3D Aptamer Biosensors Need High-End Modeling Software


An RNA aptamer complexed with biotin. By Fdardel [CC BY-SA 3.0], via Wikimedia Commons.
What if you could replace your laboratory’s antibody supply with a library of custom-built probes which served the same purpose at a fraction of the price and at a multiple of the efficacy? Enter the age of the aptamers—short oligonucleotides that can bind arbitrary targets in a cheaper and more specific way than antibodies. According to new research, using molecular dynamics simulation software to model aptamer binding activity makes aptamers easy to use, easy to configure, and better than antibodies for almost every purpose an immunologist could dream of. 1

What Are Aptamers?

As exciting as this new biotechnology sounds, most immunologists probably don’t have a working familiarity with aptamers despite vaguely understanding the concept.

Essentially, aptamers replace the long and heavy chains of an antibody with a double stranded DNA molecule that’s contorted in such a way so as to be a ligand for the target of interest. The binding characteristics of the aptamer are determined by the sequence of its nucleotides, which exert slightly different molecular forces that jut out from their bond.

As mentioned in the new research, developing the sequences for the DNA in the aptamer is a task performed computationally via a method called SELEX, which is an algorithm for testing ligand binding efficiency of nucleotide combinations. Once the sequence for the aptamer that can bind the ligand is found, it’s as easy as making it in the lab and conjugating it to a reporter.

There’s just one catch: the sequences produced by SELEX are guaranteed to bind their ligand, but only in their unmodified form. There’s not much use in having an aptamer that’s guaranteed to bind a ligand only when it hasn’t been modified with a method for detecting whether binding has occurred. As mentioned by the authors of the new research, making use of SELEX to find workable aptamer sequences requires concomitant use of molecular modeling software to ensure that the addition of reporter conjugates doesn’t interfere with ligand binding.

Predictive Aptamer Modeling and Definition

Simulation of structure is an integral part of working with aptamers experimentally, as recognized by the new research and echoed by older literature.2 Molecular dynamics is an area of particular difficulty for most researchers, as few laboratories have access to robust simulation software. This goes double for niche simulation subjects like RNA, which typically don’t require simulation to accomplish experimental goals.3 Given the fruitfulness that molecular dynamics investigations into aptamers have rendered for streamlining their use, researchers that want to access the power of aptamers need to get their hands on simulation capabilities of their own.4

With the use of molecular modeling software in combination with SELEX, researchers will be able to:

  • Identify candidate sequences which will theoretically bind to the ligand of interest
  • Simulate the molecular dynamics of the ligand of interest
  • Simulate the binding mechanics of each of the candidates without the addition of any reporter constructs
  • Simulate the binding mechanics of each of the candidates during conjugation of reporter construct to rule out denaturation
  • Simulate the completed structure of each of the binding candidates when correctly conjugated to its reporter
  • Simulate the binding candidates’ interaction with their target of interest to ensure that they can still bind when conjugated to their reporter construct
  • Simulate the biodegradation of the final aptamer product

Without modeling software, aptamers can’t hope to be effective laboratory tools.

Why Aptamers?

Aptamers require the adoption of modeling software to be used effectively, which isn’t the case for commercially available antibodies that are in mainstream use. Given that aptamers are meant to accomplish the same experimental tasks as antibodies, it’s necessary to justify using aptamers over an established technology.

The authors of the new research have a number of arguments in favor of aptamers which are quite compelling. Though antibodies can be cheap and extremely specific, the limitations of experiments using antibodies are well understood.5 Antibody-based assays like ELISPOT and ELISA, while tried and true, can’t quantify cytokine producing cell populations with enough resolution to learn anything new, according to the new research’s authors. Likewise, established antibody-based assays can’t simultaneously measure cytokine production and cytokine concentration.6

Because of the massive configurability afforded to the aptamer’s binding profile via combinations of nucleotides, aptamers can bind to many more targets than antibodies, including ions, peptides, transcription factors, and bacteria. This diversity of binding targets is one of the major upsides of using aptamers over antibodies, and it’s the reason why aptamers have been noted for their potential therapeutic uses, which would be both safer and cheaper than antibodies.7 Though the concept of therapeutic or diagnostic aptamers is more than ten years old, difficulty in producing aptamers in the laboratory held back their widespread use until very recently.8 In light of growing access to powerful simulation software, the authors of the new research claim that aptamers have overcome the practical and theoretical difficulties with their implementation.

Biosensors for All

If researchers want to take the power to produce their own aptamers into the laboratory, they’ll need robust molecular modeling software which they can use in combination with SELEX and reporter conjugation. Relying on commercially-produced aptamers will be far more expensive than making customized aptamers in-house, defeating much of the purpose of their adoption. Thankfully, there is a sophisticated piece of molecular modeling and simulation software which your lab can use to power up your assays with aptamers.

BIOVIA Biologics is the aptamer production suite which your laboratory can use to simulate the nucleotide sequences that you locate with SELEX. With Biologics, you’ll be able to cut the antibody manufacturers out of your supply chain and produce your own highly specific ligand binders in-house. Contact us today to find out how you can use Biologics to start modeling customized aptamers and expand the range of detection at a lower price than with antibodies.

  1. “Three-dimensional Modeling of Single Stranded DNA Hairpins For Aptamer-Based Biosensors.” April 2017, https://www.nature.com/articles/s41598-017-01348-5#Bib1
  2. “Molecular Dynamics Simulation Analysis of Anti-MUC1 Aptamer and Mucin 1 Peptide Binding.” 2015, http://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DC%2BC2MXotFWqur8%3D&md5=75cf6ad2fe5cb7d84a8625a72b760e19
  3. “Software For Predicting the 3D Structure of RNA Molecules. 2015, http://chemport.cas.org/cgi-bin/sdcgi?APP=ftslink&action=reflink&origin=npg&version=1.0&coi=1:CAS:528:DC%2BC2cXitFansLvL&md5=e3cee489d0af14f29983c691a44a1ce2
  4. “Investigation of Interaction of Thrombin-Binding Aptamer With Thrombin And Prethrombin-2 by Simulation of Molecular Dynamics.” May 2013, https://www.ncbi.nlm.nih.gov/pubmed/24159810?dopt=Abstract
  5. Measurement of cytokine release at the single cell level using the ELISPOT assay.” 2006,  http://www.sciencedirect.com/science/article/pii/S1046202306000053?via%3Dihub
  6. “Comparison of the ELISPOT and cytokine flow cytometry assays for the enumeration of antigen-specific T cells.” 2003, http://www.sciencedirect.com/science/article/pii/S0022175903003636?via%3Dihub
  7. “Aptamers as Therapeutics.” January 2017, https://www.ncbi.nlm.nih.gov/pubmed/28061688?dopt=Abstract
  8. “Aptamers: An Emerging Class of Molecules That Rivals Antibodies In Diagnostics.” September 1999, http://clinchem.aaccjnls.org/content/45/9/1628.long