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Special issue: Multiscale simulations of DNA from electrons to nucleosomes
This editorial for Volume 16, Issue 3 of Biophysical Reviews highlights the three-dimensional structural and dynamic information encoded in DNA sequences and introduces the topics covered in this special issue of...
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Open AccessMD-DATA: the legacy of the ABC Consortium
The ABC Consortium has been generating nucleic-acids MD trajectories for more than 20 years. This brief comment highlights the importance of this data for the field, which triggered a number of critical studie...
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Molecular strip** underpins derepression of a toxin–antitoxin system
Transcription factors control gene expression; among these, transcriptional repressors must liberate the promoter for derepression to occur. Toxin–antitoxin (TA) modules are bacterial elements that autoregulat...
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An open call for contributions to a special issue of Biophysical Reviews focused on multiscale simulations of DNA from electrons to nucleosomes
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Open AccessStructural basis of a redox-dependent conformational switch that regulates the stress kinase p38α
Many functional aspects of the protein kinase p38α have been illustrated by more than three hundred structures determined in the presence of reducing agents. These structures correspond to free forms and compl...
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Open AccessHistone H3 serine-57 is a CHK1 substrate whose phosphorylation affects DNA repair
Histone post-translational modifications promote a chromatin environment that controls transcription, DNA replication and repair, but surprisingly few phosphorylations have been documented. We report the disco...
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Open AccessCharacterization of p38α autophosphorylation inhibitors that target the non-canonical activation pathway
p38α is a versatile protein kinase that can control numerous processes and plays important roles in the cellular responses to stress. Dysregulation of p38α signaling has been linked to several diseases includi...
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Open Accessi-Motif folding intermediates with zero-nucleotide loops are trapped by 2′-fluoroarabinocytidine via F···H and O···H hydrogen bonds
G-quadruplex and i-motif nucleic acid structures are believed to fold through kinetic partitioning mechanisms. Such mechanisms explain the structural heterogeneity of G-quadruplex metastable intermediates whic...
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Deciphering the mechanical code of the genome and epigenome
Diverse DNA-deforming processes are impacted by the local mechanical and structural properties of DNA, which in turn depend on local sequence and epigenetic modifications. Deciphering this mechanical code (tha...
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Open AccessA glutamine-based single α-helix scaffold to target globular proteins
The binding of intrinsically disordered proteins to globular ones can require the folding of motifs into α-helices. These interactions offer opportunities for therapeutic intervention but their modulation with...
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MiOS, an integrated imaging and computational strategy to model gene folding with nucleosome resolution
The linear sequence of DNA provides invaluable information about genes and their regulatory elements along chromosomes. However, to fully understand gene function and regulation, we need to dissect how genes p...
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Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?
The structure of B-DNA, the physiological form of the DNA molecule, has been a central topic in biology, chemistry and physics. Far from uniform and rigid, the double helix was revealed as a flexible and struc...
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Open AccessImpact of DNA methylation on 3D genome structure
Determining the effect of DNA methylation on chromatin structure and function in higher organisms is challenging due to the extreme complexity of epigenetic regulation. We studied a simpler model system, buddi...
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Colibactin DNA-damage signature indicates mutational impact in colorectal cancer
The mucosal epithelium is a common target of damage by chronic bacterial infections and the accompanying toxins, and most cancers originate from this tissue. We investigated whether colibactin, a potent genotoxin
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Open AccessEpigenetic loss of RNA-methyltransferase NSUN5 in glioma targets ribosomes to drive a stress adaptive translational program
Tumors have aberrant proteomes that often do not match their corresponding transcriptome profiles. One possible cause of this discrepancy is the existence of aberrant RNA modification landscapes in the so-call...
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Open AccessBioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows
In the recent years, the improvement of software and hardware performance has made biomolecular simulations a mature tool for the study of biological processes. Simulation length and the size and complexity of...
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An artificial DNAzyme RNA ligase shows a reaction mechanism resembling that of cellular polymerases
DNAzymes have become attractive due to their potential biomedical and biotechnological applications, as well as their advantages in terms of stability, efficiency and synthetic accessibility with respect to pr...
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A synthetic genetic polymer with an uncharged backbone chemistry based on alkyl phosphonate nucleic acids
The physicochemical properties of nucleic acids are dominated by their highly charged phosphodiester backbone chemistry. This polyelectrolyte structure decouples information content (base sequence) from bulk p...
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Open AccessSide chain to main chain hydrogen bonds stabilize a polyglutamine helix in a transcription factor
Polyglutamine (polyQ) tracts are regions of low sequence complexity frequently found in transcription factors. Tract length often correlates with transcriptional activity and expansion beyond specific threshol...
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Challenges and guidelines toward 4D nucleome data and model standards
Due to recent advances in experimental and theoretical approaches, the dynamic three-dimensional organization (3D) of the nucleus has become a very active area of research in life sciences. We now understand t...
