Aptamers Chemistry: Chemical Modifications and Conjugation Strategies
Abstract
:1. Introduction
2. Aptamers and Selection Methods
3. Chemical Modifications of Aptamers and Their Impact on Pharmacological Properties
3.1. Modifications on Nucleic Acids Terminals
3.1.1. Terminal 3′–3′ and/or 5′–5′ Internucleotide, 3′ and 5′-Biotin Conjugates
3.1.2. 5′-End with Cholesterol and Other Lipid Moieties
3.1.3. 5′-End PEGylation
3.2. Modifications on the Sugar Ring
3.2.1. 2′-Substitutions
3.2.2. 4′-Oxygen Replacement
3.2.3. Locked and Unlocked Nucleic Acid
3.3. Modifications on the Phosphodiester Linkage
3.3.1. Methylphosphonate or Phosphorothioate
3.3.2. Triazole Modification
3.4. Modifications on the Bases and SOMAmers
3.5. Spiegelmers
3.6. Circular Aptamers
3.7. Multivalent and Dimerization of Aptamers
4. Chemical and Physical Conjugation Strategies of Aptamers to Nanoparticles
4.1. Direct and Post-Insertion
4.2. Carbodiimide Chemistry
4.3. Thiol Maleiimide and Related Chemistry
4.4. Electrostatic and cDNA Strand Conjugation
4.5. Avidin–Biotin Coupling
4.6. Sulfhydryl-Aptamer Gold Coordination
4.7. Oxidative Coupling
4.8. Click Chemistry
5. Aptamer Toxicity and Immunogenicity
6. Conclusions
Conflicts of Interest
References
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SELEX Type | Description | Ref. |
---|---|---|
Metal-Dependant Aptamers | Enrichment of oligonucleotide library with and without ion salts to generate aptamers that only function in the presence of metal ion salts. | [34] |
Crossover-SELEX | First, oligonucleotides are enriched using cell-SELEX. The product of cell-SELEX is then enriched against its purified protein to yield a higher binding affinity. Crossover-SELEX is useful for targets that are rare in their original environment. | [35] |
Subtractive SELEX | Selection of aptamers that have the ability to differentiate between two closely related targets (e.g., distinguishing between a normal cell structure and another disease-related one). This is obtained by adding rounds of negative selection against normal cells. | [36] |
Conditional SELEX | Selection of aptamers that are affected by the presence of regulatory molecules; aptamer selection is performed in two stages here: The first stage in the presence of regulatory molecules and the second in the absence of regulatory molecules. Only the sequences that successfully bind to the target in either one of the stages but not the other is selected, depending on whether the aptamer is to be used in the presence or absence of regulatory molecules. | [37] |
On-chip selection | This is similar to the microarray method. Single and double base variations are introduced using in silico methods to a pre-selected sequence with the highest affinity to its target and then embedded on a surface plasmon resonance (SPR) chip. On-chip selection is useful for aptamer selection against a large number of targets. | [38] |
Immobilization-free SELEX or GO-SELEX | First, the library is incubated with the target, and graphene oxide (GO) is then added to the mix in order to bind the unbound sequences via p–p stacking. | [39] |
Tissue slide-based SELEX | Selection of aptamers against clinical samples. Cancerous tissue is used in the first stage as a target. Then, the tissue is scraped from the slide with the bound sequences. These sequences are then eluted, and counter selection against normal tissue is performed to eliminate shared aptamers. | [40] |
Capillary Electrophoresis SELEX (CE-SELEX) | CE-SELEX separates the target bounded from unbounded sequences by the difference in electrophoretic mobility, which is a highly efficient separation method. This method enables the selection of aptamer candidates with high affinity while reducing the selection rounds to 1 to 4 from nearly 20 in conventional SELEX | [41,42] |
Microfluidic SELEX (M-SELEX) | Combining traditional SELEX with a microfluidic system. This system contains reagent-loaded micro-lines, a pressurized reagent reservoir manifold, a PCR thermocycler, and actuatable valves for selection and sample routing. | [43] |
High-Throughput Sequencing SELEX (HTS-SELEX) | Aptamers are identified through an iterative process of evolutionary selection starting from a random pool containing billions of sequences. The most predominant characteristic of HTS-SELEX is that it firstly allows for sequencing of the library across all the selection rounds. Thus, enriched sequences are visible at a much earlier round, which is more time efficient. Fewer selection rounds also avoid the potential PCR bias caused by over selection. | [44] |
Aptamers | Antibodies | |
---|---|---|
Synthesis | Chemically synthesized and easy to produce | High cost and complexity of production |
Size | Small compared to antibodies | Large |
Stability | Prone to nuclease degradation | Short biological half-life |
Targets | Wide range of targets, starting from ions to whole living cells | Produced only against immunogenic molecules, which limits the range of targets |
Toxicity and Immunogenicity | Low toxicity and non-immunogenic | Immunogenic |
Binding Specificity | High binding specificity | High binding specificity |
Binding Affinity | High binding affinity | High binding affinity |
Clearance Rate | Rapid circulation clearance | Low clearance rate |
Chemical Conjugation | Easy to conjugate to nanoparticles and drugs | More difficult to conjugate |
Chemical modification | Tolerant to chemical modifications to enhance structural and functional propertie | Modifications often lead to reduced activity |
Target | Aptamer | Nanoparticle | Drug/Imaging Molecule | Tumors | Conjugation Methodology | Ref. |
---|---|---|---|---|---|---|
Nucleolin | AS1411 | PLGA-b-PEG | Paclitaxel | Glioma | Carbodiimide chemistry | [231] |
Polyvalent mesoporous nanoparticles | Doxorubicin | Breast | Thiol-maleimide chemistry | [232] | ||
pegylated PAMAM dendrimer | Camptothecin | Colorectal | Thiol-maleimide chemistry | [233] | ||
polydopamine were surface modify a PLGA-b-TPGS polymer | Docetaxel | Breast | Thiol-maleimide related chemistry/Michael addition on dihydroxyindole unit | [234] | ||
PLGA-b-PEG | Doxorubicin and superparamagnetic iron oxide | Glioma | Carbodiimide chemistry | [235] | ||
polymersome | Doxorubicin | Breast | 3′-Cholesterol AS1411/direct conjugation | [236] | ||
PAMAM-PEG | 5-fluorouracil | Gastric cancer | Thiol-maleimide chemistry | [237] | ||
Alkyl-modified PAMAM dendrimers | Bcl-xLshRNA | Lung Cancer | Carbodiimide chemistry | [238] | ||
PSMA | A10 (F-RNA) | PEGylated liposomes | 225Ac | Prostate | Carbodiimide chemistry | [239] |
PLGA-b-PEG | Cis-Pt(IV) | Prostate | Carbodiimide chemistry | [240] | ||
TCL-SPION | Doxorubicin | Prostate | Carbodiimide chemistry of oligonucleotide linker followed by aptamer complementary base pair binding | [241] | ||
A10-3-J1 | Superparamagnetic iron oxide | Doxorubicin | Prostate | Avidin-biotin DNA linker followed by aptamer complementary base pair binding | [242] | |
A10-3.2 | Atelocollagen | miR-15a and miR-16- | Prostate | Thiol-maleimide chemistry | [243] | |
MUC1 | DNA aptamer | CuInS2 quantum dot | Daunorubicin | Prostate | Carbodiimide chemistry of oligonucleotide linker followed by aptamer complementary base pair binding | [244] |
MUC1 | DNA aptamer | Zn-doped CdTe QDs | Zn2+ doped CdTe QDs | Lung | Complementary DNA | [245] |
iron oxide nanoparticles | Hyperthermia | Breast | Avidin-biotin coupling | [246] | ||
Chitosan-coated human serum albumin | Paclitaxel | Breast | Carbodiimide chemistry | [247] | ||
Poloxamer | miRNA-29b | Lung | Carbodiimide chemistry | [248] | ||
Au@SPIONs | Photothermal therapy | Colon | SH-Aptamer gold coordination | [249] | ||
Micelle | Doxorubicin and proapoptotic peptide (KLA) | Breast, Colon | Carbodiimide chemistry | [250] | ||
5TR1 DNA aptamer | PLGA modified with chitosan | Epirubicin | Breast | Electrostatic interaction | [251] | |
DNA aptamer MA3 | Thermosensitive hydrogel | Doxorubicin | Breast | Thiol-maleimide chemistry | [252] | |
PTK7 | Sgc8 (DNA) | Polyvalent aptamer system | Doxorubicin | T-cell acute lymphoblastic leukaemia | Complementary DNA | [253] |
Au-Ag nanorods | Doxorubicin | T-cell acute lymphoblastic leukemia | SH-Aptamer gold coordination | [254] | ||
Single-walled carbon nanotubes | Daunorubicin | T-cell acute lymphoblastic leukemia | direct conjugation | [255] | ||
PTK7 | Sgc8 (DNA) | Mesoporus nanoparticles | Doxorubicin | T-cell acute lymphoblastic leukaemia | Carbodiimide chemistry | [256] |
Gold nanoparticles | Daunorubicin | T-cell acute lymphoblastic leukemia | SH-Aptamer gold coordination | [257] | ||
Au | Doxorubicin | T-cell acute lymphoblastic leukemia | SH-Aptamer gold coordination | [258] | ||
Acoustic droplets | Daunorubicin | T-cell acute lymphoblastic leukemia | Thiol-maleimide chemistry | [259] | ||
IgM | TDO5 (DNA) | PAMAM Dendrimer | Uptake study | Burkitt’s lymphoma | Carbodiimide chemistry | [260] |
HER2 | S6 aptamer | Plasmonic gold coating on magnetic nanoparticles | Fe3O4 | Breast | SH-Aptamer gold coordination | [261] |
TSA14 | PEGylated Liposomes | Doxorubicin | Breast | Thiol-maleimide chemistry | [262] | |
A6 | hybrid nanoparticles (cationic lipids and PLGA-b-PEG) | siRNA | Breast | Thiol-maleimide chemistry | [263] | |
CD44 | DNA thiolated aptamer | PEG-PAMAM | miRNA | Breast | Carbodiimide chemistry for PAMAM followed by Aptamer Thiol-maleimide chemistry | [264] |
EpCAM | EpApt | PLGA-b-PEG | Lecithisn curcumin | Colorectal | Carbodiimide chemistry | [265] |
DNA-EpCAM | mesoporous silica | Doxorubicin | colon | Carbodiimide chemistry | [266] | |
EGFR | RNA | Lipid-polymer nanoparticle | Salinomycin | Osteosarcoma CSCs | Thiol-maleimide chemistry | [267] |
Tenascin-C | GBI-10 | PEGylated Liposomes | Gadolinium Compounds | Glioma | Carbodiimide chemistry | [268] |
GBI-10 | QD–Apt nanoprobes | CdSe/ZnS | Glioma | Carbodiimide chemistry | [269] | |
PDGFR | Gint4.T | PLGA-b-PEG | PI3K-mTOR inhibitor | glioblastoma | Carbodiimide chemistry | [270] |
Cell-SELEX | SRZ1 | Cationic-liposomes | Doxorubicin | Breast cancer | Avidin-biotin coupling | [271] |
fibronectin protein | DNA aptamer AS-14 | gold-coated magnetic nanoparticles | Magnetodynamic nanotherapy | Ehrlich carcinoma | Thiol-maleimide chemistry | [272] |
Cell-SELEX | KW16-13 | gold nanorods | Photothermal therapy | Breast | Thiol-maleimide chemistry | [273] |
FGFR1 | DNA aptamer | Iron oxide nanoparticles | Hyperthermia | Osteosarcoma | Avidin-biotin coupling | [274] |
Nucliolin MUC1 ATP | AS1411 MUC1 ATP | DNA dendrimers, pH sensitive release | Epirubicin | Breast, Colon | Electrostatic interaction | [275] |
Annexin A2 | Annexin A2 aptamer | DNA/RNA hybrid Nanoparticles | Doxorubicin | Ovarian cancer | Complementary base pairing | [276] |
CD20 | DNA aptamer | Lipid-polymer Nanoparticles | Salinomycin | Melanoma | Thiol-maleimide chemistry | [277] |
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Odeh, F.; Nsairat, H.; Alshaer, W.; Ismail, M.A.; Esawi, E.; Qaqish, B.; Bawab, A.A.; Ismail, S.I. Aptamers Chemistry: Chemical Modifications and Conjugation Strategies. Molecules 2020, 25, 3. https://doi.org/10.3390/molecules25010003
Odeh F, Nsairat H, Alshaer W, Ismail MA, Esawi E, Qaqish B, Bawab AA, Ismail SI. Aptamers Chemistry: Chemical Modifications and Conjugation Strategies. Molecules. 2020; 25(1):3. https://doi.org/10.3390/molecules25010003
Chicago/Turabian StyleOdeh, Fadwa, Hamdi Nsairat, Walhan Alshaer, Mohammad A. Ismail, Ezaldeen Esawi, Baraa Qaqish, Abeer Al Bawab, and Said I. Ismail. 2020. "Aptamers Chemistry: Chemical Modifications and Conjugation Strategies" Molecules 25, no. 1: 3. https://doi.org/10.3390/molecules25010003
APA StyleOdeh, F., Nsairat, H., Alshaer, W., Ismail, M. A., Esawi, E., Qaqish, B., Bawab, A. A., & Ismail, S. I. (2020). Aptamers Chemistry: Chemical Modifications and Conjugation Strategies. Molecules, 25(1), 3. https://doi.org/10.3390/molecules25010003