SASDAU7: Aptamer AIR-3 FdU (AIR3-FdU)

基本情報

• 登録情報: データベース: SASBDB / ID: SASDAU7

試料

Aptamer AIR-3 FdU

• AIR3-FdU (RNA)

• 引用: ジャーナル: RNA Biol / 年: 2016; タイトル: Structure and target interaction of a G-quadruplex RNA-aptamer.; 著者: 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 / ; 要旨: 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.

登録者

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

モデル

• モデル #295: ; タイプ: dummy / ソフトウェア: DAMMIF / ダミー原子の半径: 3.00 A / カイ2乗値: 0.7225; Omokage検索でこの集合体の類似形状データを探す (詳細)

試料

• 試料: 名称: Aptamer AIR-3 FdU / 試料濃度: 0.2 mg/ml
• バッファ: 名称: water / pH: 7.5

要素 #166

タイプ: RNA / 記述: AIR3-FdU / 分子量: 34.39 / 分子数: 2
配列:

GGAAGAAAGA GGUCUGAGAC AUUCUCUUAU AGGGGAGGCU GUGGUGAGGG AAUAUUAAGA GAAUUAACGG UCUAGUUCAC CUCGACUUCU GGAGUUGACG UUGCUU

実験情報

• ビーム: 設備名称: PETRA III P12 / 地域: Hamburg / 国: Germany / 線源: X-ray synchrotron / 波長: 0.12 Å / スペクトロメータ・検出器間距離: 3.1 mm
• 検出器: 名称: Pilatus 2M

スキャン

タイトル: Aptamer AIR-3 FDU / 測定日: 2013年10月31日 / 保管温度: 10 °C / セル温度: 10 °C / 照射時間: 0.05 sec. / フレーム数: 20 / 単位: 1/nm /

	Min	Max
Q	0.0291	4.4884

距離分布関数 P(R)

ソフトウェア P(R): GNOM 4.6 / ポイント数: 309 /

	Min	Max
Q	0.1594	1.781
P(R) point	50	358
R	0	16

結果

カーブのタイプ: single_conc /

	実験値	Porod
分子量	67 kDa	67 kDa
体積	-	67 nm3

	P(R)	Guinier
前方散乱 I0	16950	17500
慣性半径, Rg	5 nm	5 nm

	Min	Max
D	-	16
Guinier point	50	89