Engineering RNA sequence specificity of Pumilio repeats

CG Cheong, TMT Hall - Proceedings of the National …, 2006 - National Acad Sciences
Puf proteins bind RNA sequence specifically and regulate translation and stability of target
mRNAs. A “code” for RNA recognition has been deduced from crystal structures of the Puf …

Protein–RNA interactions: exploring binding patterns with a three-dimensional superposition analysis of high resolution structures

N Morozova, J Allers, J Myers, Y Shamoo - Bioinformatics, 2006 - academic.oup.com
Motivation: The recognition of specific RNA sequences and structures by proteins is critical
to our understanding of RNA processing, gene expression and viral replication. The diversity …

DNA Protection against Damages Induced by Low-Energy Electrons: Absolute Cross Sections for Arginine–DNA Complexes

X Wang, H Liao, W Liu, Y Shao, Y Zheng… - The Journal of …, 2023 - ACS Publications
Histone proteins protect cellular DNA from radiation damage. We find that arginine, a major
component of histone proteins, protects DNA from lesions induced by low-energy secondary …

Characterization of the stacking interactions between DNA or RNA nucleobases and the aromatic amino acids

LR Rutledge, LS Campbell-Verduyn… - Chemical physics letters, 2007 - Elsevier
MP2/6-31G∗(0.25) gas-phase potential energy surfaces of stacked dimers between the four
aromatic amino acids and the natural (DNA or RNA) nucleobases were considered as a …

Analysis of evolutionarily independent protein-RNA complexes yields a criterion to evaluate the relevance of prebiotic scenarios

C Blanco, M Bayas, F Yan, IA Chen - Current Biology, 2018 - cell.com
A central difficulty facing study of the origin of life on Earth is evaluating the relevance of
different proposed prebiotic scenarios. Perhaps the most established feature of the origin of …

Can DNA-binding proteins of replisome tautomerize nucleotide bases? Ab initio model study

OO Brovarets', YP Yurenko, IY Dubey… - Journal of …, 2012 - Taylor & Francis
Ab initio quantum-chemical study of specific point contacts of replisome proteins with DNA
modeled by acetic acid with canonical and mutagenic tautomers of DNA bases methylated …

Absolute binding-free energies between standard RNA/DNA nucleobases and amino-acid sidechain analogs in different environments

A de Ruiter, B Zagrovic - Nucleic acids research, 2015 - academic.oup.com
Despite the great importance of nucleic acid–protein interactions in the cell, our
understanding of their physico-chemical basis remains incomplete. In order to address this …

Modulating Anticancer Potential by Modifying the Structural Properties of a Family of Zinc Metal–Organic Chains Based on 4-Nitro-1H-pyrazole

B Fernández, I Fernández, J Cepeda… - Crystal Growth & …, 2018 - ACS Publications
We have synthesized a novel family of metal–organic chains based on 4-nitro-1 H-pyrazole
linker and zinc as metal center. We report the formation of these coordination polymers …

Directing the formation of adenine coordination polymers from tunable copper (II)/dicarboxylato/adenine paddle-wheel building units

S Pérez-Yáñez, G Beobide, O Castillo… - Crystal growth & …, 2012 - ACS Publications
Coordination polymers containing paddle-wheel shaped building units of general formula
[Cu2 (μ-adeninato) 2 (μ-carboxylato) 2](1–3) and [Cu2 (μ-carboxylato) 4 (methyladenine) …

Energetics of protein–DNA interactions

JE Donald, WW Chen… - Nucleic Acids Research, 2007 - academic.oup.com
Protein–DNA interactions are vital for many processes in living cells, especially
transcriptional regulation and DNA modification. To further our understanding of these …