RNA Probes for Visualization of Sarcin/ricin Loop Depurination without Background Fluorescence

被引：1

作者：

Klimek, Robin ^{[1
]}

Kaiser, Christoph ^{[2
]}

Murmann, Nina S. ^{[1
]}

Kaltenschnee, Nina ^{[1
]}

Spano, Teresa ^{[3
]}

Wachtveitl, Josef ^{[2
]}

Schuman, Erin M. ^{[3
]}

Heckel, Alexander ^{[1
]}

机构：

[1] Goethe Univ Frankfurt, Inst Organ Chem & Chem Biol, Max von Laue Str 79, D-60438 Frankfurt, Germany

[2] Goethe Univ Frankfurt, Inst Phys & Theoret Chem, Max von Laue Str 79, D-60438 Frankfurt, Germany

[3] Max Planck Inst Brain Res, Teresa Spano, Max von Laue Str 4, D-60438 Frankfurt, Germany

来源：

CHEMISTRY-AN ASIAN JOURNAL | 2022年 / 17卷 / 24期

关键词：

Sarcin-ricin-loop; molecular beacon; fluorescence; ribosome; depurination; MOLECULAR BEACONS; EUKARYOTIC RIBOSOMES; NUCLEOSIDE ANALOG; RICIN LOOP; SITE; STRATEGIES; SIGNALS;

D O I：

10.1002/asia.202201077

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

Protein synthesis via ribosomes is a fundamental process in all known living organisms. However, it can be completely stalled by removing a single nucleobase (depurination) at the sarcin/ricin loop of the ribosomal RNA. In this work, we describe the preparation and optimization process of a fluorescent probe that can be used to visualize depurination. Starting from a fluorescent thiophene nucleobase analog, various RNA probes that fluoresce exclusively in the presence of a depurinated sarcin/ricin-loop RNA were designed and characterized. The main challenge in this process was to obtain a high fluorescence signal in the hybridized state with an abasic RNA strand, while keeping the background fluorescence low. With our new RNA probes, the fluorescence intensity and lifetime can be used for efficient monitoring of depurinated RNA.

引用

页数：6

共 23 条

[1] Differences in Ribosome Binding and Sarcin/Ricin Loop Depurination by Shiga and Ricin Holotoxins
Li, Xiao-Ping
Tumer, Nilgun E.
TOXINS, 2017, 9 (04):
[2] THE SARCIN RICIN LOOP, A MODULAR RNA
SZEWCZAK, AA
MOORE, PB
JOURNAL OF MOLECULAR BIOLOGY, 1995, 247 (01) : 81 - 98
[3] Differences in Ribosome Binding and Sarcin/Ricin Loop Depurination by Shiga and Ricin Holotoxins (vol 9, 133, 2017)
TOXINS, 2018, 10 (03):
[4] New insights into the mechanism of cleavage of sarcin ricin loop (SRL) RNA
Jain, Swapan S.
Suero, Orlando
Tullius, Thomas D.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 2007, 24 (06): : 631 - 631
[5] Vinyldeoxyadenosine in a sarcin-ricin RNA loop and its binding to ricin toxin A-chain
Roday, Setu
Saen-oon, Suwipa
Schramm, Vern L.
BIOCHEMISTRY, 2007, 46 (21) : 6169 - 6182
[6] Pokeweed antiviral protein regulates the stability of its own mRNA by a mechanism that requires depurination but can be separated from depurination of the α-sarcin/ricin loop of rRNA
Parikh, BA
Coetzer, C
Tumer, NE
JOURNAL OF BIOLOGICAL CHEMISTRY, 2002, 277 (44) : 41428 - 41437
[7] THE CONFORMATION OF THE SARCIN RICIN LOOP FROM 28S RIBOSOMAL-RNA
SZEWCZAK, AA
MOORE, PB
CHAN, YL
WOOL, IG
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1993, 90 (20) : 9581 - 9585
[8] Sarcin ricin loop RNA interactions with a Ru(III)/Pt(II) metal complex
Sapse, Iden A.
Jain, Swapan S.
Anderson, Craig M.
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2014, 248
[9] Linkage between substrate recognition and catalysis during cleavage of sarcin/ricin loop RNA by restrictocin
Korennykh, Alexei V.
Plantinga, Matthew J.
Correll, Carl C.
Piccirilli, Joseph A.
BIOCHEMISTRY, 2007, 46 (44) : 12744 - 12756
[10] Application of dipolar coupling data to the refinement of the solution structure of the Sarcin-Ricin loop RNA
J.J. Warren
P.B. Moore
Journal of Biomolecular NMR, 2001, 20 : 311 - 323

← 1 2 3 →