Enzymatic approaches to probing of RNA secondary and tertiary structure.

Methods in Enzymology
G Knapp

Abstract

To make strong statements about possible tertiary structure or the relative stability of regions of secondary structure, the structure-probing experiments must go further than single-hit reactions. Some elements of the environment of the RNA molecule must be altered systematically. Knowledge of the effects of ions or other interacting factors on the activity or physical parameters (e.g., NMR and melting cooperativity) of the RNA help in experimental design. For example, the copious work on tRNA(Phe) compared the crystal and solution structures and allowed the direct correlation of Mg2+ stabilization of the tertiary structure of that molecule. Figure 3 demonstrates that pre-tRNA(Leu-3) responds to Mg2+ depletion in the same manner as detected by the appearance of highly sensitive RNase cleavage sites in the D and T psi C loops. Similar experiments titrating polyamine concentrations suggested that secondary structure was more efficiently stabilized by polyamines than by Mg2+. The variation of Mg2+ concentrations has been used to gain additional information about other RNA structures. Others have used protein-RNA interactions to approach the question of the functional structure of a RNA (for examples, see Ref. 3). Thus, the ideal ...Continue Reading

Citations

Jan 10, 1998·The Journal of Biological Chemistry·M Napierała, W J Krzyzosiak
Sep 1, 1996·Nature Biotechnology·S KlussmannJ P Fürste
Sep 1, 1996·Nature Biotechnology·A NolteJ P Fürste
Dec 13, 2007·Quarterly Reviews of Biophysics·Christopher S Fraser, Jennifer A Doudna
Apr 23, 2008·Current Protocols in Nucleic Acid Chemistry·S E Rokita, C J Burrows
Jun 19, 2014·Current Protocols in Bioinformatics·David H Mathews
Feb 13, 2016·Annual Review of Plant Biology·Lee E VandivierBrian D Gregory
Jul 1, 2017·Wiley Interdisciplinary Reviews. RNA·Shawn W FoleyBrian D Gregory
Jun 18, 2019·Chembiochem : a European Journal of Chemical Biology·Sushree Prangya P PanyP I Pradeepkumar
Nov 14, 2001·The Journal of Biological Chemistry·Marc MeliMarie-Christine Maurel
Apr 23, 2008·Current Protocols in Bioinformatics·David H Mathews
Apr 23, 2008·Current Protocols in Bioinformatics·David Mathews
Jan 16, 2009·Journal of Virology·Priscilla M Van Wynsberghe, Paul Ahlquist
Oct 15, 2013·Biotechnology Journal·James ChappellJulius Lucks
Apr 23, 2015·Cellular and Molecular Life Sciences : CMLS·Rosa Díaz-Toledano, Jordi Gómez
Jun 19, 2014·Current Protocols in Bioinformatics·David H Mathews
Dec 3, 2016·Biochemical Society Transactions·Chun Kit Kwok
Apr 23, 2008·Current Protocols in Nucleic Acid Chemistry·David H MathewsMichael Zuker
Dec 6, 2003·The EMBO Journal·Caroline RouauxAnne-Laurence Boutillier
Apr 23, 2008·Current Protocols in Nucleic Acid Chemistry·W A Ziehler, D R Engelke
Dec 3, 2016·Current Protocols in Nucleic Acid Chemistry·David H MathewsRichard M Watson
Jun 7, 2018·Frontiers in Plant Science·Xiaofei YangYiliang Ding
Feb 23, 2019·Genome Biology·Krishna ChoudharySharon Aviran
May 5, 2004·Proceedings of the National Academy of Sciences of the United States of America·David H MathewsDouglas H Turner
Dec 23, 2008·Nature·Partho Sarothi RayPaul L Fox
Oct 13, 2011·Nucleic Acids Research·Ascensión Ariza-MateosJordi Gómez
Jan 26, 2016·International Journal of Molecular Sciences·Kun YanAirong Qian
Dec 7, 2013·International Journal of Molecular Sciences·Irina V NovikovaKarissa Y Sanbonmatsu
Apr 30, 2015·Briefings in Bioinformatics·Youhuang BaiMing Chen
Jul 29, 2018·Nature Reviews. Genetics·Eric J StrobelJulius B Lucks
May 24, 2012·Nucleic Acids Research·Elisa BiondiDonald H Burke

❮ 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.