DNA vs RNA Aptamers

In our “What is an aptamer” blog, we described that aptamers are synthetically made, single-stranded DNA or RNA molecules. There are inherent differences between DNA and RNA when found naturally. DNA is typically a double-stranded biomolecule composed of A, T, C, and G bases. RNA is single-stranded and composed of A, U, C, and G bases that are not as stable within the cell as it usually acts as a messenger for other systems. 

Choosing Between DNA and RNA Aptamers

When designing a selection strategy for an aptamer binding to a target, the innate differences and their associated positives and negatives need to be considered. The first thing that needs to be decided would be the application of the aptamer. This is because as mentioned above, RNA naturally acts as a messenger system for the cell, which means native RNA is meant to be degraded within seconds in plasma. Native DNA has a longer half-life within plasma, closer to 60 minutes. There are chemical modifications that can be done to RNA, like the substitution of a fluorine instead of the natural hydroxyl group at the 2’ position on the RNA bases. This modification, along with others, can increase the half-life of RNA to match, or exceed, that of native DNA. This means that if an aptamer is desired to have no modifications in your application, then DNA would be preferential due to the stability being better.

	DNA	RNA
Native Stability in Plasma	60-90 minutes	Seconds
Library Structural Diversity	Large structural diversity	Large structural diversity
Sequence Structural Diversity	More stable structures, therefore more reliable binding	More structural diversity within a sequence, can cause weak binding
Selection time	Short (compared to RNA)	Long (need to transcribe after every round)

 

Structural Differences

The only structural difference between the backbone of single-stranded RNA and single-stranded DNA is the hydroxyl group at the 5’ position on RNA. The presence of this group could cause some steric hindrance and thus less flexibility within the RNA molecule. While more structures have been characterized in RNA, that is because RNA has been studied more extensively. Due to this, it cannot be ruled out that either have a larger structural diversity.

RNA, however, has been shown to be more likely to have an increased number of conformations within a sequence, with only a few of them being able to participate in target binding. Meanwhile, DNA tends to form more stable secondary structures that are available for binding to the target. 

 

Time for Selection

When looking to do a selection for a target, the time that it takes to do a selection also needs to be considered. While this seems like it is a smaller issue than the previously mentioned considerations, there are large differences between the two.  A selection with RNA will take longer as there is the extra step of converting the RNA library into DNA to allow it to be amplified for further rounds. It subsequently needs to be converted back into RNA for the next round of selection. This makes the selection longer than DNA, where the library just needs to be amplified between rounds. At NeoVentures, this selection time is greatly reduced with our Neomers platform. This new reproducible aptamer selection method, we can identify highly specific aptamers in only one round of selection. This means that for the time needed for selection is greatly reduced for both RNA and DNA libraries. 

 

The success of an aptamer selection also heavily depends on the consideration of positive and negative selections. At NeoVentures, we have the most experience in designing the best strategy that will work for your target and application. Get in touch with our team to learn more about which you should use for your unique application.