On the power and challenges of atomistic molecular dynamics to investigate RNA molecules.

Muscat S, Martino G, Manigrasso J, Marcia M, De Vivo M

Journal of chemical theory and computation, 2024

doi:10.1021/acs.jctc.4c00773.

Targeting the conserved active site of splicing machines with specific and selective small molecule modulators.

Silvestri I, Manigrasso J, Andreani A, Brindani N, Mas C, Reiser JB, Vidossich P, Martino G, McCarthy AA, De Vivo M, Marcia M

Nature communications, 2024

doi:10.1038/s41467-024-48697-0.

The new world of RNA diagnostics and therapeutics.

Blandino G, Dinami R, Marcia M, Anastasiadou E, Ryan BM, Palcau AC, Fattore L, Regazzo G, Sestito R, Loria R, Díaz Méndez AB, Cappelletto MC, Pulito C, Monteonofrio L, Calin GA, Sozzi G, Cheong JK, Aharonov R, Ciliberto G

Journal of experimental & clinical cancer research : CR, 2023

doi:10.1186/s13046-023-02752-8.

G·U base pairing motifs in long non-coding RNAs.

Sabalette KB, Makarova L, Marcia M

Biochimie, 2023

doi:10.1016/j.biochi.2023.06.003.

ADAR RNA editing on antisense RNAs results in apparent U-to-C base changes on overlapping sense transcripts.

Pecori R, Chillón I, Lo Giudice C, Arnold A, Wüst S, Binder M, Marcia M, Picardi E, Papavasiliou FN

Frontiers in cell and developmental biology, 2023

doi:10.3389/fcell.2022.1080626.

The multiple molecular dimensions of long noncoding RNAs that regulate gene expression and tumorigenesis.

Marcia M

Current opinion in oncology, 2022

doi:10.1097/CCO.0000000000000813.

Author Correction: Visualizing group II intron dynamics between the first and second steps of splicing.

Manigrasso J, Chillón I, Genna V, Vidossich P, Somarowthu S, Pyle AM, De Vivo M, Marcia M

Nature communications, 2022

doi:10.1038/s41467-021-27699-2.

Noncoding RNAs: biology and applications-a Keystone Symposia report.

Cable J, Heard E, Hirose T, Prasanth KV, Chen LL, Henninger JE, Quinodoz SA, Spector DL, Diermeier SD, Porman AM, Kumar D, Feinberg MW, Shen X, Unfried JP, Johnson R, Chen CK, Wilusz JE, Lempradl A, McGeary SE, Wahba L, Pyle AM, Hargrove AE, Simon MD, Marcia M, Przanowska RK, Chang HY, Jaffrey SR, Contreras LM, Chen Q, Shi J, Mendell JT, He L, Song E, Rinn JL, Lalwani MK, Kalem MC, Chuong EB, Maquat LE, Liu X

Annals of the New York Academy of Sciences, 2021

doi:10.1111/nyas.14713.

Computer-aided design of RNA-targeted small molecules: a growing need in drug discovery.

Manigrasso J, Marcia M, De Vivo M

CHEM, 2021

doi:10.1016/j.chempr.2021.05.021.

Screening strategies for identifying RNA- and ribonucleoprotein-targeted compounds.

Martin WJ, Grandi P, Marcia M

Trends in pharmacological sciences, 2021

doi:10.1016/j.tips.2021.06.001.

Finding the ion in the RNA-stack: can computational models accurately predict key functional elements in large macromolecular complexes?

Marcia M, Manigrasso J, De Vivo M

Journal of chemical information and modeling, 2021

doi:10.1021/acs.jcim.1c00572.

The molecular structure of long non-coding RNAs: emerging patterns and functional implications.

Chillón I, Marcia M

Critical reviews in biochemistry and molecular biology, 2020

doi:10.1080/10409238.2020.1828259.

Visualizing group II intron dynamics between the first and second steps of splicing.

Manigrasso J, Chillón I, Genna V, Vidossich P, Somarowthu S, Pyle AM, De Vivo M, Marcia M

Nature communications, 2020

doi:10.1038/s41467-020-16741-4.

Visualizing the functional 3D shape and topography of long noncoding RNAs by single-particle atomic force microscopy and in-solution hydrodynamic techniques.

Uroda T, Chillon I, Annibale P, Teulon JM, Pessey O, Karuppasamy M, Pellequer JL, Marcia M

NATURE PROTOCOLS, 2020

doi:10.1038/s41596-020-0323-7.

Conserved pseudoknots in incRNA MEG3 are essential for stimulation of the p53 pathway.

Uroda T, Anastasakou E, Rossi A, Teulon JM, Pellequer JL, Annibale P, Pessey O, Inga A, Chillón I, Marcia M

Molecular cell, 2019

doi:10.1016/j.molcel.2019.07.025.

A transient and flexible cation-π interaction promotes hydrolysis of nucleic acids in DNA and RNA nucleases.

Genna V, Marcia M, Vivo M

Journal of the American Chemical Society, 2019

doi:10.1021/jacs.9b03663.

A group II intron-encoded protein interacts with the cellular replicative machinery through the β-sliding clamp.

García-Rodríguez FM, Neira JL, Marcia M, Molina-Sánchez MD, Toro N

Nucleic acids research, 2019

doi:10.1093/nar/gkz468.

Topology and enzymatic properties of a canonical Polycomb repressive complex 1 isoform.

Colombo M, Pessey O, Marcia M

FEBS letters, 2019

doi:10.1002/1873-3468.13442.

Second-Shell Basic Residues Expand the Two-Metal-Ion Architecture of DNA and RNA Processing Enzymes.

Genna V, Colombo M, De Vivo M, Marcia M

Structure (London, England : 1993), 2017

doi:10.1016/j.str.2017.11.008.

Identification of high-confidence RNA regulatory elements by combinatorial classification of RNA-protein binding sites.

Li YE, Xiao M, Shi B, Yang YT, Wang D, Wang F, Marcia M, Lu ZJ

Genome biology, 2017

doi:10.1186/s13059-017-1298-8.

Using Molecular Replacement Phasing to Study the Structure and Function of RNA.

Marcia M

Methods in molecular biology (Clifton, N.J.), 2016

doi:10.1007/978-1-4939-2763-0_15.

Native Purification and Analysis of Long RNAs.

Chillón I, Marcia M, Legiewicz M, Liu F, Somarowthu S, Pyle AM

Methods in enzymology, 2015

doi:10.1016/bs.mie.2015.01.008.

Crystal structure of group II intron domain 1 reveals a template for RNA assembly.

Zhao C, Rajashankar KR, Marcia M, Pyle AM

Nature chemical biology, 2015

doi:10.1038/nchembio.1949.

HOTAIR forms an intricate and modular secondary structure.

Somarowthu S, Legiewicz M, Chillón I, Marcia M, Liu F, Pyle AM

Molecular cell, 2015

doi:10.1016/j.molcel.2015.03.006.

Principles of ion recognition in RNA: insights from the group II intron structures

Marcia M, Pyle AM

RNA (New York, N.Y.), 2014

doi:10.1261/rna.043414.113.

Production of fully assembled and active Aquifex aeolicus F1FO ATP synthase in Escherichia coli

Zhang C, Allegretti M, Vonck J, Langer JD, Marcia M, Peng G, Michel H

Biochimica et biophysica acta, 2013

doi:10.1016/j.bbagen.2013.08.023.

Solving nucleic acid structures by molecular replacement: examples from group II intron studies

Marcia M, Humphris-Narayanan E, Keating KS, Somarowthu S, Rajashankar K, Pyle AM

Acta crystallographica. Section D, Biological crystallography, 2013

doi:10.1107/s0907444913013218.

Role of the N-terminal signal peptide in the membrane insertion of Aquifex aeolicus F1F0 ATP synthase c-subunit

Zhang C, Marcia M, Langer JD, Peng G, Michel H

The FEBS journal, 2013

doi:10.1111/febs.12336.

Now on display: a gallery of group II intron structures at different stages of catalysis

Marcia M, Somarowthu S, Pyle AM

Mobile DNA, 2013

doi:10.1186/1759-8753-4-14.

Visualizing group II intron catalysis through the stages of splicing

Marcia M, Pyle AM

Cell, 2012

doi:10.1016/j.cell.2012.09.033.

Ion binding and internal hydration in the multidrug resistance secondary active transporter NorM investigated by molecular dynamics simulations

Vanni S, Campomanes P, Marcia M, Rothlisberger U

Biochemistry, 2012

doi:10.1021/bi2015184.

PICKScreens, A New Database for the Comparison of Crystallization Screens for Biological Macromolecules

Hedderich T, Marcia M, Kopke J, Michel H

CRYSTAL GROWTH & DESIGN, 2011

doi:10.1021/cg101267n.

Characterizing a monotopic membrane enzyme. Biochemical, enzymatic and crystallization studies on Aquifex aeolicus sulfide:quinone oxidoreductase

Marcia M, Langer JD, Parcej D, Vogel V, Peng G, Michel H

Biochimica et biophysica acta, 2010

doi:10.1016/j.bbamem.2010.07.033.

A new structure-based classification of sulfide:quinone oxidoreductases

Marcia M, Ermler U, Peng G, Michel H

Proteins, 2010

doi:10.1002/prot.22665.

The structure of Aquifex aeolicus sulfide:quinone oxidoreductase, a basis to understand sulfide detoxification and respiration

Marcia M, Ermler U, Peng G, Michel H

Proceedings of the National Academy of Sciences of the United States of America, 2009

doi:10.1073/pnas.0904165106.