SASDAT7: Aptamer AIR-3 5FU (AIR3-5FU)

Basic information

• Entry: Database: SASBDB / ID: SASDAT7

Sample

Aptamer AIR-3 5FU

• AIR3-5FU (RNA)

• Citation: Journal: RNA Biol / Year: 2016; Title: Structure and target interaction of a G-quadruplex RNA-aptamer.; Authors: Kristina Szameit / Katharina Berg / Sven Kruspe / Erica Valentini / Eileen Magbanua / Marcel Kwiatkowski / Isaure Chauvot de Beauchêne / Boris Krichel / Kira Schamoni / Charlotte Uetrecht / Dmitri I Svergun / Hartmut Schlüter / Martin Zacharias / Ulrich Hahn / ; Abstract: G-quadruplexes have recently moved into focus of research in nucleic acids, thereby evolving in scientific significance from exceptional secondary structure motifs to complex modulators of gene regulation. Aptamers (nucleic acid based ligands with recognition properties for a specific target) that form Gquadruplexes may have particular potential for therapeutic applications as they combine the characteristics of specific targeting and Gquadruplex mediated stability and regulation. We have investigated the structure and target interaction properties of one such aptamer: AIR-3 and its truncated form AIR-3A. These RNA aptamers are specific for human interleukin-6 receptor (hIL-6R), a key player in inflammatory diseases and cancer, and have recently been exploited for in vitro drug delivery studies. With the aim to resolve the RNA structure, global shape, RNA:protein interaction site and binding stoichiometry, we now investigated AIR-3 and AIR-3A by different methods including RNA structure probing, Small Angle X-ray scattering and microscale thermophoresis. Our findings suggest a broader spectrum of folding species than assumed so far and remarkable tolerance toward different modifications. Mass spectrometry based binding site analysis, supported by molecular modeling and docking studies propose a general Gquadruplex affinity for the target molecule hIL-6R.

Contact author

• Erica Valentini (EMBL-Hamburg, European Molecular Biology Laboratory (EMBL) - Hamburg outstation, Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany)

Models

• Model #294: ; Type: dummy / Software: DAMMIF / Radius of dummy atoms: 3.50 A / Symmetry: P1 / Chi-square value: 0.786769; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Aptamer AIR-3 5FU / Specimen concentration: 0.3 mg/ml
• Buffer: Name: water / pH: 7.5

Entity #165

Type: RNA / Description: AIR3-5FU / Formula weight: 34.39 / Num. of mol.: 2
Sequence:

GGAAGAAAGA GGUCUGAGAC AUUCUCUUAU AGGGGAGGCU GUGGUGAGGG AAUAUUAAGA GAAUUAACGG UCUAGUUCAC CUCGACUUCU GGAGUUGACG UUGCUU

Experimental information

• Beam: Instrument name: PETRA III P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotron / Wavelength: 0.12 Å / Dist. spec. to detc.: 3.1 mm
• Detector: Name: Pilatus 2M

Scan

Title: Aptamer AIR-3 FUH / Measurement date: Oct 31, 2013 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 0.05 sec. / Number of frames: 20 / Unit: 1/nm /

	Min	Max
Q	0.0291	4.4884

Distance distribution function P(R)

Sofotware P(R): GNOM 4.6 / Number of points: 299 /

	Min	Max
Q	0.2279	1.796
P(R) point	76	374
R	0	16.5

Result

Type of curve: single_conc /

	Experimental	Porod
MW	77 kDa	77 kDa
Volume	-	77 nm3

	P(R)	Guinier	P(R) error	Guinier error
Forward scattering, I0	19290	18200	-	-
Radius of gyration, Rg	4.8 nm	4.3 nm	0.3	0.3

	Min	Max	Error
D	-	16	0.5
Guinier point	76	104	-