Electron Paramagnetic Resonance Dynamic Signatures of TAR RNA-Small Molecule Complexes Provide Insight into RNA Structure and Recognition

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• 作者：Thomas E. Edwards and Snorri Th. Sigurdsson
• 刊名：Biochemistry
• 出版年：2002
• 出版时间：December 17, 2002
• 年：2002
• 卷：41
• 期：50
• 页码：14843 - 14847
• 全文大小：70K
• 年卷期：v.41,no.50(December 17, 2002)
• ISSN：1520-4995

文摘

Electron paramagnetic resonance (EPR) spectroscopy was utilized to investigate the correlationbetween RNA structure and RNA internal dynamics in complexes of HIV-1 TAR RNA with smallmolecules. TAR RNAs containing single nitroxide spin-labels in the 2'-position of U23, U25, U38, orU40 were incubated with compounds known to inhibit TAR-Tat complex formation. The combinedchanges in nucleotide mobility at all four sites, as monitored by their EPR spectral width, yield a dynamicsignature for each compound. The multicyclic dyes Hoechst 33258, DAPI, and berenil bind to TAR RNAin a similar manner and gave nearly identical signatures. Different signatures were obtained for the acridinederivative CGP 40336A and the aminoglycoside antibiotic neomycin, which bind to different regions ofthe RNA. The dynamic signature for guanidinoneomycin was remarkably similar to that obtained forargininamide and is evidence for guanidinoneomycin binding to the same site as arginine 52 of the Tatprotein, rather than to the neomycin binding site. The data presented here show that the dynamic signaturesprovide strong insights into RNA structure and recognition and demonstrate the value of EPR spectroscopyfor the investigation of small molecule binding to RNA.