1
|
Study on the binding mode of aptamer to ampicillin and its electrochemical response behavior in two different reaction media. Anal Bioanal Chem 2021; 413:6877-6887. [PMID: 34595555 DOI: 10.1007/s00216-021-03646-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 10/20/2022]
Abstract
A study was carried out to investigate the binding mode of aptamer to ampicillin (AMP) and its electrochemical response behavior. The binding mode was confirmed using the molecular dynamics (MD) simulation method to obtain the corresponding binding dynamic change process. Following the confirmed binding mode, a qualitative elucidation was provided on the electrochemical response characteristics of a single-probe aptamer-based folding sensor. The results show that there exist two different binding modes in two different solution systems, Phys2 and H2O (0.1 M NaCl). These two binding modes can respectively induce two different contraction changes, thereby driving the methylene blue (MB)-modified aptamer probe to show a "close-to-interface" convergence behavior with different degrees on the actual electrode surface, which validates two apparently different electrochemical response behavior characteristics of "signal-on" for the sensor. By contrast, H2O (0.1 M NaCl) as the reaction medium is more conducive to the formation of a stable aptamer/AMP complex and the development of a high-sensitivity analytical method with a low detection limit of 0.033 μM. The simulation results effectively support the experimental results, which is helpful in gaining a deeper understanding of the relationship between the signaling mechanism and practical analytical performance for aptamer-based folding sensors at the molecular level.
Collapse
|
2
|
Cai S, Yan J, Xiong H, Liu Y, Peng D, Liu Z. Investigations on the interface of nucleic acid aptamers and binding targets. Analyst 2019; 143:5317-5338. [PMID: 30357118 DOI: 10.1039/c8an01467a] [Citation(s) in RCA: 158] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nucleic acid aptamers are single-stranded DNA or RNA of 20-100 nucleotides in length that have attracted substantial scientific interest due to their ability to specifically bind to target molecules via the formation of three-dimensional structures. Compared to traditional protein antibodies, aptamers have several advantages, such as their small size, high binding affinity, specificity, flexible structure, being chemical synthesizable and modifiable, good biocompatibility, high stability and low immunogenicity, which all contribute to their widely applications in the biomedical field. To date, much progress has been made in the study and applications of aptamers, however, detailed information on how aptamers bind to their targets is still scarce. Over the past few 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 programs 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 in 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. The binding forces mediating the aptamer-target interactions, such as hydrogen bonding, electrostatic interaction, the hydrophobic effect, π-π stacking and van der Waals forces are summarized. The challenges and future perspectives are also discussed.
Collapse
Affiliation(s)
- Shundong Cai
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, PR China.
| | | | | | | | | | | |
Collapse
|
3
|
Gülbakan B, Barylyuk K, Schneider P, Pillong M, Schneider G, Zenobi R. Native Electrospray Ionization Mass Spectrometry Reveals Multiple Facets of Aptamer–Ligand Interactions: From Mechanism to Binding Constants. J Am Chem Soc 2018; 140:7486-7497. [DOI: 10.1021/jacs.7b13044] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Basri Gülbakan
- Department of Chemistry and Applied Bioscience, ETH Zürich, CH-8093 Zürich, Switzerland
- Hacettepe University Institute of Child Health, Ihsan Dogramaci Children’s Hospital, Sıhhiye Square, 06100 Ankara, Turkey
| | - Konstantin Barylyuk
- Department of Chemistry and Applied Bioscience, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Petra Schneider
- Department of Chemistry and Applied Bioscience, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Max Pillong
- Department of Chemistry and Applied Bioscience, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Gisbert Schneider
- Department of Chemistry and Applied Bioscience, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Bioscience, ETH Zürich, CH-8093 Zürich, Switzerland
| |
Collapse
|
5
|
Kahsai AW, Wisler JW, Lee J, Ahn S, Cahill TJ, Dennison SM, Staus DP, Thomsen ARB, Anasti KM, Pani B, Wingler LM, Desai H, Bompiani KM, Strachan RT, Qin X, Alam SM, Sullenger BA, Lefkowitz RJ. Conformationally selective RNA aptamers allosterically modulate the β2-adrenoceptor. Nat Chem Biol 2016; 12:709-16. [PMID: 27398998 PMCID: PMC4990464 DOI: 10.1038/nchembio.2126] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/09/2016] [Indexed: 01/08/2023]
Abstract
G-protein-coupled receptor (GPCR) ligands function by stabilizing multiple, functionally distinct receptor conformations. This property underlies the ability of 'biased agonists' to activate specific subsets of a given receptor's signaling profile. However, stabilizing distinct active GPCR conformations to enable structural characterization of mechanisms underlying GPCR activation remains difficult. These challenges have accentuated the need for receptor tools that allosterically stabilize and regulate receptor function through unique, previously unappreciated mechanisms. Here, using a highly diverse RNA library combined with advanced selection strategies involving state-of-the-art next-generation sequencing and bioinformatics analyses, we identify RNA aptamers that bind a prototypical GPCR, the β2-adrenoceptor (β2AR). Using biochemical, pharmacological, and biophysical approaches, we demonstrate that these aptamers bind with nanomolar affinity at defined surfaces of the receptor, allosterically stabilizing active, inactive, and ligand-specific receptor conformations. The discovery of RNA aptamers as allosteric GPCR modulators significantly expands the diversity of ligands available to study the structural and functional regulation of GPCRs.
Collapse
Affiliation(s)
- Alem W. Kahsai
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710
| | - James W. Wisler
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710
| | - Jungmin Lee
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | - Seungkirl Ahn
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710
| | - Thomas J. Cahill
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710
| | - S. Moses Dennison
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710
| | - Dean P. Staus
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710
| | - Alex R. B. Thomsen
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710
| | - Kara M. Anasti
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710
| | - Biswaranjan Pani
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710
| | - Laura M. Wingler
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710
| | - Hemant Desai
- The University of North Carolina School of Medicine, Chapel Hill, NC 27516
| | - Kristin M. Bompiani
- Department of Surgery, Duke University Medical Center, Durham, NC, 27710
- Duke Translational Research Institute, Duke University Medical Center, Durham, NC, 27710
- The University of California, San Diego, Moores Cancer Center, La Jolla, CA 92093
| | | | - Xiaoxia Qin
- Genome Sequencing and Analysis Core Resource, Duke University, Durham, NC, 27710
| | - S. Munir Alam
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710
| | - Bruce A. Sullenger
- Department of Surgery, Duke University Medical Center, Durham, NC, 27710
- Duke Translational Research Institute, Duke University Medical Center, Durham, NC, 27710
| | - Robert J. Lefkowitz
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710
- Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC, 27710
| |
Collapse
|