Minimizing base loss and internal fragmentation in collisionally activated dissociation of multiply deprotonated RNA.

Journal of the American Society for Mass Spectrometry
Monika TaucherKathrin Breuker

Abstract

In recent years, new classes of nonprotein-coding ribonucleic acids (ncRNAs) with important cellular functions have been discovered. Of particular interest for biomolecular research and pharmaceutical developments are small ncRNAs that are involved in gene regulation, such as small interfering RNAs (21-28 nt), pre-microRNAs (70-80 nt), or riboswitches (34-200 nt). De novo sequencing of RNA by top-down mass spectrometry has so far been limited to RNA consisting of up to approximately 20 nt. We report here complete sequence coverage for 34 nt RNA (10.9 kDa), along with 30 out of 32 possible complementary ion pairs from collisionally activated dissociation (CAD) experiments. The key to minimizing undesired base loss and internal fragmentation is to minimize the internal energy of fragment ions from primary backbone cleavage. This can be achieved by collisional cooling of primary fragment ions and selection of precursor ions of relatively low negative net charge (about -0.2/nt).

References

Feb 1, 1995·Current Opinion in Biotechnology·P A LimbachJ A McCloskey
Aug 31, 2002·Angewandte Chemie·Ronald Micura
Sep 10, 2002·Journal of the American Society for Mass Spectrometry·Stefan SchürchChristian J Leumann
Mar 14, 2003·Nature·Ruedi Aebersold, Matthias Mann
Aug 19, 2004·Mass Spectrometry Reviews·Valérie Gabelica, Edwin De Pauw
Jun 28, 2005·Journal of the American Society for Mass Spectrometry·Jan M Tromp, Stefan Schürch
Jul 15, 2006·Rapid Communications in Mass Spectrometry : RCM·Jan M Tromp, Stefan Schürch
Oct 7, 2006·Science·Brian T Chait
Sep 19, 2008·Journal of the American Society for Mass Spectrometry·Teng-Yi HuangScott A McLuckey
Oct 25, 2008·Analytical Chemistry·Teng-Yi HuangScott A McLuckey
Feb 4, 2009·Biopolymers·Herbert Oberacher, Florian Pitterl
Apr 22, 2009·Chembiochem : a European Journal of Chemical Biology·Ulrike RiederRonald Micura
May 15, 2009·Analytical Chemistry·Julie Farand, Francis Gosselin
Jan 1, 1992·Journal of the American Society for Mass Spectrometry·S A McLuckeyG L Glish

❮ Previous
Next ❯

Citations

Apr 7, 2010·Journal of the American Society for Mass Spectrometry·Monika Taucher, Kathrin Breuker
Aug 10, 2011·The Analyst·Weidong CuiMichael L Gross
Sep 29, 2011·Nucleic Acids Research·John J TurnerSven Klussmann
Nov 1, 2013·Journal of the American Society for Mass Spectrometry·Majlinda KullolliSharon J Pitteri
Dec 14, 2011·Journal of Bioscience and Bioengineering·Yoshihiro IzumiEiichiro Fukusaki
Mar 5, 2016·Journal of the American Society for Mass Spectrometry·Moritz SchennachKathrin Breuker
Oct 9, 2012·Angewandte Chemie·Monika Taucher, Kathrin Breuker
Apr 24, 2015·Nucleic Acids Research·Christian RimlKathrin Breuker
Oct 31, 2019·Journal of Mass Spectrometry : JMS·Mellie June PaulinesPatrick A Limbach
Feb 23, 2020·Nucleic Acids Research·Felix HagelskampStefanie Kellner
Dec 14, 2018·Chemical Science·Eva-Maria Schneeberger, Kathrin Breuker
Nov 15, 2020·Nature Communications·Eva-Maria SchneebergerKathrin Breuker
Feb 25, 2020·Analytical Chemistry·Trenton M Peters-ClarkeJoshua J Coon

❮ 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.