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Investigations on the Interface of Nucleic Acid Aptamers and Binding Targets


Nucleic acid aptamers are single-stranded DNA or RNA with 20-100 nucleotides in length that can specifically bind to target molecules via formed three-dimensional structures, which have attracted substantial scientific interest. Compared to traditional protein antibodies, aptamers have several advantages, such as small size, high binding affinity, specificity, flexible structure, chemical synthesizable and modifiable, good biocompatibility, high stability and low immunogenicity, which all contribute to their widely applications in biomedical field. To date, much progress has been made in the study and applications of aptamers, however, the detailed information of how aptamers bind to their targets is still scarce. Over the past decades, many methods have been introduced to investigate the aptamer-target binding process, such as measuring the main kinetic or thermodynamic parameters, detecting the structural changes of the binding complexes, etc. Apart from traditional physicochemical methods, various types of molecular docking software have been applied to simulate the aptamer-target interactions, while these simulations also have limitations. To facilitate the further research on the interactions, herein, we provide a brief review to illustrate the recent advances on the study of aptamer-target interactions. We summarize the binding targets of aptamers, such as small molecules, macromolecules, and even cells. Their binding constants (KD) are also summarized. Methods to probe the aptamer-target binding process, such as surface plasmon resonance (SPR), circular dichroism spectroscopy (CD), isothermal titration calorimetry (ITC), footprinting assay, truncation and mutation assay, nuclear magnetic resonance spectroscopy (NMR), X-ray crystallography and molecular docking simulation are indicated. Binding forces mediating the aptamer-ligand interactions, such as hydrogen bonding, electrostatic interaction, hydrophobic effect, π-π stacking and Van der Waals forces are summarized. The challenges and future perspectives are also discussed.

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Publication details

The article was received on 01 Aug 2018, accepted on 08 Oct 2018 and first published on 08 Oct 2018

Article type: Minireview
DOI: 10.1039/C8AN01467A
Citation: Analyst, 2018, Accepted Manuscript
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    Investigations on the Interface of Nucleic Acid Aptamers and Binding Targets

    S. Cai, J. H. Yan, H. xiong, Y. Liu, D. Peng and Z. Liu, Analyst, 2018, Accepted Manuscript , DOI: 10.1039/C8AN01467A

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