SASDA84: RNA Aptamer (SRB2m)

基本情報

• 登録情報: データベース: SASBDB / ID: SASDA84

試料

RNA Aptamer

• SRB2m (RNA), SRB2m

• 引用: ジャーナル: Anal Biochem / 年: 2009; タイトル: Characterization of a fluorophore binding RNA aptamer by fluorescence correlation spectroscopy and small angle X-ray scattering.; 著者: Arne Werner / Petr V Konarev / Dmitri I Svergun / Ulrich Hahn / ; 要旨: Using fluorescence correlation spectroscopy (FCS), we have established an in vitro assay to study RNA dynamics by analyzing fluorophore binding RNA aptamers at the single molecule level. The RNA aptamer SRB2m, a minimized variant of the initially selected aptamer SRB-2, has a high affinity to the disulfonated triphenylmethane dye sulforhodamine B. A mobility shift of sulforhodamine B after binding to SRB2m was measured. In contrast, patent blue V (PBV) is visible only if complexed with SRB2m due to increased molecular brightness and minimal background. With small angle X-ray scattering (SAXS), the three-dimensional structure of the RNA aptamer was characterized at low resolution to analyze the effect of fluorophore binding. The aptamer and sulforhodamine B-aptamer complex was found to be predominantly dimeric in solution. Interaction of PBV with SRB2m led to a dissociation of SRB2m dimers into monomers. Radii of gyration and hydrodynamic radii, gained from dynamic light scattering, FCS, and fluorescence cross-correlation experiments, led to comparable conclusions. Our study demonstrates how RNA-aptamer fluorophore complexes can be simultaneously structurally and photophysically characterized by FCS. Furthermore, fluorophore binding RNA aptamers provide a tool for visualizing single RNA molecules.

登録者

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

モデル

• モデル #48: ; タイプ: dummy / カイ2乗値: 3.265249; 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: RNA Aptamer / Sample MW: 35 kDa / 試料濃度: 0.5 mg/ml
• バッファ: 名称: Hepes / pH: 7.4

要素 #46

名称: SRB2m / タイプ: RNA / 記述: SRB2m / 分子量: 16.55 / 分子数: 2
配列:

GGAACCUCGC UUCGGCGAUG AUGGAGAGGC GCAAGGUUAA CCGCCUCAGG UUCC

実験情報

• ビーム: 設備名称: DORIS III X33 / 地域: Hamburg / 国: Germany / 線源: X-ray synchrotron
• 検出器: 名称: MAR 345 Image Plate

スキャン

タイトル: SRB2m with PBV / 測定日: 2007年10月24日 / 保管温度: 15 °C / セル温度: 15 °C / 照射時間: 120 sec. / フレーム数: 2 / 単位: 1/nm /

	Min	Max
Q	0.2449	5.0717

距離分布関数 P(R)

ソフトウェア P(R): GNOM 4.5a / ポイント数: 512 /

	Min	Max
Q	0.2483	4.98
P(R) point	1	512
R	0	8

結果

D max: 8 / カーブのタイプ: single_conc /

	実験値	Porod
分子量	20 kDa	-
体積	-	24 nm3

	P(R)	Guinier
前方散乱 I0	177	180.23
慣性半径, Rg	2.27 nm	2.25 nm