Light-regulated catalysis by an RNA-cleaving deoxyribozyme

Journal of Molecular Biology
Yong Liu, Dipankar Sen

Abstract

We describe light-induced switches for the catalytic activity of the small, RNA-cleaving 8-17 deoxyribozyme (DNAzyme), based on photochemically induced cis-trans isomerization of azobenzene (Az) moieties covalently tethered at various locations within the DNAzyme. Prior studies have shown that trans-azobenzene is able to stack comfortably within a DNA double helix, stabilizing it, while cis-azobenzene has a helix-destabilizing effect. We designed two classes of Az-modified 8-17DNAzyme constructs, in each of which two azobenzene molecules substituted for nucleotides, either in the substrate-binding arm (SBA); or, within the catalytic core. Measurement of single-turnover kinetics for RNA cleavage revealed that in the SBA constructs Ell and E13, five- to sixfold higher catalytic rates were obtained when the reaction mixture was irradiated with visible light (favouring trans-Az) as compared to ultraviolet light (which promotes cis-Az), consistent with trans-Az in these constructs stabilizing the enzyme-substrate complex. Surprisingly, the reverse result was obtained with the catalytic core construct E17, where ultraviolet irradiation resulted in a five- to sixfold faster catalytic activity relative to visible light irradiation. The...Continue Reading

References

Apr 29, 1997·Proceedings of the National Academy of Sciences of the United States of America·S W Santoro, G F Joyce
Sep 28, 1998·Biochemistry·S W Santoro, G F Joyce
Mar 31, 1999·Proceedings of the National Academy of Sciences of the United States of America·G A Soukup, R R Breaker
Jan 22, 2002·Journal of Molecular Biology·A R Feldman, D Sen
Feb 28, 2002·Journal of the American Chemical Society·Xingguo LiangMakoto Komiyama
May 23, 2002·Cellular and Molecular Life Sciences : CMLS·G M Emilsson, R R Breaker
Jul 12, 2002·Nature·Jennifer A Doudna, Thomas R Cech
Aug 31, 2002·Chembiochem : a European Journal of Chemical Biology·Hiroyuki AsanumaMakoto Komiyama
Mar 19, 2004·Nature·Wade C WinklerRonald R Breaker

❮ Previous
Next ❯

Citations

Apr 26, 2013·Chemical Reviews·Wiktor SzymańskiBen L Feringa
Apr 24, 2007·Organic Letters·Hrvoje LusicAlexander Deiters
May 8, 2010·Chemical Communications : Chem Comm·Johann ElbazItamar Willner
Aug 22, 2012·Physical Chemistry Chemical Physics : PCCP·Jahur A MondalDipak K Palit
Sep 13, 2008·Nucleosides, Nucleotides & Nucleic Acids·Keita TanakaMakoto Komiyama
Dec 7, 2007·Nucleic Acids Research·XinJing TangIvan J Dmochowski
Feb 19, 2010·Nucleic Acids Research·XinJing TangZhongJin Li
Sep 25, 2012·Nucleic Acids Research·Yuan WangXinjing Tang
Jan 30, 2013·Beilstein Journal of Organic Chemistry·Subhas SamantaG Andrew Woolley
Jul 11, 2008·Expert Opinion on Biological Therapy·Weihua Pan, Gary A Clawson
Nov 19, 2015·Journal of the American Chemical Society·Chun-Hua LuItamar Willner
Dec 17, 2015·ACS Chemical Biology·Xiaoyan WangYu Xiang
Jul 1, 2008·Journal of Molecular Biology·Yong Liu, Dipankar Sen
Jul 10, 2007·Journal of Molecular Biology·Hyun-Wu LeeDipankar Sen
Jun 18, 2010·The FEBS Journal·Dazhi JiangJin Zhang
Jul 8, 2015·Journal of the American Chemical Society·Tae-Gon ChaJong Hyun Choi
Jul 19, 2016·The Journal of Physical Chemistry Letters·Addie KingslandLutz Maibaum
Jun 10, 2017·Chemical Reviews·Wenhu ZhouJuewen Liu
Jan 28, 2017·Chemical Society Reviews·Anouk S LubbeBen L Feringa
Dec 19, 2014·Angewandte Chemie·Fuan WangItamar Willner
Jul 11, 2006·Angewandte Chemie·Günter Mayer, Alexander Heckel
Jul 25, 2007·Biopolymers·Claudia Höbartner, Scott K Silverman
Apr 12, 2008·Chembiochem : a European Journal of Chemical Biology·Douglas D Young, Alexander Deiters
Jun 18, 2009·Chembiochem : a European Journal of Chemical Biology·Douglas D YoungAlexander Deiters
Jan 16, 2010·Chembiochem : a European Journal of Chemical Biology·Julia L RichardsIvan J Dmochowski
Mar 10, 2010·Chembiochem : a European Journal of Chemical Biology·Kenny Schlosser, Yingfu Li
Feb 23, 2010·Angewandte Chemie·Mengguang ZhouHiroyuki Asanuma
Jan 25, 2007·Molecular BioSystems·XinJing Tang, Ivan J Dmochowski
Mar 23, 2007·Organic & Biomolecular Chemistry·Douglas D Young, Alexander Deiters
Sep 26, 2019·Chembiochem : a European Journal of Chemical Biology·Daria D NedorezovaDmitry M Kolpashchikov
Aug 30, 2008·Chembiochem : a European Journal of Chemical Biology·Fuzhong ZhangG Andrew Woolley
Apr 24, 2018·Chembiochem : a European Journal of Chemical Biology·Yukiko KamiyaHiroyuki Asanuma
Dec 6, 2006·Chemical Communications : Chem Comm·Hiroyuki AsanumaMakoto Komiyama
Jan 27, 2019·Chemical Communications : Chem Comm·Ayaka BannoMasato Ikeda

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.