HPV-16 E7 oncoprotein aptamer

May 9, 2024 • Jiali Wang, Bo Fu

Description

In 2011, Toscano-Garibay JD, Benítez-Hess ML, Alvarez-Salas LM selexed an RNA aptamer targeting HPV-16 E7 protein from a randomized oligonucleotide library using an improved SELEX method. This aptamer is named G5a3N. 4, which has high affinity and specificity for binding specifically to HPV-16 E7 protein. The discovery of this aptamer may provide a valuable tool for detecting papillomavirus infection and cervical cancer^[1].

SELEX

In 2011, Toscano-Garibay JD, Benítez-Hess ML, Alvarez-Salas LM used a synthetic single stranded DNA (ssDNA) library called APTLIB, which contains 15 randomized nucleotide positions (approximately 10⁹ variants). The APTLIB RNA library is first subjected to three rounds of counter selection to remove aptamers that may bind to purified GST proteins. Then, the library was mixed with glutathione agarose beads coupled with the GST-E7 fusion protein and subjected to ten rounds of SELEX selection. After 10 rounds of selection, sequence analysis revealed the presence of a major motif in the selected library, namely 50-TSTTGTGTK-3, which mainly binds specifically to GST proteins. After removing the sequence binding to GST, an additional four rounds of SELEX were performed, including reverse selection rounds, to generate a G5α3N library, ultimately resulting in the RNA aptamer G5α3N.4 that specifically binds to HPV-16 E7 protein^[1].
Detailed information are accessible on SELEX page.

Structure

The 2D structure of the figure is based on the article by ribodraw tool to draw. G5α3N.4 apatamer binds to Human papillomavirus type 16 (HPV-16) E7 oncoprotein^[1].

5'-GGAGACCCAAGCCGAUUUAUUUUGUGCAGCUUUUGUUCCCUUUAGUGAGGGUUAAUU-3'

Ligand information

SELEX ligand

Plays a role in viral genome replication by driving entry of quiescent cells into the cell cycle. Stimulation of progression from G1 to S phase allows the virus to efficiently use the cellular DNA replicating machinery to achieve viral genome replication. E7 protein has both transforming and trans-activating activities. Induces the disassembly of the E2F1 transcription factor from RB1, with subsequent transcriptional activation of E2F1-regulated S-phase genes. Interferes with host histone deacetylation mediated by HDAC1 and HDAC2, leading to transcription activation. Also plays a role in the inhibition of both antiviral and antiproliferative functions of host interferon alpha. Interaction with host TMEM173/STING impairs the ability of TMEM173/STING to sense cytosolic DNA and promote the production of type I interferon (IFN-alpha and IFN-beta).-----From Uniprot

Name	Uniprot ID	Pfam	MW	Amino acids sequences	PDB	Gene ID
Human papillomavirus type 16 (HPV-16) E7 oncoprotein	P03129	IPR000148	11.022 kDa	MHGDTPTLHEYMLDLQPETTDLYCYEQLNDSSEEEDEIDGPAGQAEPDRAHYNIVTFCCKCDSTLRLCVQSTHVDIRTLEDLLMGTLGIVCPICSQKP	4YOZ 6APN	K02718

Some isolated sequences bind to the affinity of the protein.

Name	Sequence	Ligand	Affinity
G5α3N.4	5'-GGAGACCCAAGCCGAUUUAUUUUGUGCAGCUUUUGUUCCCUUUAGUGAGGGUUAAUU-3'	HPV-16 E7 protein	1.9 μM

References

[1] Isolation and characterization of an RNA aptamer for the HPV-16 E7 oncoprotein.
Toscano-Garibay, J. D., Benítez-Hess, M. L., & Alvarez-Salas, L. M.
Archives of medical research, 42(2), 88–96. (2011)