CH391L/S13/In vitro Selection of FNAs

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Functional nucleic acids (FNAs), as described by Dr. S.K. Silverman, are DNA and RNA aptamers that bind targets, or they are deoxyribozymes (single stranded DNA) and ribozymes (RNA) that have catalytic activity.[1] Aptamers, Ribozymes, and Deoxyribozymes are grouped into three main categories that are further classified into either natural or artificial depending on their origin. The exception being Deoxyribozymes as they have yet to be discovered in a living organism. Although the first ribozyme was discovered only in the 1980s, the search for new and better FNAs continues. This has led the development of new methodologies, such as the SELEX [2, 3] or In vitro selection, as we strive to expand their potential both as tools for exploring biology and solving real world problem solving.

Functional Nucleic Acid Chronology [2, 3],[4],[5],[6],[7],[8].
Functional Nucleic Acid Chronology [2, 3],[4],[5],[6],[7],[8].

Functional Nucleic Acids


Most natural ribozymes, RNA catalysts, catalyze mostly some type of scission or ligation that involves some type of phosphodiester chemistry. In vitro selected ribozymes are displaying a versatile level of sophistication of the sort required for cellular metabolism.[9]

Examples of Natural Ribozymes


Bimolecular Construct of 8-17 Deoxyribozyme and its Ribose Likage Substrate Cleaving Site
Bimolecular Construct of 8-17 Deoxyribozyme and its Ribose Likage Substrate Cleaving Site

An interesting discovery was made in the early 1990s, when for the first time DNA was shown that, besides being a genetic information storage molecule, it could also be both an enzyme and an aptamer. In the figure below you can observe 8-17, an RNA cleaving DNA enzyme. This molecule with 10-23 were the first to be described and tested in vivo as potential new therapies for cleaving the expressed mRNA of a virus. [7] Although proteins offer a larger diversity chemistries, depending on amino acids vs. both kinds of nucleic acids, as the latter ones depend on a limited array of nucleotides. Until know around a dozen distinct types of reactions. These include the following activities such as self-phosphorylation, RNA labeling, depurination,etc [10]

Aptamers and Riboswitches

The word aptamer from the latin aptus and translates as the past participle of "to fit" were originally identified by employing the protocol SELEX[2, 3]. Therefore, the word Aptamer describes their basic function as RNA or single stranded DNA (ssDNA)that can bind a ligand by assuming an specific structure.[11, 12] Yet, it would take several years until the discovery of the first in vivo aptamer or riboswitch [13].

In vitro Selection of Functional Nucleic Acids

SELEX or In vivo Selection Experiment
SELEX or In vivo Selection Experiment

A SELEX or In vitro Selection Experiment , describes the basic method for performing a SELEX or uses single stranded nucleic acids that are chemically synthesized,with a constant region (CR) and a fixed random region of length n. The random region of length n has only 4 nucleotides available, so the size of sequence space tested increases as 4n. Since only 1014 molecules can be sample in any given experiment, a point where the sequence space is larger, we can only sample sparse regions of this sequence space. Case in point, for a pool where "n" = 60 the actual sequence space is 1036 molecules [1].

The In vitro selection experiment

The first step is subjecting the population of single stranded nucleic acids or "pools" to specific selective condition in which function is possible. Then a (2) diverse subset of the population will perform the desired function and will be then (3) PCR (Polymerase Chain Reaction) amplified to regenerate the single stranded nucleic acids making use of CR introduced previously. The previous step is necessary for the selection's continuation into the next selection round, while at the same time a sample is obtained and can be sequenced. The reason why several rounds of selection are required is that we want to enrich the portion of the population with our desired function from the background noise, cheater sequences (non-function), that exist at the beginning of the experiment.

Examples of Functional Nucleic Acids

Deoxyribozyme-Catalyzed RNA labeling

Deoxyribozyme-catalyze labeling (DECAL), by 10DM24 deozyribozyme, "approach for site-specific internal RNA modification" that is attached to a labelled target RNA.[14]

The Flexizyme

One of the most interesting FNAs now available to new tool are flexizymes that perform a self-aminoacylating reaction on an in vitro selected tRNA with a N70 region and that can add nonnatural amino acids by reprogramming genetic code [15].

iGEM Link

TheTPP ribozyme biobrick made by the Pekin 2011 team combines both an aptamer and a ribozyme for regulatory purposes.


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  1. Error fetching PMID 23088677: [Silverman2012]
  2. Error fetching PMID 2200121: [Gold1990]
  3. Error fetching PMID 6297745: [Cech1982]
  4. Error fetching PMID 6197186: [Altman1983]
  5. Error fetching PMID 1697402: [Ellington1990]
  6. Error fetching PMID 12110898: [Cech2002]
  7. Error fetching PMID 11187837: [Breaker2000]
  8. isbn:978-0-387-73711-9. [Silverman2009]
  9. Error fetching PMID 10872462: [Wilson1999]
  10. Error fetching PMID 12410317: [Winkler2002]
  11. Error fetching PMID 17150804: [GoTo2006]
  12. Error fetching PMID 12022469: [Breaker2002]
  13. Error fetching PMID 12824337: [Zucker2003]
  14. Error fetching PMID 17846637: [Patel2007]
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