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View article: Tumor Patterns and Cancer Risk in Carriers of <i>TP53</i> exonic Germline Variants that alter mRNA Splicing
Tumor Patterns and Cancer Risk in Carriers of <i>TP53</i> exonic Germline Variants that alter mRNA Splicing Open
Pathogenic germline variants in the TP53 gene cause Li-Fraumeni syndrome (LFS), a highly penetrant cancer predisposition disorder. Most of these variants arise from single-nucleotide variations (SNVs) in TP53 exons, causing missense mutati…
View article: Arsenic-sensing domain controls ACR3 transporter trafficking and function in Marchantia polymorpha
Arsenic-sensing domain controls ACR3 transporter trafficking and function in Marchantia polymorpha Open
Arsenic, a toxic and carcinogenic metalloid, is a pervasive environmental contaminant that threatens human health through contaminated water and food. The efflux of As(III) via ACR3 transporters is an ancient detoxification mechanism conse…
View article: Mechanistic insights into ASO-RNA complexation: Advancing antisense oligonucleotide design strategies
Mechanistic insights into ASO-RNA complexation: Advancing antisense oligonucleotide design strategies Open
Oligonucleotide drugs, an emerging modulator class, hold promise for targeting previously undruggable biomacromolecules. To date, only 18 oligonucleotide drugs, including sought-after antisense oligonucleotides (ASOs) and splice-switching …
View article: Mechanistic Insights into ASO-RNA Complexation: Advancing Antisense Oligonucleotide Design Strategies
Mechanistic Insights into ASO-RNA Complexation: Advancing Antisense Oligonucleotide Design Strategies Open
Oligonucleotide drugs, an emerging modulator class, hold promise for targeting previously undruggable biomacromolecules. To date, only 18 oligonucleotide drugs, including sought-after antisense oligonucleotides (ASO) and splice-switching o…
View article: Structural dynamics of therapeutic nucleic acids with phosphorothioate backbone modifications
Structural dynamics of therapeutic nucleic acids with phosphorothioate backbone modifications Open
Antisense oligonucleotides (ASOs) offer ground-breaking possibilities for selective pharmacological intervention for any gene product-related disease. Therapeutic ASOs contain extensive chemical modifications that improve stability to enzy…
View article: RETRACTED: A moduli-selective antibody inhibits the pain receptor TRPV1 in cynomolgus monkeys without adverse temperature dysregulation
RETRACTED: A moduli-selective antibody inhibits the pain receptor TRPV1 in cynomolgus monkeys without adverse temperature dysregulation Open
The authors have requested that this preprint be removed from Research Square.
View article: Supplemental data for Structural dynamics of therapeutic nucleic acids with phosphorothioate backbone modification, Carlesso et al.
Supplemental data for Structural dynamics of therapeutic nucleic acids with phosphorothioate backbone modification, Carlesso et al. Open
Description of the parameterization strategy for phosphorothioate-modified therapeutic nucleic acids, and files related to the system preparation, MD trajectories and analysis.
View article: Supplemental data for Structural dynamics of therapeutic nucleic acids with phosphorothioate backbone modification, Carlesso et al.
Supplemental data for Structural dynamics of therapeutic nucleic acids with phosphorothioate backbone modification, Carlesso et al. Open
Description of the parameterization strategy for phosphorothioate-modified therapeutic nucleic acids, and files related to the system preparation, MD trajectories and analysis.
View article: Decoding the Dual Recognition Mechanism of Glucocorticoid Receptor for DNA and RNA: Sequence vs. Shape
Decoding the Dual Recognition Mechanism of Glucocorticoid Receptor for DNA and RNA: Sequence vs. Shape Open
Transcription factors (TFs) regulate eukaryotic transcription through selecting DNA-binding, can also specifically interact with RNA, which may present another layer of transcriptional control. The mechanisms of the TFs-DNA recognition are…
View article: Decoding the Dual Recognition Mechanism of Glucocorticoid Receptor for DNA and RNA: Sequence vs. Shape
Decoding the Dual Recognition Mechanism of Glucocorticoid Receptor for DNA and RNA: Sequence vs. Shape Open
1. STRUCTURES_GR_RNA_PROJECT Zip file contains starting, last snapshot, and average structures for the unbound and GR-bounds DNA, dsRNA, Gas5(model1 and model2), and GRE_RNA. 2. CONTACTS_CONTACTS_GR_RNA_PROJECT Zip file contains the specif…
View article: Recommendation: Abnormal methylation in the NDUFA13 gene promoter of breast cancer cells breaks the cooperative DNA recognition by transcription factors — R2/PR4
Recommendation: Abnormal methylation in the NDUFA13 gene promoter of breast cancer cells breaks the cooperative DNA recognition by transcription factors — R2/PR4 Open
Selective DNA binding by transcription factors (TFs) is crucial for the correct regulation of DNA transcription. In healthy cells, promoters of active genes are hypomethylated. A single CpG methylation within a TF response element (RE) may…
View article: Recommendation: Abnormal methylation in the NDUFA13 gene promoter of breast cancer cells breaks the cooperative DNA recognition by transcription factors — R1/PR3
Recommendation: Abnormal methylation in the NDUFA13 gene promoter of breast cancer cells breaks the cooperative DNA recognition by transcription factors — R1/PR3 Open
Selective DNA binding by transcription factors (TFs) is crucial for the correct regulation of DNA transcription. In healthy cells, promoters of active genes are hypomethylated. A single CpG methylation within a TF response element (RE) may…
View article: Recommendation: Abnormal methylation in the NDUFA13 gene promoter of breast cancer cells breaks the cooperative DNA recognition by transcription factors — R0/PR2
Recommendation: Abnormal methylation in the NDUFA13 gene promoter of breast cancer cells breaks the cooperative DNA recognition by transcription factors — R0/PR2 Open
Selective DNA binding by transcription factors (TFs) is crucial for the correct regulation of DNA transcription. In healthy cells, promoters of active genes are hypomethylated. A single CpG methylation within a TF response element (RE) may…
View article: Methylation in NDUFA13 gene promoter disrupts communication between collaborative transcription factors – potential mechanism for onset of breast cancer
Methylation in NDUFA13 gene promoter disrupts communication between collaborative transcription factors – potential mechanism for onset of breast cancer Open
Selective DNA binding by transcription factors (TFs) is crucial for the correct regulation of DNA transcription. In healthy cells, promoters of active genes are hypomethylated. A single CpG methylation within a TF response element may chan…
View article: Decision: Homologous BHLH transcription factors induce distinct deformations of torsionally-stressed DNA: a potential transcription regulation mechanism — R2/PR5
Decision: Homologous BHLH transcription factors induce distinct deformations of torsionally-stressed DNA: a potential transcription regulation mechanism — R2/PR5 Open
Changing torsional restraints on DNA is essential for the regulation of transcription. Torsional stress, introduced by RNA polymerase, can propagate along chromatin facilitating topological transitions and modulating the specific binding o…
View article: Decision: Homologous BHLH transcription factors induce distinct deformations of torsionally-stressed DNA: a potential transcription regulation mechanism — R1/PR4
Decision: Homologous BHLH transcription factors induce distinct deformations of torsionally-stressed DNA: a potential transcription regulation mechanism — R1/PR4 Open
Changing torsional restraints on DNA is essential for the regulation of transcription. Torsional stress, introduced by RNA polymerase, can propagate along chromatin facilitating topological transitions and modulating the specific binding o…
View article: Decision: Homologous BHLH transcription factors induce distinct deformations of torsionally-stressed DNA: a potential transcription regulation mechanism — R0/PR3
Decision: Homologous BHLH transcription factors induce distinct deformations of torsionally-stressed DNA: a potential transcription regulation mechanism — R0/PR3 Open
Changing torsional restraints on DNA is essential for the regulation of transcription. Torsional stress, introduced by RNA polymerase, can propagate along chromatin facilitating topological transitions and modulating the specific binding o…
View article: Homologous BHLH transcription factors induce distinct deformations of torsionally-stressed DNA: a potential transcription regulation mechanism
Homologous BHLH transcription factors induce distinct deformations of torsionally-stressed DNA: a potential transcription regulation mechanism Open
Changing torsional restraints on DNA is essential for the regulation of transcription. Torsional stress, introduced by RNA polymerase, can propagate along chromatin facilitating topological transitions and modulating the specific binding o…
View article: Abnormal methylation in the <i>NDUFA13</i> gene promoter of breast cancer cells breaks the cooperative DNA recognition by transcription factors
Abnormal methylation in the <i>NDUFA13</i> gene promoter of breast cancer cells breaks the cooperative DNA recognition by transcription factors Open
Selective DNA binding by transcription factors (TFs) is crucial for the correct regulation of DNA transcription. In healthy cells, promoters of active genes are hypomethylated. A single CpG methylation within a TF response element (RE) may…
View article: Homologous basic helix–loop–helix transcription factors induce distinct deformations of torsionally-stressed DNA: a potential transcription regulation mechanism
Homologous basic helix–loop–helix transcription factors induce distinct deformations of torsionally-stressed DNA: a potential transcription regulation mechanism Open
Changing torsional restraints on DNA is essential for the regulation of transcription. Torsional stress, introduced by RNA polymerase, can propagate along chromatin facilitating topological transitions and modulating the specific binding o…
View article: Sequence-specific dynamics of DNA response elements and their flanking sites regulate the recognition by AP-1 transcription factors
Sequence-specific dynamics of DNA response elements and their flanking sites regulate the recognition by AP-1 transcription factors Open
Activator proteins 1 (AP-1) comprise one of the largest families of eukaryotic basic leucine zipper transcription factors. Despite advances in the characterization of AP-1 DNA-binding sites, our ability to predict new binding sites and exp…
View article: Rational antibody design for undruggable targets using kinetically controlled biomolecular probes
Rational antibody design for undruggable targets using kinetically controlled biomolecular probes Open
This newly developed biological probes/proteomics method yields functional antibodies targeting previously undruggable targets.
View article: Michler’s hydrol blue elucidates structural differences in prion strains
Michler’s hydrol blue elucidates structural differences in prion strains Open
Significance Amyloids are protein fiber aggregates that are associated with both pathology, e.g., neurodegenerative diseases, and functionality, e.g., adaptation to environmental changes in yeasts. A particular property of amyloid fibrils …
View article: Dataset for molecular simulations of human IRE1 tetramer models.
Dataset for molecular simulations of human IRE1 tetramer models. Open
Dataset from SymmDock protein-protein docking of different conformers of IRE1 tetramers (dimer of back-to-back dimers); input files scripts and trajectories from subsequent MD simulations using Gromacs. Videos showing PC1 and PC2 of tetram…
View article: Dataset for molecular simulations of human IRE1 tetramer models.
Dataset for molecular simulations of human IRE1 tetramer models. Open
Dataset from SymmDock protein-protein docking of different conformers of IRE1 tetramers (dimer of back-to-back dimers); input files scripts and trajectories from subsequent MD simulations using Gromacs. Videos showing PC1 and PC2 of tetram…
View article: Sequence-specific dynamics of DNA response elements and their flanking sites regulate the recognition by AP-1 transcription factors
Sequence-specific dynamics of DNA response elements and their flanking sites regulate the recognition by AP-1 transcription factors Open
Activator proteins 1 (AP-1) comprise one of the largest families of eukaryotic basic leucine zipper transcription factors. Despite advances in the characterization of AP-1 DNA-binding sites, our ability to predict new binding sites and exp…