Petr Stadlbauer
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View article: Structural basis of bis-quinolinium ligands binding to quadruplex-duplex hybrids from PIM1 oncogene.
Structural basis of bis-quinolinium ligands binding to quadruplex-duplex hybrids from PIM1 oncogene. Open
Our study investigates the interaction of two bis-quinolinium ligands, Phen-DC3 and 360A, with the quadruplex-duplex hybrid (QDH) derived from the promoter region of the PIM1 oncogene. While the QDH is polymorphic in vitro, with a hybrid a…
View article: RNA G-quadruplexes emerge from a compacted coil-like ensemble via multiple pathways
RNA G-quadruplexes emerge from a compacted coil-like ensemble via multiple pathways Open
RNA G-quadruplexes (rG4s) are emerging as vital structural elements involved in processes like gene regulation, translation, and genome stability. Found in untranslated regions of messenger RNAs (mRNAs), they influence translation efficien…
View article: Atomistic Insights Into Interaction of Doxorubicin With <scp>DNA</scp>: From Duplex to Nucleosome
Atomistic Insights Into Interaction of Doxorubicin With <span>DNA</span>: From Duplex to Nucleosome Open
Doxorubicin (DOX) is a widely used chemotherapeutic agent known for intercalating into DNA. However, the exact modes of DOX interactions with various DNA structures remain unclear. Using molecular dynamics (MD) simulations, we explored DOX…
View article: Can We Ever Develop an Ideal RNA Force Field? Lessons Learned from Simulations of the UUCG RNA Tetraloop and Other Systems
Can We Ever Develop an Ideal RNA Force Field? Lessons Learned from Simulations of the UUCG RNA Tetraloop and Other Systems Open
Molecular dynamics (MD) simulations are an important and well-established tool for investigating RNA structural dynamics, but their accuracy relies heavily on the quality of the employed force field (ff). In this work, we present a …
View article: RNA G-Quadruplex Emerges from a Coil-Like Ensemble via Multiple Pathways
RNA G-Quadruplex Emerges from a Coil-Like Ensemble via Multiple Pathways Open
RNA G-quadruplexes (rG4s) are vital structural elements in gene regulation and genome stability. In untranslated regions of mRNAs, rG4s influence translation efficiency and mRNA localization. Additionally, rG4s of long non-coding RNAs and …
View article: Computer Folding of Parallel <scp>DNA</scp> G‐Quadruplex: Hitchhiker's Guide to the Conformational Space
Computer Folding of Parallel <span>DNA</span> G‐Quadruplex: Hitchhiker's Guide to the Conformational Space Open
Guanine quadruplexes (GQs) play crucial roles in various biological processes, and understanding their folding pathways provides insight into their stability, dynamics, and functions. This knowledge aids in designing therapeutic strategies…
View article: Can We Ever Develop an Ideal RNA Force Field? Lessons Learned from Simulations of UUCG RNA Tetraloop and Other Systems
Can We Ever Develop an Ideal RNA Force Field? Lessons Learned from Simulations of UUCG RNA Tetraloop and Other Systems Open
Molecular dynamics (MD) simulations are an important and well-established tool for investigating RNA structural dynamics, but their accuracy relies heavily on the quality of the employed force field ( ff ). In this work, we present a compr…
View article: Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations
Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations Open
Guanine quadruplex (GQ) is a noncanonical nucleic acid structure formed by guanine-rich DNA and RNA sequences. Folding of GQs is a complex process, where several aspects remain elusive, despite being important for understanding structure f…
View article: Mechanical stability and unfolding pathways of parallel tetrameric G-quadruplexes probed by pulling simulations
Mechanical stability and unfolding pathways of parallel tetrameric G-quadruplexes probed by pulling simulations Open
Guanine-quadruplex (GQ) is a noncanonical nucleic acid structure formed by guanine-rich DNA and RNA sequences. Folding of GQs is a complex process, many aspects of which remain elusive, despite being important for understanding of structur…
View article: Photoinduced charge separation and DNA self-repair depend on sequence directionality and stacking pattern
Photoinduced charge separation and DNA self-repair depend on sequence directionality and stacking pattern Open
The exposure of DNA to UV light may result in electron transfer between the bases. It can entail self-repair of common DNA lesions and the efficiency of these two processes is controlled by stacking overlap of the nucleobases.
View article: DNA Quadruplex Structure with a Unique Cation Dependency
DNA Quadruplex Structure with a Unique Cation Dependency Open
DNA quadruplex structures provide an additional layer of regulatory control in genome maintenance and gene expression and are widely used in nanotechnology. We report the discovery of an unprecedented tetrastranded structure formed from a …
View article: Simple Adjustment of Intranucleotide Base-Phosphate Interaction in the OL3 AMBER Force Field Improves RNA Simulations
Simple Adjustment of Intranucleotide Base-Phosphate Interaction in the OL3 AMBER Force Field Improves RNA Simulations Open
Molecular dynamics (MD) simulations represent an established tool to study RNA molecules. The outcome of MD studies depends, however, on the quality of the force field (ff). Here we suggest a correction for the widely used AMBER OL3…
View article: Parallel G-quadruplex folds via multiple paths involving G-tract stacking and structuring from coil ensemble
Parallel G-quadruplex folds via multiple paths involving G-tract stacking and structuring from coil ensemble Open
G-quadruplexes (G4s) are non-canonical nucleic acid structures that fold through complex processes. Characterization of G4 folding landscape contributes to comprehending G4 roles in gene regulation but is challenging for experiments and co…
View article: Simple Adjustment of Intra-nucleotide Base-phosphate Interaction in OL3 AMBER Force Field Improves RNA Simulations
Simple Adjustment of Intra-nucleotide Base-phosphate Interaction in OL3 AMBER Force Field Improves RNA Simulations Open
Molecular dynamics (MD) simulations represent an established tool to study RNA molecules. Outcome of MD studies depends, however, on the quality of the used force field ( ff ). Here we suggest a correction for the widely used AMBER OL3 ff …
View article: PARALLEL G-QUADRUPLEX FOLDS VIA MULTIPLE PATHS INVOLVING G-TRACT STACKING AND STRUCTURING FROM COIL ENSEMBLE
PARALLEL G-QUADRUPLEX FOLDS VIA MULTIPLE PATHS INVOLVING G-TRACT STACKING AND STRUCTURING FROM COIL ENSEMBLE Open
Data from all-atom molecular dynamics simulations of DNA G-quadruplex and various G-hairpins: input files (Gromacs and Amber), stripped trajectory files (reactive trajectories and reference replicas for G4, and reactive trajectories, and r…
View article: PARALLEL G-QUADRUPLEX FOLDS VIA MULTIPLE PATHS INVOLVING G-TRACT STACKING AND STRUCTURING FROM COIL ENSEMBLE
PARALLEL G-QUADRUPLEX FOLDS VIA MULTIPLE PATHS INVOLVING G-TRACT STACKING AND STRUCTURING FROM COIL ENSEMBLE Open
Data from all-atom molecular dynamics simulations of DNA G-quadruplex and various G-hairpins: input files (Gromacs and Amber), stripped trajectory files (reactive trajectories and reference replicas for G4, and reactive trajectories, and r…
View article: Topology of DNA G-Quadruplexes Can Be Harnessed in Holliday Junction-Based DNA Suprastructures to Control and Optimize Their Biocatalytic Properties
Topology of DNA G-Quadruplexes Can Be Harnessed in Holliday Junction-Based DNA Suprastructures to Control and Optimize Their Biocatalytic Properties Open
International audience
View article: Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations
Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations Open
Guanine quadruplexes (GQs) are non-canonical nucleic acid structures involved in many biological processes. GQs formed in single-stranded regions often need to be unwound by cellular machinery, so their mechanochemical properties are impor…
View article: Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations
Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations Open
Guanine quadruplexes (GQs) are non-canonical nucleic acid structures involved in many biological processes. GQs formed in single-stranded regions often need to be unwound by cellular machinery, so their mechanochemical properties are impor…
View article: Spontaneous binding of single-stranded RNAs to RRM proteins visualized by unbiased atomistic simulations with a rescaled RNA force field
Spontaneous binding of single-stranded RNAs to RRM proteins visualized by unbiased atomistic simulations with a rescaled RNA force field Open
Recognition of single-stranded RNA (ssRNA) by RNA recognition motif (RRM) domains is an important class of protein–RNA interactions. Many such complexes were characterized using nuclear magnetic resonance (NMR) and/or X-ray crystallography…
View article: Spontaneous binding of single-stranded RNAs to RRM proteins visualised by unbiased atomistic simulations with rescaled RNA force field
Spontaneous binding of single-stranded RNAs to RRM proteins visualised by unbiased atomistic simulations with rescaled RNA force field Open
Recognition of single-stranded RNA (ssRNA) by RNA recognition motif (RRM) domains is an important class of protein-RNA interactions. Many such complexes were characterized using NMR and/or X-ray crystallography techniques, revealing ensemb…
View article: Early steps of oxidative damage in DNA quadruplexes are position-dependent: quantum mechanical and molecular dynamics analysis of human telomeric sequence containing ionized Guanine.
Early steps of oxidative damage in DNA quadruplexes are position-dependent: quantum mechanical and molecular dynamics analysis of human telomeric sequence containing ionized Guanine. Open
Guanine radical cation (G+ ) is a key intermediate in many oxidative processes occurring in nucleic acids. Here, by combining mixed Quantum Mechanical/Molecular Mechanics calculations and Molecular Dynamics (MD) simulations, we study how …
View article: Exploring Sequence Space to Design Controllable G-Quadruplex Topology Switches
Exploring Sequence Space to Design Controllable G-Quadruplex Topology Switches Open
International audience
View article: The beginning and the end: flanking nucleotides induce a parallel G-quadruplex topology
The beginning and the end: flanking nucleotides induce a parallel G-quadruplex topology Open
Genomic sequences susceptible to form G-quadruplexes (G4s) are always flanked by other nucleotides, but G4 formation in vitro is generally studied with short synthetic DNA or RNA oligonucleotides, for which bases adjacent to the G4 core ar…
View article: 2,6-diaminopurine promotes repair of DNA lesions under prebiotic conditions
2,6-diaminopurine promotes repair of DNA lesions under prebiotic conditions Open
High-yielding and selective prebiotic syntheses of RNA and DNA nucleotides involve UV irradiation to promote the key reaction steps and eradicate biologically irrelevant isomers. While these syntheses were likely enabled by UV-rich prebiot…
View article: Insights into G-Quadruplex–Hemin Dynamics Using Atomistic Simulations: Implications for Reactivity and Folding
Insights into G-Quadruplex–Hemin Dynamics Using Atomistic Simulations: Implications for Reactivity and Folding Open
Guanine quadruplex nucleic acids (G4s) are involved in key biological processes such as replication or transcription. Beyond their biological relevance, G4s find applications as biotechnological tools since they readily bind hemin and enha…
View article: Insight into formation propensity of pseudocircular DNA G-hairpins
Insight into formation propensity of pseudocircular DNA G-hairpins Open
We recently showed that Saccharomyces cerevisiae telomeric DNA can fold into an unprecedented pseudocircular G-hairpin (PGH) structure. However, the formation of PGHs in the context of extended sequences, which is a prerequisite for their …
View article: Insights into G-Quadruplex–Hemin Dynamics Using Atomistic Simulations: Implications for Reactivity and Folding
Insights into G-Quadruplex–Hemin Dynamics Using Atomistic Simulations: Implications for Reactivity and Folding Open
Guanine quadruplex nucleic acids (G4s) are involved in key biological processes such as replication or transcription. Beyond their biological relevance, G4s find applications as biotechnological tools since they readily bind hemin and enha…
View article: Primitive RNA-catalysis with guanine-rich oligonucleotide sequences – the case of a (GGC)<sub>3</sub>nonamer
Primitive RNA-catalysis with guanine-rich oligonucleotide sequences – the case of a (GGC)<sub>3</sub>nonamer Open
A cornerstone of molecular evolution leading to the emergence of life on our planet is associated with appearance of the first catalytic RNA molecules. A question remains regarding the nature of the simplest catalytic centers that could me…
View article: Interactive Modeling of Cellular Structures on Surfaces with Application to Additive Manufacturing
Interactive Modeling of Cellular Structures on Surfaces with Application to Additive Manufacturing Open
The rich and evocative patterns of natural tessellations endow them with an unmistakable artistic appeal and structural properties which are echoed across design, production, and manufacturing. Unfortunately, interactive control of such pa…