Protein-binding RNA aptamers affect molecular interactions distantly from their binding sites

PloS One
Daniel Miotto DupontP A Andreasen

Abstract

Nucleic acid aptamer selection is a powerful strategy for the development of regulatory agents for molecular intervention. Accordingly, aptamers have proven their diligence in the intervention with serine protease activities, which play important roles in physiology and pathophysiology. Nonetheless, there are only a few studies on the molecular basis underlying aptamer-protease interactions and the associated mechanisms of inhibition. In the present study, we use site-directed mutagenesis to delineate the binding sites of two 2´-fluoropyrimidine RNA aptamers (upanap-12 and upanap-126) with therapeutic potential, both binding to the serine protease urokinase-type plasminogen activator (uPA). We determine the subsequent impact of aptamer binding on the well-established molecular interactions (plasmin, PAI-1, uPAR, and LRP-1A) controlling uPA activities. One of the aptamers (upanap-126) binds to the area around the C-terminal α-helix in pro-uPA, while the other aptamer (upanap-12) binds to both the β-hairpin of the growth factor domain and the kringle domain of uPA. Based on the mapping studies, combined with data from small-angle X-ray scattering analysis, we construct a model for the upanap-12:pro-uPA complex. The results sugges...Continue Reading

References

Aug 30, 1990·Nature·A D Ellington, J W Szostak
Jan 1, 1994·European Biophysics Journal : EBJ·J S PedersenR Bauer
Jul 3, 1997·International Journal of Cancer. Journal International Du Cancer·P A AndreasenM J Duffy
Jun 30, 2000·Journal of Molecular Biology·P E PjuraA G Gittis
Jun 1, 2005·Biophysical Journal·Maxim V Petoukhov, Dmitri I Svergun
Nov 23, 2005·Bioinformatics·Konstantin ArnoldTorsten Schwede
Sep 19, 2006·Journal of Molecular Biology·Cyril BarinkaJacek Lubkowski
Oct 5, 2006·The Journal of Biological Chemistry·Daniel M DupontTroels Wind
Apr 1, 2008·Nature Structural & Molecular Biology·Qing HuaiMingdong Huang
Jun 27, 2008·Bioinformatics·Shantanu SharmaNikolay V Dokholyan
Oct 31, 2008·RNA·Stephen B LongBruce A Sullenger
Mar 11, 2009·Frontiers in Bioscience (Landmark Edition)·Daniel Miotto DupontPeter Andre Andreasen
Jul 2, 2010·Nature Reviews. Drug Discovery·Anthony D KeefeAndrew Ellington
Sep 3, 2010·Nature Reviews. Drug Discovery·Marcin Drag, Guy S Salvesen
Oct 22, 2010·RNA·Daniel Miotto DupontPeter André Andreasen
Jun 30, 2011·Current Pharmaceutical Design·Maria Vincenza Carriero, Maria Patrizia Stoppelli
Aug 16, 2011·Current Medicinal Chemistry·D M DupontP A Andreasen
Jun 21, 2012·Methods in Enzymology·Manja A BehrensKlaus H Nielsen
Oct 22, 2013·Cancer Treatment Reviews·Nadia HarbeckSophie Doisneau-Sixou
Apr 1, 2009·Journal of Applied Crystallography·Daniel Franke, Dmitri I Svergun

❮ Previous
Next ❯

Citations

Mar 5, 2016·The Review of Scientific Instruments·Linda K BruetzelJan Lipfert
Mar 2, 2016·Bioconjugate Chemistry·Daniel M DupontJan K Jensen
Jan 5, 2017·Nucleic Acid Therapeutics·Nils BjerregaardPeter A Andreasen
May 14, 2016·Wiley Interdisciplinary Reviews. RNA·Nils BjerregaardDaniel M Dupont
Dec 14, 2018·Journal of Applied Crystallography·Saskia BucciarelliBente Vestergaard
Jun 4, 2020·Nucleic Acid Therapeutics·Nasim Shahidi HamedaniBernd Pötzsch
Jul 31, 2021·BioMed Research International·Homayoun AsadzadehMohammad R K Mofrad

❮ Previous
Next ❯

Methods Mentioned

BETA
SELEX
X-ray
surface plasmon resonance
ELISA
electrophoresis
chip

Software Mentioned

SUPERSAXS
DAMMIF
SAXS
DAMAVER
iFoldRNA
SUBCOMB
PyMOL
SASREF
PyMOL Molecular Graphics System
WIFT

Related Concepts

Related Feeds

Aminoglycosides

Aminoglycoside is a medicinal and bacteriologic category of traditional Gram-negative antibacterial medications that inhibit protein synthesis and contain as a portion of the molecule an amino-modified glycoside. Discover the latest research on aminoglycoside here.

Aminoglycosides (ASM)

Aminoglycoside is a medicinal and bacteriologic category of traditional Gram-negative antibacterial medications that inhibit protein synthesis and contain as a portion of the molecule an amino-modified glycoside. Discover the latest research on aminoglycoside here.