Polyadenylic acid (also known as poly(A), poly(A) carrier or carrier RNA) is a synthetic homopolymer composed of a long single-stranded (100-500 kDa) sequence of adenine (A) nucleotides available in lyophilized form. Its charge, shape and ability to residue-stack is modulated by solvent composition.

It is structurally identical to poly(A) tails, an endogenous stretch of about 50 to 250 adenine residues located at the 3'-end of (most) mature messenger RNAs (mRNAs), ubiquitously found in eukaryotic and some prokaryotic cells and a variety of viruses. Even SARS-CoV-2 was found to have a poly(A) tail.

The eukaryotic poly(A) tail is synthesized in the nucleus (called polyadenylation) by poly(A) polymerase, one of the subunits of a more than 80-protein complex (in humans), which uses ATP to add AMP moieties to the 3'-end of (cleaved) pre-messenger RNA. This process is important for transcription termination, mRNA stability, export to the cytoplasm and translation efficiency. Moreover, aberrant polyadenylation is associated with expression defects leading to human diseases.

Since the first accounts of a poly(A) tail in the 1970’s, synthetic poly(A) has been proven to be a versatile tool to:

A) Enhance DNA extraction from biological samples prior to amplification

Poly(A) is used as a carrier molecule in solid-phase and microfluidic-based silica monolith extraction methodologies to significantly enhance DNA extraction (via precipitation) from (low yield or degraded) biological samples.^[1,2]

B) Enhance (viral) RNA extraction from biological samples prior to amplification

It is also commonly being added to the extraction buffer (found in many commercial kits) in worldwide SARS-CoV-2 extraction from clinical samples prior to RT-qPCR or droplet digital PCR (ddPCR) amplifications for detection.^[3] Novel CRISPR-based diagnostics that use poly(A)-extracted viral RNA have also been developed. These methods are reported to be faster, ultrasensitive, easy to implement and quickly mobilized for future emerging viruses.^[4,5]

C) Resuspend lyophilized gBlocks

Poly(A) was used to resuspend lyophilized gBlocks containing synthetic double-stranded (control) DNA in the validation of a ddPCR assay.^[6]

D) Partially inhibit Exo1’s exonuclease activity

Following DNA double-strand breaks, poly(ADP-ribose) (PAR) is synthesized, which binds to Exo1, mediating early end resection and inhibiting its exonuclease activity. Poly(A) was found to only partially inhibit Exo1’s exonuclease activity in vitro.^[7]

E) Characterize A-U molecular recognition in biomedical membrane mimetic systems

Poly(A) was found to form a lipoplex with a novel cationic liposomal formulation doped with lauroyl uridine (LU), a non-ionic nucleolipid. Adenine-uridine (A-U) hydrogen bonds hold the lipoplex together, while also serving to spatially arrange the adenine bases to promote pi-pi interactions.^[8]

F) Explore the pharmacological activity of small molecules that interact with mRNA adenine residues, providing insight for nucleic acid targeted drug development

Three small isoquinoline alkaloids (coralyne, berberine and palmatine) were found to bind to poly(A) with high affinity. The mode of binding was either full or partial intercalation and the binding of coralyne for instance led to self-structure formation.^[9]

Furthermore, berberine was found to regulate gene expression by interacting with DNA TATA boxes concurrently with poly (A) tails.^[10]

Related Product

433347 Polyadenylic acid potassium salt, 85% (CAS: 26763-19-9)

Reference

1. Shaw, K. J., Thain, L., Docker, P. T., Dyer, C. E., Greenman, J., Greenway, G. M., & Haswell, S. J. (2009). The use of carrier RNA to enhance DNA extraction from microfluidic-based silica monoliths. Analytica chimica acta, 652(1-2), 231–233.
2. Kishore, R., Reef Hardy, W., Anderson, V. J., Sanchez, N. A., & Buoncristiani, M. R. (2006). Optimization of DNA extraction from low-yield and degraded samples using the BioRobot EZ1 and BioRobot M48. Journal of forensic sciences, 51(5), 1055–1061.
3. Yu, F., Yan, L., Wang, N., Yang, S., Wang, L., Tang, Y., Gao, G., Wang, S., Ma, C., Xie, R., Wang, F., Tan, C., Zhu, L., Guo, Y., & Zhang, F. (2020). Quantitative Detection and Viral Load Analysis of SARS-CoV-2 in Infected Patients. Clinical infectious diseases: an official publication of the Infectious Diseases Society of America, 71(15), 793–798.
4. Broughton, J.P., Deng, X., Yu, G. et al. CRISPR–Cas12-based detection of SARS-CoV-2. Nat Biotechnol, 38, 870–874 (2020).
5. Ding, X., Yin, K., Li, Z. et al. Ultrasensitive and visual detection of SARS-CoV-2 using all-in-one dual CRISPR-Cas12a assay. Nat Commun 11, 4711 (2020).
6. Miyaoka, Y., Berman, J. R., Cooper, S. B., Mayerl, S. J., Chan, A. H., Zhang, B., Karlin-Neumann, G. A., & Conklin, B. R. (2016). Systematic quantification of HDR and NHEJ reveals effects of locus, nuclease, and cell type on genome-editing. Scientific reports, 6, 23549.
7. Cheruiyot, A., Paudyal, S. C., Kim, I. K., Sparks, M., Ellenberger, T., Piwnica-Worms, H., & You, Z. (2015). Poly(ADP-ribose)-binding promotes Exo1 damage recruitment and suppresses its nuclease activities. DNA repair, 35, 106–115.
8. Cuomo, F., Ceglie, A., Colafemmina, G., Germani, R., Savelli, G., Lopez, F. (2011). Polyadenylic acid binding on cationic liposomes doped with the non-ionic nucleolipid Lauroyl Uridine. Colloids and Surfaces B: Biointerfaces, 82(2), 277-282.
9. Giri, P., Kumar, G. S. (2010). Isoquinoline Alkaloids and their Binding with Polyadenylic Acid: Potential Basis of Therapeutic Action. Mini-Reviews in Medicinal Chemistry, 10(7), 568-577.
10. Yuan, ZY., Lu, X., Lei, F. et al. (2016). TATA boxes in gene transcription and poly (A) tails in mRNA stability: New perspective on the effects of berberine. Sci Rep 5, 18326.