Anna M Popova

Anna M Popova
The Scripps Research Institute | scripps · Department of Integrative Structural and Computational Biology

PhD

About

13
Publications
654
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299
Citations
Introduction
I use modern tools of mass spectrometry for identification and quantitative analysis of ribosomal RNA (rRNA) modifications found in bacteria, yeast, and human cells. I develop methods to efficiently incorporate stable isotopes into prokaryotic and eukaryotic rRNA to measure changes in rRNA modifications as a result of mutations or diseases. Also, I am actively working on automating LC-MS/MS analysis of complex mixtures of RNAs by making a new computational tool to assist in discovery of new RNA modifications.
Additional affiliations
November 2018 - September 2019
The Scripps Research Institute
Position
  • Researcher
April 2006 - May 2011
University of Southern California
Position
  • PhD Student
Description
  • Developed methods for studying nucleic acids structure and dynamics using nitroxide labeling and Electron Paramagnetic Resonance.

Publications

Publications (13)
Article
Full-text available
Mass spectrometry is an important method for analysis of modified nucleosides ubiquitously present in cellular RNAs, in particular for ribosomal and transfer RNAs that play crucial roles in mRNA translation and decoding. Furthermore, modifications have effect on the lifetimes of nucleic acids in plasma and cells and are consequently incorporated in...
Article
RNA helicases play various roles in ribosome biogenesis depending on the ribosome assembly pathway and stress state of the cell. However, it is unclear how most RNA helicases interact with ribosome assembly intermediates or on other cell processes to regulate ribosome assembly. SrmB is a DEAD-box helicase that acts early in the ribosome assembly pr...
Article
Full-text available
Ribosomal RNA (rRNA) modifications, including ribose, base methylations and pseudouridines, are important players in the ribosome biogenesis process and translation. Here we introduce mass spectrometry (MS) combined with stable isotope labeling to quantitatively monitor rRNA modifications in bacteria and yeast. By looking at the ribosome assembly i...
Article
Full-text available
Spin labels, which are chemically stable radicals attached at specific sites of a bio-molecule, enable investigations on structure and dynamics of proteins and nucleic acids using techniques such as site-directed spin labeling and paramagnetic NMR. Among spin labels developed, the class of rigid labels have limited or no independent motions between...
Article
Post-transcriptional RNA modifications that are introduced during the multi-step ribosome biogenesis process are essential for protein synthesis. The current lack of a comprehensive method for a fast quantitative analysis of ribosomal RNA modifications significantly limits our understanding of how individual modification steps are coordinated durin...
Article
The behavior of the nitroxide spin labels 1-oxyl-4-bromo-2,2,5,5-tetramethylpyrroline (R5a) and 1-oxyl-2,2,5,5-tetramethylpyrroline (R5) attached at a phosphorothioate-substituted site in a DNA duplex is modulated by the DNA in a site- and stereospecific manner. A better understanding of the mechanisms of R5a/R5 sensing of the DNA microenvironment...
Article
In this report, stereospecific structural and dynamic features in DNA are studied using the site-directed spin labeling technique. A stable nitroxide radical, 1-oxyl-4-bromo-2,2,5,5-tetramethylpyrroline (R5a), was attached postsynthetically to phosphorothioates that were chemically introduced, one at a time, at five sites of a DNA duplex. The two p...
Article
In site-directed spin labeling, structural and dynamic information on a parent macromolecule is obtained by monitoring a covalently linked nitroxide radical using electron paramagnetic resonance (EPR) spectroscopy. Our group have developed a method of attaching nitroxide species, such as 1-oxyl-4-bromo-2,2,5,5-tetramethylpyrroline (R5a), to a speci...
Article
In site-directed spin labeling, a covalently attached nitroxide probe containing a chemically inert unpaired electron is utilized to obtain information on the local environment of the parent macromolecule. Studies presented here examine the feasibility of probing local DNA structural and dynamic features using a class of nitroxide probes that are l...
Article
Site-directed spin labeling (SDSL) obtains structural and dynamic information of a macromolecule using a site-specifically attached stable nitroxide radical. SDSL studies of arbitrary DNA and RNA sequences can be achieved using an efficient phosphorothioate labeling scheme, where a nitroxide is attached to a phosphorothioate substituted at a target...
Article
Individual stationary phases for gas chromatography based on 18-crown-6 and dibenzo-18-crown-6 (10% on Inerton N AW) and a stationary phase of a mixed composition (polyethylene glycol PEG-3000 and cyclodextrin β-CD) are prepared. These stationary phases are characterized using the McReynolds system and the Abraham solvation parameter model. It is s...
Article
Full-text available
The possibility of evaluating stability constants in the analyte-macrocycle system by capillary zone electrophoresis was exemplified in the separation of a mixture of acids (homovanillic acid, vanilmandelic acid, 5-hydroxyindole-3-acetic acid, and 3,4-dihydroxyphenylalanine) or bases (adrenalin, noradrenalin, dopamine, serotonin, and metanephrine)...
Article
Full-text available
This protocol describes the procedures for measuring nanometer distances in nucleic acids using a nitroxide probe that can be attached to any nucleotide within a given sequence. Two nitroxides are attached to phosphorothioates that are chemically substituted at specific sites of DNA or RNA. Inter-nitroxide distances are measured using a four-pulse...

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Projects

Projects (2)
Project
Develop a software for automated annotation and database matching of the RNA oligonucleotide MS/MS spectra. With Pytheas, we envision making high-throughput analysis of RNA tandem MS data more customizable and statistically reliable, providing support of flexible labeling schemes, RNA modifications, and statistical validation.
Project
Using LC-MS/MS and stable-isotope labeling, identify presence of unknown rRNA modifications in gram-positive bacteria.