The authors acknowledge the Institute for Mental and Physical Health and Clinical Translation (IMPACT) SEED funding, the &#34;Alfred Deakin Postdoctoral Research Fellowship&#34; program at Deakin University, and the &#34;Australian Government Research Training Program Scholarship&#34;.&#160;

NOTE: Prior to starting the experiment, wear personal protective equipment, including a lab coat, gloves, and goggles. See the Table of Materials for details about materials, reagents, equipment, and software used in this protocol.
1. Buffers required for the assay
<ol>
	<li>Prepare the buffers required for this experiment-the SELEX buffer required for aptamer folding, Blocking Buffer (BB), Wash Buffer (WB), and Binding Buffer (BiB) (Table 1...

<ol>
	<li>Cancer. World Health Organization Available from: <a target="_blank" href="https://www.who.int/news-room/fact-sheets/detail/cancer#:~:text=Cancer%20is%20a%20leading%20cause.and%20rectum%20and%20prostate%20cancers">https://www.who.int/news-room/fact-sheets/detail/cancer#:~:text=Cancer%20is%20a%20leading%20cause.and%20rectum%20and%20prostate%20cancers</a> (2022)</li><li>Liu, J. K. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+history+of+monoclonal+antibody+development+-+Progress,+remaining+challenges+and+future+innovations.">The history of monoclonal antibody development - Progress, remaining challenges and future innovations.</a> Annals of Medicine and Surgery. 3 (4), 113-116 (2014).</li><li>Nakhjavani, M., Shigdar, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Future+of+PD-1/PD-L1+axis+modulation+for+the+treatment+of+triple-negative+breast+cancer.">Future of PD-1/PD-L1 axis modulation for the treatment of triple-negative breast cancer.</a> Pharmacological Research. 175, 106019 (2022).</li><li>Bukari, B., Samarasinghe, R. M., Noibanchong, J., Shigdar, S. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Non-invasive+delivery+of+therapeutics+into+the+brain:+the+potential+of+aptamers+for+targeted+delivery.">Non-invasive delivery of therapeutics into the brain: the potential of aptamers for targeted delivery.</a> Biomedicines. 8 (5), 120 (2020).</li><li>Wu, X., Chen, J., Wu, M., Zhao, J. X. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Aptamers:+active+targeting+ligands+for+cancer+diagnosis+and+therapy.">Aptamers: active targeting ligands for cancer diagnosis and therapy.</a> Theranostics. 5 (4), 322 (2015).</li><li>Feng, X., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+aptamer+functionalized+nanocomposite+used+for+prostate+cancer+diagnosis+and+therapy.">The aptamer functionalized nanocomposite used for prostate cancer diagnosis and therapy.</a> Journal of Nanomaterials. 2022, (2022).</li><li>Huang, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Advances+in+aptamer-based+biomarker+discovery.">Advances in aptamer-based biomarker discovery.</a> Frontiers in Cell and Developmental Biology. 9, 571 (2021).</li><li>Ashrafuzzaman, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Aptamers+as+both+drugs+and+drug-carriers.">Aptamers as both drugs and drug-carriers.</a> BioMed Research International. 2014, (2014).</li><li>Nakhjavani, M., Samarasinghe, R. M., Shigdar, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Triple-negative+breast+cancer+brain+metastasis:+an+update+on+druggable+targets,+current+clinical+trials,+and+future+treatment+options.">Triple-negative breast cancer brain metastasis: an update on druggable targets, current clinical trials, and future treatment options.</a> Drug Discovery Today. , (2022).</li><li>Macdonald, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Development+of+a+bifunctional+aptamer+targeting+the+transferrin+receptor+and+epithelial+cell+adhesion+molecule+(EpCAM)+for+the+treatment+of+brain+cancer+metastases.">Development of a bifunctional aptamer targeting the transferrin receptor and epithelial cell adhesion molecule (EpCAM) for the treatment of brain cancer metastases.</a> ACS Chemical Neuroscience. 8 (4), 777-784 (2017).</li><li>Macdonald, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Bifunctional+aptamer-doxorubicin+conjugate+crosses+the+blood-brain+barrier+and+selectively+delivers+its+payload+to+EpCAM-positive+tumor+cells.">Bifunctional aptamer-doxorubicin conjugate crosses the blood-brain barrier and selectively delivers its payload to EpCAM-positive tumor cells.</a> Nucleic Acid Therapeutics. 30 (2), 117-128 (2020).</li><li>Shigdar, S., Agnello, L., Fedele, M., Camorani, S., Cerchia, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Profiling+cancer+cells+by+cell-SELEX:+use+of+aptamers+for+discovery+of+actionable+biomarkers+and+therapeutic+applications+thereof.">Profiling cancer cells by cell-SELEX: use of aptamers for discovery of actionable biomarkers and therapeutic applications thereof.</a> Pharmaceutics. 14 (1), 28 (2021).</li><li>Rahimizadeh, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Development+of+cell-specific+aptamers:+recent+advances+and+insight+into+the+selection+procedures.">Development of cell-specific aptamers: recent advances and insight into the selection procedures.</a> Molecules. 22 (12), 2070 (2017).</li><li>Chen, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Development+of+cell-SELEX+technology+and+its+application+in+cancer+diagnosis+and+therapy.">Development of cell-SELEX technology and its application in cancer diagnosis and therapy.</a> International Journal of Molecular Sciences. 17 (12), 2079 (2016).</li><li>Shigdar, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+use+of+sensitive+chemical+antibodies+for+diagnosis:+detection+of+low+levels+of+EpCAM+in+breast+cancer.">The use of sensitive chemical antibodies for diagnosis: detection of low levels of EpCAM in breast cancer.</a> PLoS One. 8 (2), 57613 (2013).</li><li>Ni, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Role+of+the+EpCAM+(CD326)+in+prostate+cancer+metastasis+and+progression.">Role of the EpCAM (CD326) in prostate cancer metastasis and progression.</a> Cancer and Metastasis Reviews. 31 (3), 779-791 (2012).</li><li>Ni, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Epithelial+cell+adhesion+molecule+(EpCAM)+is+associated+with+prostate+cancer+metastasis+and+chemo/radioresistance+via+the+PI3K/Akt/mTOR+signaling+pathway.">Epithelial cell adhesion molecule (EpCAM) is associated with prostate cancer metastasis and chemo/radioresistance via the PI3K/Akt/mTOR signaling pathway.</a> The International Journal of Biochemistry &amp; Cell Biology. 45 (12), 2736-2748 (2013).</li><li>McKeague, M., Kruse, P. F., Patterson, M. K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Tissue Culture. , 395-397 (1973).</li><li>McKeague, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+minimum+aptamer+publication+standards+(MAPS+guidelines)+for+de+novo+aptamer+selection.">The minimum aptamer publication standards (MAPS guidelines) for de novo aptamer selection.</a> Aptamers. 6, 10-18 (2022).</li><li>Schoofs, G., Van Hout, A., D'huys, T., Schols, D., Van Loy, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+flow+cytometry-based+assay+to+identify+compounds+that+disrupt+binding+of+fluorescently-labeled+CXC+Chemokine+ligand+12+to+CXC+Chemokine+receptor+4.">A flow cytometry-based assay to identify compounds that disrupt binding of fluorescently-labeled CXC Chemokine ligand 12 to CXC Chemokine receptor 4.</a> Journal of Visualized Experiments. (133), e57271 (2018).</li><li>McKinnon, K. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Flow+cytometry:+an+overview.">Flow cytometry: an overview.</a> Current Protocols in Immunology. 120 (1), 1-11 (2018).</li><li>Kamiloglu, S., Sari, G., Ozdal, T., Capanoglu, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Guidelines+for+cell+viability+assays.">Guidelines for cell viability assays.</a> Food Frontiers. 1 (3), 332-349 (2020).</li><li>Ruscito, A., DeRosa, M. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Small-molecule+binding+aptamers:+Selection+strategies,+characterization,+and+applications.">Small-molecule binding aptamers: Selection strategies, characterization, and applications.</a> Frontiers in Chemistry. 4, 14 (2016).</li><li>McKeague, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comprehensive+analytical+comparison+of+strategies+used+for+small+molecule+aptamer+evaluation.">Comprehensive analytical comparison of strategies used for small molecule aptamer evaluation.</a> Analytical Chemistry. 87 (17), 8608-8612 (2015).</li><li>Henri, J., Bayat, N., Macdonald, J., Shigdar, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+guide+to+using+nucleic+acid+aptamers+in+cell+based+assays.">A guide to using nucleic acid aptamers in cell based assays.</a> Aptamers. 23, (2019).</li><li>Mao, H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+mechanism+and+regularity+of+quenching+the+effect+of+bases+on+fluorophores:+the+base-quenched+probe+method.">The mechanism and regularity of quenching the effect of bases on fluorophores: the base-quenched probe method.</a> Analyst. 143 (14), 3292-3301 (2018).</li><li>McKeague, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analysis+of+in+vitro+aptamer+selection+parameters.">Analysis of in vitro aptamer selection parameters.</a> Journal of Molecular Evolution. 81 (5), 150-161 (2015).</li><li>Chen, B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Targeting+negative+surface+charges+of+cancer+cells+by+multifunctional+nanoprobes.">Targeting negative surface charges of cancer cells by multifunctional nanoprobes.</a> Theranostics. 6 (11), 1887 (2016).</li><li>Shigdar, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RNA+aptamers+targeting+cancer+stem+cell+marker+CD133.">RNA aptamers targeting cancer stem cell marker CD133.</a> Cancer Letters. 330 (1), 84-95 (2013).</li><li>Amraee, M., Oloomi, M., Yavari, A., Bouzari, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DNA+aptamer+identification+and+characterization+for+E.+coli+O157+detection+using+cell+based+SELEX+method.">DNA aptamer identification and characterization for E. coli O157 detection using cell based SELEX method.</a> Analytical Biochemistry. 536, 36-44 (2017).</li><li>Yu, X. -. X., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Selection+and+characterization+of+a+novel+DNA+aptamer,+Apt-07S+specific+to+hepatocellular+carcinoma+cells.">Selection and characterization of a novel DNA aptamer, Apt-07S specific to hepatocellular carcinoma cells.</a> Drug Design, Development and Therapy. 14, 1535 (2020).</li></ol>

The key challenge with developing new aptamers is the lack of standard guidelines that applies to different steps of this process. McKeague et al. have recently demonstrated some of the associated challenges, which lead to unclear presentations of data in publications and failure to replicate the research. They proposed fundamental guidelines necessary for consideration in characterizing aptamers19. An aptamer binding assay is a critical step in screening and/or characterizing aptamers<sup class="...

Cancer is still one of the leading causes of mortality worldwide1. Despite the significant improvement in cancer treatment in recent decades, anticancer drug development is still a highly debated topic. This is because chemotherapy, as the mainstay of cancer treatment, is accompanied by serious side effects that limit patient compliance with the treatment. Moreover, chemotherapy-induced cancer resistance to treatment has restricted its application as the sole choice of medical intervention. The application of monoclonal antibodies (mAbs) introduced an enhanced response to cancer treatments2. The rationale of using mAbs was to improve the efficacy of chemotherapeutics and minimize their adverse reactions. However, the administration of mAbs also became a challenge. This was not only because of the mAb-induced immunological reactions but also due to the animal-dependent and expensive production costs and difficult storage conditions3. Introduction of aptamers in the 1990s4 raised new hopes in cancer treatment, as the application of aptamers could address the challenges associated with mAbs.
Aptamers are short nucleic acid sequences that are specifically produced for a certain target. Systematic evolution of ligands by exponential enrichment (SELEX) is a common method in aptamer production. In SELEX, the protein of interest is incubated with a library of random nucleotide sequences, and through a series of iterative cycles, the aptamer specific for that protein is purified. Aptamers have similar target selectivity and specificity to mAbs, and therefore drug development in this field shows promising future applications. Aptamers specific for cancer biomarkers could be applied as single drugs and cancer diagnostic tools5,6,7. Due to their nano-sized structure, these aptamers could also act as drug carriers to deliver cytotoxic agents specifically to the tumor8. This would increase the efficacy of targeted drug delivery and decrease chemotherapy-associated, off-target adverse reactions. Moreover, these nanomedicines have a high tissue penetration, which makes them a desirable candidate for deep-tumor drug delivery and treatment. Aptamers can also be designed to target the transporters expressed on the blood-brain barrier (BBB) to improve drug delivery to brain tumors9. A good example of such an aptamer are bifunctional aptamers, targeting the transferrin receptor (TfR)10 to enhance drug delivery across the BBB, and delivering a cytotoxic drug payload to tumor cells11.
Despite all the advantages of aptamers, drug development in this field has not yet yielded a marketed, successful anticancer drug. One reason for this could be the lack of standard and reproducible methods that could be followed globally by researchers in the field. In this paper, a step-by-step protocol of an aptamer binding to a native protein expressed on the cell surface is demonstrated. This protocol is a prerequisite step in the preclinical assessment of anticancer aptamers. The assay is performed to show the selectivity and specificity of the purified aptamer collected from SELEX or a published aptamer sequence for confirmation of selectivity and specificity. This flow cytometric-based assay is a rapid, reliable, sensitive assay that accurately shows the selectivity and specificity of the aptamer, where the aptamer is being tested against proteins on the cell surface12,13,14. This method is demonstrated using the binding of an aptamer specific for EpCAM shown in this paper15. EpCAM, as a transmembrane glycoprotein, plays roles in tumor cell signaling, progression, migration, and metastasis16,17. To show the selectivity and specificity of this aptamer, EpCAM-positive and -negative cancer cells were used. The previously developed EpCAM specific aptamer, TEPP (5&#8242;-GC GCG GTAC CGC GC TA ACG GA GGTTGCG TCC GT-3&#8242;), and a negative control aptamer, TENN (5&#8242;-GC GCG TGCA CGC GC TA ACG GA TTCCTTT TCC GT-3), were used as EpCAM-binding and -non-binding aptamers, respectively10. The 3&#39; end of both TEPP and TENN were labeled with a TYE665 fluorophore.
TEPP is a bifunctional aptamer that targets EpCAM from one end and TfR on the other. This has made TEPP a suitable candidate for drug delivery to EpCAM+ brain tumors. Using its TfR-specific end, TEPP traverses the blood-brain barrier, and using the EpCAM-specific end, finds the tumor and delivers its cargo (e.g., cytotoxic drugs) to the tumor. TENN has a similar length and 2D structure as TEPP, but it does not have affinity for the EpCAM or TfR, and hence is a suitable negative control aptamer. Using TEPP and TENN, testing the binding of an aptamer to the target protein using flow cytometry is shown in this paper. This protocol applies to the development of cell-specific aptamers. It is also applicable to further complementary and confirmation analyses of the aptamer sequences available in the literature. The protocol can also be used by those new to the aptamer field who are looking at using a previously published aptamer for their research and development (R&#38;D) purposes. In this paper, two aptamer sequences available in the literature are studied.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>1.5 mL microcentrifuge tubes with attached lid</td>
			<td>Sigma-Aldrich</td>
			<td>T6649</td>
			<td></td>
		</tr>
		<tr>
			<td>15 mL CellStar blue screw cap, conical bottom tube</td>
			<td>Greiner Bio One</td>
			<td>188271</td>
			<td></td>
		</tr>
		<tr>
			<td>5 mL serological pipettes</td>
			<td>Greiner Bio One</td>
			<td>606180</td>
			<td></td>
		</tr>
		<tr>
			<td>BD FACSCanto II Flow Becton Dickinson Cytometer</td>
			<td>Becton Dickinson</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>BD FACSDiva V9.0</td>
			<td>BD Biosciences</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Bovine Serum Albumin (BSA), Lyophilized powder</td>
			<td>Sigma-AldrichTM</td>
			<td>A7906-50G</td>
			<td></td>
		</tr>
		<tr>
			<td>Bright-line Hemocytometer</td>
			<td>Sigma-Aldrich</td>
			<td>Z359629</td>
			<td></td>
		</tr>
		<tr>
			<td>Dulbecco&#8217;s Modified Eagle Medium (DMEM) High Glucose Media Powder</td>
			<td>Life Technologies</td>
			<td>12100046</td>
			<td></td>
		</tr>
		<tr>
			<td>Dulbecco&#8217;s Phosphate- Buffered Saline (DPBS)</td>
			<td>Life Technologies</td>
			<td>21300025</td>
			<td></td>
		</tr>
		<tr>
			<td>FlowJo, LLC 10.8.1</td>
			<td>BD Biosciences</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Foetal Bovine Serum (FBS)</td>
			<td>Bovogen</td>
			<td>SFBS-F</td>
			<td></td>
		</tr>
		<tr>
			<td>HEK293T</td>
			<td>American Type Culture Collection</td>
			<td>ACS-4500</td>
			<td></td>
		</tr>
		<tr>
			<td>Heracell 150i CO2 Incubator</td>
			<td>Thermo Fisher Scientific</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Heraeus Megafuge 16R Centrifuge</td>
			<td>Thermo Fisher Scientific</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Magnesium Chloride (MgCl2)</td>
			<td>Sigma-Aldrich</td>
			<td>M8266</td>
			<td></td>
		</tr>
		<tr>
			<td>MDA-MB-231</td>
			<td>American Type Culture Collection</td>
			<td>CRM-HTB-26</td>
			<td></td>
		</tr>
		<tr>
			<td>Microplate, PS, 96 well, F-bottom (Chimney well), Black</td>
			<td>Greiner Bio One</td>
			<td>655076</td>
			<td></td>
		</tr>
		<tr>
			<td>MiniAmp Thermal Cycler</td>
			<td>Thermo Fisher Scientific</td>
			<td>A37834</td>
			<td></td>
		</tr>
		<tr>
			<td>Phosphate-Buffered Saline (PBS) tablets</td>
			<td>Life Technologies</td>
			<td>18912014</td>
			<td></td>
		</tr>
		<tr>
			<td>Pyrogen- and RNase-free ultrapure water</td>
			<td>Milli-Q</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>T75 Cell Culture flask</td>
			<td>Cellstar</td>
			<td>658170</td>
			<td></td>
		</tr>
		<tr>
			<td>TENN</td>
			<td>Integrated DNA Technologies</td>
			<td>N/A</td>
			<td>5&#8242;-GC GCG TGCA CGC GC TA ACG GA TTCCTTT TCC GT-3</td>
		</tr>
		<tr>
			<td>TEPP</td>
			<td>Integrated DNA Technologies</td>
			<td>N/A</td>
			<td>5&#8242;-GC GCG GTAC CGC GC TA ACG GA GGTTGCG TCC GT-3&#8242;</td>
		</tr>
		<tr>
			<td>Transfer RNA (tRNA)</td>
			<td>Sigma-Aldrich</td>
			<td>R8508-5X1ML</td>
			<td></td>
		</tr>
		<tr>
			<td>Trypan Blue Solution</td>
			<td>Life Technologies</td>
			<td>15250061</td>
			<td></td>
		</tr>
		<tr>
			<td>Trypsin-EDTA</td>
			<td>Gibco</td>
			<td>15400054</td>
			<td></td>
		</tr>
	</tbody>
</table>

a flow cytometry-based cell surface protein binding assay for assessing selectivity and specificity of an anticancer aptamer

A key challenge in developing an anticancer aptamer is to efficiently determine the selectivity and specificity of the developed aptamer to the target protein. Due to its several advantages over monoclonal antibodies, aptamer development has gained enormous popularity among cancer researchers. Systematic evolution of ligands by exponential enrichment (SELEX) is the most common method of developing aptamers specific for proteins of interest. Following SELEX, a quick and efficient binding assay accelerates the process of identification, confirming the selectivity and specificity of the aptamer. 
This paper explains a step-by-step flow cytometric-based binding assay of an aptamer specific for epithelial cellular adhesion molecule (EpCAM). The transmembrane glycoprotein EpCAM is overexpressed in most carcinomas and plays roles in cancer initiation, progression, and metastasis. Therefore, it is a valuable candidate for targeted drug delivery to tumors. To evaluate the selectivity and specificity of the aptamer to the membrane-bound EpCAM, EpCAM-positive and -negative cells are required. Additionally, a non-binding EpCAM aptamer with a similar length and 2-dimensional (2D) structure to the EpCAM-binding aptamer is required. The binding assay includes different buffers (blocking buffer, wash buffer, incubation buffer, and FACS buffer) and incubation steps. 
The aptamer is incubated with the cell lines. Following the incubation and washing steps, the cells will be evaluated using a sensitive flow cytometry assay. Analysis of the results shows the binding of the EpCAM-specific aptamer to EpCAM-positive cells and not the EpCAM-negative cells. In EpCAM-positive cells, this is depicted as a band shift in the binding of the EpCAM aptamer to the right compared to the non-binding aptamer control. In EpCAM-negative cells, the corresponding bands of EpCAM-binding and -non-binding aptamers overlap. This demonstrates the selectivity and specificity of the EpCAM aptamer. While this protocol is focused on the EpCAM aptamer, the protocol is applicable to other published aptamers.

An important aspect of new drug discovery and development is assuring the selectivity and specificity of the drug candidate. This means that the drug candidate should be able to discriminate between different cells and only affect the cell population of interest (selectivity). Selectivity is studied using cell lines that differ in terms of expression of the protein of interest. In this study, MDA-MB-231 and HEK 293T cell lines were chosen as EpCAM-positive and -negative cells. Specificity is another determinant that show...

Watch this Scientific Journal Video about A Flow Cytometry-Based Cell Surface Protein Binding Assay for Assessing Selectivity and Specificity of an Anticancer Aptamer at JoVE.com

A Flow Cytometry-Based Cell Surface Protein Binding Assay for Assessing Selectivity and Specificity of an Anticancer Aptamer

A necessary step in anticancer aptamer development is to test its binding to the target. We demonstrate a flow cytometric-based assay to study this binding, emphasizing the importance of including a negative control aptamer and cancer cells that are positive or negative for that particular protein.&#160;

A key challenge in developing an anticancer aptamer is to efficiently determine the selectivity and specificity of the developed aptamer to the target ...

This protocol will help researchers new to working with aptamers to be able to use them in their projects and also to understand the individual little steps that are required to complete the protocol. Aptamers are very versatile, and this protocol demonstrates how easy and simple they are in an immunophenotyping assay. Aptamers can be used for both diagnostic and therapeutic applications.This protocol is the first steps undertaken to confirm their specificity and sensitivity. While this particular assay demonstrates staining of one cell surface receptor, aptamers can very easily be used for multi-parametric flow cytometry, providing a high level of phenotypic knowledge. The important aspects of working with aptamers are ensuring that they are folded correctly prior to use, and also that the buffer and the ionic strength conditions are the same as when they were selected.After collecting and discarding the media in the flask, add three milliliters of PBS and spread it over the cells. After adding one milliliter of 0.25%of Trypsin-EDTA to each flask, incubate for five to 10 minutes at 37 degrees Celsius and visualize the detachment of cells under a microscope. Next, add one milliliter of complete medium to the cells and pipette the cells up and down to make a single cell suspension.Pipette the cells into an appropriate tube and centrifuge at 200 G for five minutes. After discarding the supernatant, resuspend the cells in one milliliter of fresh medium and count the cells using trypan blue staining by diluting certain volume of cell suspension with trypan blue. Distribute approximately 15 microliters of the mixture between a hemocytometer and a cover glass to count the cells.Collect the required number of cells, making sure to have a hundred thousand cells per test sample. Then incubate the cells at 37 degrees Celsius for two hours to allow the stabilization of the protein of interest on the cell membrane following enzymatic detachment. Following the two hours incubation, centrifuge the cells at 500 G for five minutes.After discarding the supernatant, resuspend the cells in 500 microliters of blocking buffer. Incubate the cells at four degrees Celsius for 30 minutes with intermittent mixing. During this 30 minute incubation, perform aptamer folding by preparing twice the concentrations of aptamers as described in the manuscript.Then mix and incubate the aptamers with the thermocycler machine according to the required folding conditions while ensuring to protect the aptamers from light. Following the 30 minutes incubation, centrifuge the cells as demonstrated previously and remove the supernatant. Then add one milliliter of wash buffer and centrifuge the cells again.After removing the supernatant, resuspend the cells in a suitable volume of the binding buffer. Next, pipette 50 microliters of the resuspended cells into each well of an ice cold 96 well black plate. Then pipette 50 microliters of the aptamers onto a 50 microliters volume of cells, mix and incubate in darkness at four degrees Celsius for 30 minutes.After centrifuge and removing the supernatant, carefully resuspend the pellet in wash buffer and again centrifuge at 500 G for five minutes. Then resuspend in 100 microliters of wash buffer for flow cytometric analysis while repeating the wash step twice. First, turn on the flow cytometer and then the computer.Next, open the flow cytometry analysis software, log into the program, and under the cytometer tab run fluid startup. To create a new experiment, under the experiment tab, click new folder, and name the folder slash experiment appropriately. Click on the new folder to highlight it.Then under the experiment tab again, click new experiment and name the experiment appropriately. To add the first sample slash specimen, under the experiment tab click new specimen and name the specimen appropriately. To add a tube sample, highlight the specimen and under the experiment tab, click new tube.Then add the appropriate number of tubes and name. To prepare the required graphs, under a worksheet tab, open a new worksheet. Once the new worksheet window pops up, prepare a dot blot graph of side scatter versus forward scatter to select the population of interest.Prepare a dot blot graph of forward scatter height versus forward scatter area to select the single cell population. Next, prepare a histogram of the number of events against the fluorophore of interest. Ensure that the acquisition dashboard for controlling the sample acquisition, inspector and cytometer to adjust voltage parameters as well as the worksheet with all the graphs is open before starting flow cytometry.First, run the untreated cells. Make sure the arrow pointing to the tube is green. If this arrow is not green, click on the arrow to make it green.Using up pipette, transfer each sample from the 96 well black plate to a flow cytometry tube. On the acquisition dashboard, choose an appropriate number of events to record, change the flow rate to low, and click Acquire Data. Adjust the voltage for the FSC and SCC parameters, ensuring that the cell population is centralized within the dot plot and that no cells are touching either axis of the graph to avoid losing the cells of interest.Define the first gate by identifying and selecting the population of interest in a forward and side scattered density plot while excluding the debris, which constitutes the population with the lowest forward scatter signal. Define the second gate by excluding doublet cell populations, as doublet cells considerably affect the results and conclusions. Increase the acquisition speed to medium or high to analyze the samples faster, but do not exceed more than 200 to 300 events per second.Then click record data. After adjusting the voltage and gating and recording the data, take out the sample and click Next Tube. Insert the next sample and repeat recording data for all control and test samples.Once all the data are collected, wash the flow cytometer by running three tubes of 50%bleach, FACSRinse and ultrapure water, each for five minutes at a high flow rate. Then from the cytometer dropdown menu, click fluidics shut down. Export the result as fsc files to a USB drive to transfer.Analyze them using the analysis software by pressing the new button to create a new document and window to handle the analysis, and drag the sample files into the new window. Double click to open the unstained sample. To gate the single cell population, choose the P1 population and double click on the P1 population to create an FSCH versus FSCA graph.Double click on the gated single cells to create a histogram of events against the used fluorochrome. In the original window select P1 and single cells and drag them to all samples so that all samples now contain the same gating. Next, click on the layout editor button to open the layouts window and drag two samples over one another to create overlay histogram.In EpCAM positive MDA-MB-231 cells, overlaying the histograms representing cells treated with TEPP and TENN shows that the TEPP treated cells are shifted to the right, compared to the TENN treated cells demonstrating that the binding of the TEPP aptamer occurs to the protein of interest. In negative control, HEK 293T cells overlaying histograms of TEPP and TENN do not reflect any shift indicating that in EpCAM expressing cells TEPP is the EpCAM aptamer attached to its receptor. And furthermore, no binding was observed in EpCAM negative cells, which confirms the selectivity and specificity of the developed aptamer.Ensure the aptamers are protected from light, the aptamers and cells are mixed on the plate, and the correct voltages are set on the flow cytometer. This is highly dependent on future applications for the aptamers. For example, we are focused on drug delivery.So the next step for us would be to assess if the aptamers are internalized using fluorescent microscopy. This protocol has demonstrated how easy it is for aptamers to replace monoclonal and polyclonal antibodies in immunophenotyping assays.

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JoVE Journal

Cancer Research

3.0K vistas.  Deakin University. Este protocolo ayudará a los investigadores nuevos en el trabajo con aptámeros a poder usarlos en sus proyectos y también a comprender los pequeños pasos individuales que se requieren para completar el protocolo. Los aptámeros son muy versátiles, y este protocolo demuestra lo fáciles y simples que son en un ensayo de inmunofenotipado. Los aptámeros se pueden utilizar tanto para aplicaciones diagnósticas como terapéuticas.Este protocolo es el primer paso dado para confirmar su...