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Nucleic Acid Aptamers
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Nucleic Acid Aptamers

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Bioorganic Chemistry".

Deadline for manuscript submissions: closed (10 March 2018) | Viewed by 52817

Special Issue Editor

Prof. Dr. Masayasu Kuwahara

E-Mail Website
Guest Editor
Graduate School of Integrated Basic Sciences, Nihon University, 3-25-40 Sakurajosui, Setagaya-ku, Tokyo 156-8550, Japan
Interests: bioanalytical chemistry; nucleic acid aptamers; xenonucleic acids; polymerases

Special Issue Information

Dear Colleagues,

Nucleic acid aptamers are DNA or RNA molecules that can specifically bind to their targets to form stable target/aptamer complexes. Since the establishment of the systematic evolution of ligands by exponential enrichment method around 1990, nucleic acid aptamers for various targets have been developed. Numerous improved methodologies for their selections and various applications, such as bioimaging, diagnoses, molecular therapies, logic gates, and DNA origami technology, have been reported to date. To achieve improved binding affinity and specificity, increased in vivo stability, and further expanded applications, computational predictions, engineering, and chemical modifications have also been attempted. Among these, some attempts have been successful in efficient acquisition of high affinity aptamers and practical uses. However, technical issues still remain in aptamer development. The present Special Issue is aimed at covering a new aspect of research and development pertaining to nucleic acid aptamers. For example, papers regarding novel methodologies for selections and structural/functional characterizations, newly acquired aptamers, engineering/modification strategies, in silico studies, and diverse applications, as well as related elemental technologies and materials for the potential uses will be invited.

Prof. Masayasu Kuwahara
Guest Editor

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Keywords

  • aptamers
  • riboswitches
  • xenonucleic acids
  • polymerase variants
  • therapeutic and diagnositic nucleic acids
  • biosensors

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Published Papers (7 papers)

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Research

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12 pages, 2105 KiB  
Article
CpG Methylation Changes G-Quadruplex Structures Derived from Gene Promoters and Interaction with VEGF and SP1
by Kaori Tsukakoshi, Shiori Saito, Wataru Yoshida, Shinichi Goto and Kazunori Ikebukuro
Molecules 2018, 23(4), 944; https://doi.org/10.3390/molecules23040944 - 18 Apr 2018
Cited by 30 | Viewed by 6622
Abstract
G-quadruplex (G4) is a DNA/RNA conformation that consists of two or more G-tetrads resulting from four-guanine bases connected by Hoogsteen-type hydrogen bonds, which is often found in the telomeres of chromatin, as well as in the promoter regions of genes. The function of [...] Read more.
G-quadruplex (G4) is a DNA/RNA conformation that consists of two or more G-tetrads resulting from four-guanine bases connected by Hoogsteen-type hydrogen bonds, which is often found in the telomeres of chromatin, as well as in the promoter regions of genes. The function of G4 in the genomic DNA is being elucidated and some G4-protein interactions have been reported; these are believed to play a role in vital cellular functions. In this study, we focused on CpG methylation, a well-known epigenetic modification of the genomic DNA, especially found in the promoter regions. Although many G4-forming sequences within the genomic DNA harbor CpG sites, the relationship between CpG methylation and the binding properties of associated proteins remains unclear. We demonstrated that the binding ability of vascular endothelial growth factor (VEGF) G4 DNA to VEGF165 protein was significantly decreased by CpG methylation. We identified the binding activity of G4 DNA oligonucleotides derived from gene promoter regions to SP1, a transcription factor that interacts with a G4-forming DNA and is also altered by CpG methylation. The effect of methylation on binding affinity was accompanied by changes in G4 structure and/or topology. Therefore, this study suggested that CpG methylation might be involved in protein binding to G4-forming DNA segments for purposes of transcriptional regulation. Full article
(This article belongs to the Special Issue Nucleic Acid Aptamers)
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7 pages, 3768 KiB  
Article
Electrochemical Aptamer-Based Sensors for Rapid Point-of-Use Monitoring of the Mycotoxin Ochratoxin A Directly in a Food Stream
by Jacob Somerson and Kevin W. Plaxco
Molecules 2018, 23(4), 912; https://doi.org/10.3390/molecules23040912 - 15 Apr 2018
Cited by 38 | Viewed by 6778
Abstract
The ability to measure the concentration of specific small molecules continuously and in real-time in complex sample streams would impact many areas of agriculture, food safety, and food production. Monitoring for mycotoxin taint in real time during food processing, for example, could improve [...] Read more.
The ability to measure the concentration of specific small molecules continuously and in real-time in complex sample streams would impact many areas of agriculture, food safety, and food production. Monitoring for mycotoxin taint in real time during food processing, for example, could improve public health. Towards this end, we describe here an inexpensive electrochemical DNA-based sensor that supports real-time monitor of the mycotoxin ochratoxin A in a flowing stream of foodstuffs. Full article
(This article belongs to the Special Issue Nucleic Acid Aptamers)
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12 pages, 1640 KiB  
Article
A Lateral Flow Strip Based Aptasensor for Detection of Ochratoxin A in Corn Samples
by Guilan Zhang, Chao Zhu, Yafei Huang, Jiao Yan and Ailiang Chen
Molecules 2018, 23(2), 291; https://doi.org/10.3390/molecules23020291 - 31 Jan 2018
Cited by 48 | Viewed by 6666
Abstract
Ochratoxin A (OTA) is a mycotoxin identified as a contaminant in grains and wine throughout the world, and convenient, rapid and sensitive detection methods for OTA have been a long-felt need for food safety monitoring. Herein, we presented a new competitive format based [...] Read more.
Ochratoxin A (OTA) is a mycotoxin identified as a contaminant in grains and wine throughout the world, and convenient, rapid and sensitive detection methods for OTA have been a long-felt need for food safety monitoring. Herein, we presented a new competitive format based lateral flow strip fluorescent aptasensor for one-step determination of OTA in corn samples. Briefly, biotin-cDNA was immobilized on the surface of a nitrocellulose filter on the test line. Without OTA, Cy5-labeled aptamer combined with complementary strands formed a stable double helix. In the presence of OTA, however, the Cy5-aptamer/OTA complexes were generated, and therefore less free aptamer was captured in the test zone, leading to an obvious decrease in fluorescent signals on the test line. The test strip showed an excellent linear relationship in the range from 1 ng·mL−1 to 1000 ng·mL−1 with the LOD of 0.40 ng·mL−1, IC15 value of 3.46 ng·mL−1 and recoveries from 96.4% to 104.67% in spiked corn samples. Thus, the strip sensor developed in this study is an acceptable alternative for rapid detection of the OTA level in grain samples. Full article
(This article belongs to the Special Issue Nucleic Acid Aptamers)
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5184 KiB  
Communication
In Vitro Selection of DNA Aptamers that Binds Geniposide
by Aozhe Zhang, Dingran Chang, Zijian Zhang, Fan Li, Weihong Li, Xu Wang, Yingfu Li and Qian Hua
Molecules 2017, 22(3), 383; https://doi.org/10.3390/molecules22030383 - 28 Feb 2017
Cited by 9 | Viewed by 6497
Abstract
Geniposide is a key iridoid glycoside from Gardenia jasminoides fructus widely used in traditional Chinese herbal medicine. However, detection of this small molecule represents a significant challenge mostly due to the lack of specific molecular recognition elements. In this study, we have performed [...] Read more.
Geniposide is a key iridoid glycoside from Gardenia jasminoides fructus widely used in traditional Chinese herbal medicine. However, detection of this small molecule represents a significant challenge mostly due to the lack of specific molecular recognition elements. In this study, we have performed in vitro selection experiments to isolate DNA aptamers that can specifically bind geniposide. Using a stringent selection procedure, we have isolated DNA aptamers that can distinguish geniposide from genipin and glucose, two structural analogs of geniposide. Two top aptamers exhibit low micromolar binding affinity towards geniposide, but show significantly reduced affinity to genipin and glucose. These aptamers have the potential to be further developed into analytical tools for the detection of geniposide. Full article
(This article belongs to the Special Issue Nucleic Acid Aptamers)
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Review

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20 pages, 7808 KiB  
Review
Applications of Cancer Cell-Specific Aptamers in Targeted Delivery of Anticancer Therapeutic Agents
by Minhee Kim, Dong-Min Kim, Keun-Sik Kim, Woong Jung and Dong-Eun Kim
Molecules 2018, 23(4), 830; https://doi.org/10.3390/molecules23040830 - 4 Apr 2018
Cited by 80 | Viewed by 9734
Abstract
Aptamers are single-stranded oligonucleotides that specifically bind and interact with their corresponding targets, including proteins and cells, through unique three-dimensional structures. Numerous aptamers have been developed to target cancer biomarkers with high specificity and affinity, and some are employed as versatile guiding ligands [...] Read more.
Aptamers are single-stranded oligonucleotides that specifically bind and interact with their corresponding targets, including proteins and cells, through unique three-dimensional structures. Numerous aptamers have been developed to target cancer biomarkers with high specificity and affinity, and some are employed as versatile guiding ligands for cancer-specific drug delivery and anti-cancer therapeutics. In this review, we list the aptamers that target tumor surface biomarkers and summarize the representative applications of aptamers as agonists and antagonists that activate anti-cancer and inactivate pro-cancer biomarkers, respectively. In addition, we describe applications of aptamer-drug or aptamer-oligonucleotide conjugates that can deliver therapeutic agents, including small interfering RNAs, micro RNAs, short hairpin RNAs, and chemotherapeutic molecules, to cancer cells. Moreover, we provide examples of aptamer- conjugated nano-vehicles, in which cancer-targeting oligonucleotide aptamers are conjugated with nano-vehicles such as liposomes, micelles, polymeric nanoparticles, and quantum dots. Conjugation of aptamers with anti-cancer drugs and nano-vehicles will facilitate innovative applications of aptamer-based cancer therapeutics. Full article
(This article belongs to the Special Issue Nucleic Acid Aptamers)
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25 pages, 504 KiB  
Review
Practical Application of Aptamer-Based Biosensors in Detection of Low Molecular Weight Pollutants in Water Sources
by Wei Zhang, Qing Xiu Liu, Zhi Hou Guo and Jun Sheng Lin
Molecules 2018, 23(2), 344; https://doi.org/10.3390/molecules23020344 - 7 Feb 2018
Cited by 68 | Viewed by 8698
Abstract
Water pollution has become one of the leading causes of human health problems. Low molecular weight pollutants, even at trace concentrations in water sources, have aroused global attention due to their toxicity after long-time exposure. There is an increased demand for appropriate methods [...] Read more.
Water pollution has become one of the leading causes of human health problems. Low molecular weight pollutants, even at trace concentrations in water sources, have aroused global attention due to their toxicity after long-time exposure. There is an increased demand for appropriate methods to detect these pollutants in aquatic systems. Aptamers, single-stranded DNA or RNA, have high affinity and specificity to each of their target molecule, similar to antigen-antibody interaction. Aptamers can be selected using a method called Systematic Evolution of Ligands by EXponential enrichment (SELEX). Recent years we have witnessed great progress in developing aptamer selection and aptamer-based sensors for low molecular weight pollutants in water sources, such as tap water, seawater, lake water, river water, as well as wastewater and its effluents. This review provides an overview of aptamer-based methods as a novel approach for detecting low molecular weight pollutants in water sources. Full article
(This article belongs to the Special Issue Nucleic Acid Aptamers)
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1130 KiB  
Review
Development of Cell-Specific Aptamers: Recent Advances and Insight into the Selection Procedures
by Kamal Rahimizadeh, Hadi AlShamaileh, Milena Fratini, Madhuri Chakravarthy, Michelle Stephen, Sarah Shigdar and Rakesh N. Veedu
Molecules 2017, 22(12), 2070; https://doi.org/10.3390/molecules22122070 - 27 Nov 2017
Cited by 35 | Viewed by 6994
Abstract
Systematic evolution of ligands by exponential enrichment (SELEX) is an established procedure for developing short single-stranded nucleic acid ligands called aptamers against a target of choice. This approach has also been used for developing aptamers specific to whole cells named Cell-SELEX. Aptamers selected [...] Read more.
Systematic evolution of ligands by exponential enrichment (SELEX) is an established procedure for developing short single-stranded nucleic acid ligands called aptamers against a target of choice. This approach has also been used for developing aptamers specific to whole cells named Cell-SELEX. Aptamers selected by Cell-SELEX have the potential to act as cell specific therapeutics, cell specific markers or cell specific drug delivery and imaging agents. However, aptamer development is a laborious and time-consuming process which is often challenging due to the requirement of frequent optimization of various steps involved in Cell-SELEX procedures. This review provides an insight into various procedures for selection, aptamer enrichment, regeneration and aptamer-binding analysis, in addition to a very recent update on all aptamers selected by Cell-SELEX procedures. Full article
(This article belongs to the Special Issue Nucleic Acid Aptamers)
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