Moselio Schaechter


  • The purpose of this blog is to share my appreciation for the width and depth of the microbial activities on this planet. I will emphasize the unusual and the unexpected phenomena for which I have a special fascination... (more)

    For the memoirs of my first 21 years of life, click here.

Associate Bloggers



  • (Click photo for more information.)

Bloggers Emeriti


  • (Click photo for more information.)

Meetings & Sponsors



« Frost Flowers Come to Life | Main | Retrospective, May 2011 »

May 19, 2011

Of Terms in Biology: Aptamer

by Elio

Aptamer

A DNA aptamer nestled on its
target. Source.

Picture yourself looking for a molecule that specifically inhibits an enzyme, impairs the binding of a ligand to a receptor, or does some other such wonder. Classically, one thinks of antibodies, but these require a lot of work and are not easy to come by. Easier is to fish out the desired molecule from a large pool of oligonucleotides or peptides. You do this by mixing the gemisch with whatever target you have in mind and looking for what binds to it. In the case of oligonucleotides, the candidate molecules can then be readily amplified. What you get are called aptamers. Typically, aptamers bind to their targets with high affinity and specificity, comparable to that of monoclonal antibodies.

The term "aptamer" derives from the Latin aptus, to fit. RNA and DNA aptamers have the ability to form complex 3-D structures, which endows them with a high degree of specificity for the target molecule. Aptamers can detect very small structural changes in their targets, such as the presence or absence of a methyl or hydroxyl group, or different enantiomers. For example, an aptamer to theophylline binds with 10,000-fold lower affinity to caffeine—two molecules that differ by only a single methyl group (1,3-dimethylxanthine and 1,3,7-trimethylxanthine, respectively).

To look for nucleic acid aptamers, one screens a large library of oligos (containing as many as 1020 different ones, each usually 40-60 nucleotides long) by repeated rounds of selection and amplification. This is called the SELEX process. Since this is all done in a test tube, one can select for aptamers that work under specific binding conditions, such as salt concentration, pH, and temperature. SELEX can be automated. Usually, aptamers have a long shelf life plus they have other attributes that make them good candidates for therapeutics.

For a more detailed account, click here or here. If you want to see videos of live people playing the aptamer game or animations thereof, search for “aptamer” with Google Video.

 

Comments

I like 3-D structure it seems everything clear Aptamers have a long shelf life plus they have other attributes that make them good candidates for therapeutics.

Here is a great paper where someone has gone the next step. An aptamer binding to the herbicide atrazine was created by a SELEX and deployed in a synthetic biological circuit. The circuit causes the bacteria to chemotaxi to the atrazine and destroy it.

http://www.nature.com/nchembio/journal/v6/n6/full/nchembio.369.html

Elio says: Wow!

Verify your Comment

Previewing your Comment

This is only a preview. Your comment has not yet been posted.

Working...
Your comment could not be posted. Error type:
Your comment has been saved. Comments are moderated and will not appear until approved by the author. Post another comment

The letters and numbers you entered did not match the image. Please try again.

As a final step before posting your comment, enter the letters and numbers you see in the image below. This prevents automated programs from posting comments.

Having trouble reading this image? View an alternate.

Working...

Post a comment

Comments are moderated, and will not appear until the author has approved them.

Teachers' Corner

Podcast

How to Interact with This Blog

  • We welcome readers to answer queries and comment on our musings. To leave a comment or view others, remarks, click the "Comments" link in red following each blog post. We also occasionally publish guest blog posts from microbiologists, students, and others with a relevant story to share. If you are interested in authoring an article, please email us at elios179 at gmail dot com.

Subscribe via email

Translate




Search




MicrobeWorld News

Membership