential Ovarian Cancer Biomarker Using Aptamers Selected by Cell Systematic Evolution of Ligands by Exponential Enrichment

Molecular recognition of live methicillin-resistant staphylococcus aureus cells using DNA aptamers

Polyethylene-based polymeric prodrugs have been prepared by acyclic diene metathesis (ADMET) polymerization; this condensation type, step growth polymerization, affords controlled polymer architectures via exact methylene run lengths between drug branches. Polyethylene was synthesized with the nonsteroidal anti-inflammatory drug (NSAID) branches ibuprofen and naproxen attached at every 21st backbone carbon through a hydrolysable ester linkage. These ester linkages can have their reactivity tuned by using a variety of spacers that link the drug to the polymer backbone. Two types of spacers, tetraethylene glycol (TEG, hydrophilic) and decanediol (hydrophobic), were incorporated between the drugs and the polymer backbone to observe the effect of spacer properties on the rate of drug release. The rate of hydrolysis and subsequent release of drug was monitored as a direct effect of the spacer and type of reactive linker. With the primary structure of the polymers perfectly known, making such subtle changes to these structures has a dramatic influence on their physical properties. The polymers discussed herein are characterized with NMR, IR, TGA, and DSC. The rate at which these materials hydrolyze and release their pharmaceutical species via enzymatic or chemical hydrolysis was monitored by UV-vis. Tailoring the type of spacer and hydrolysable linker to a particular drug offers a new class of polyethylene with controllable features that can be used in the application of a new drug delivery material.

Polyethylene Prodrugs Using Precisely Placed Pharmaceutical Agents

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In vitro selection with artificial expanded genetic information systems

Identification of Cell Membrane Protein Stress-Induced Phosphoprotein 1 as a Potential Ovarian Cancer Biomarker Using Aptamers Selected by Cell Systematic Evolution of Ligands by Exponential Enrichment

Molecular recognition of live methicillin-resistant staphylococcus aureus cells using DNA aptamers

Polyethylene Prodrugs Using Precisely Placed Pharmaceutical Agents