scholarly journals Y box-binding protein-1 binds preferentially to single-stranded nucleic acids and exhibits 3'->5' exonuclease activity

2001 ◽  
Vol 29 (5) ◽  
pp. 1200-1207 ◽  
Author(s):  
H. Izumi
Keyword(s):  
Nucleic Acids ◽  
Binding Protein ◽  
Exonuclease Activity

scholarly journals Design of the Crosslinking Reactions for Nucleic Acids-Binding Protein and Evaluation of the Reactivity

2020 ◽  
Vol 10 (21) ◽  
pp. 7709
Author(s):  
Kenta Odaira ◽  
Ken Yamada ◽  
Shogo Ishiyama ◽  
Hidenori Okamura ◽  
Fumi Nagatsugi
Keyword(s):  
Nucleic Acids ◽  
Binding Protein ◽  
Molecular Study ◽  
Pyrimidine Derivative ◽  
Major Groove ◽  
Covalent Bonds ◽  
Biological Studies ◽  
Selective Chemical ◽  
Crosslinking Reactions ◽  
Vinyl Group

Selective chemical reactions of biomolecules are some of the important tools for investigations by biological studies. We have developed the selective crosslinking reactions to form covalent bonds to DNA or RNA using crosslinking oligonucleotides (CFO) bearing reactive bases. In this study, we designed the cross-linkable 4-amino-6-oxo-2-vinyltriazine derivative with an acyclic linker (acyAOVT) to react with the nucleic acids-binding protein based on our previous results. We hypothesized that the acyAOVT base would form a stable base pair with guanine by three hydrogen bonds at the positions of the vinyl group in the duplex DNA major groove, and the vinyl group can react with the nucleophilic species in the proximity, for example, the cysteine or lysine residue in the nucleic acids-binding protein. The synthesized oligonucleotides bearing the acyAOVT derivative showed a higher reactivity than that of the corresponding pyrimidine derivative without one nitrogen. The duplex containing acyAOVT-guanine (G) formed complexes with Hha1 DNMT even in the presence of 2-mercaptoethanol. We expect that our system will provide a useful tool for the molecular study of nucleic acids-binding proteins.

scholarly journals NABP1, a novel RORγ-regulated gene encoding a single-stranded nucleic-acid-binding protein

2006 ◽  
Vol 397 (1) ◽  
pp. 89-99 ◽  
Author(s):  
Hong Soon Kang ◽  
Ju Youn Beak ◽  
Yong-Sik Kim ◽  
Robert M. Petrovich ◽  
Jennifer B. Collins ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Binding Protein ◽  
Size Exclusion ◽  
Binding Motif ◽  
Nucleic Acid Binding ◽  
Wild Type ◽  
Gene Encoding ◽  
Nucleic Acid Binding Protein ◽  
Acid Binding Protein

RORγ2 (retinoid-related orphan receptor γ2) plays a critical role in the regulation of thymopoiesis. Microarray analysis was performed in order to uncover differences in gene expression between thymocytes of wild-type and RORγ−/− mice. This analysis identified a novel gene encoding a 22 kDa protein, referred to as NABP1 (nucleic-acid-binding protein 1). This subsequently led to the identification of an additional protein, closely related to NABP1, designated NABP2. Both proteins contain an OB (oligonucleotide/oligosaccharide binding) motif at their N-terminus. This motif is highly conserved between the two proteins. NABP1 is highly expressed in the thymus of wild-type mice and is greatly suppressed in RORγ−/− mice. During thymopoiesis, NABP1 mRNA expression is restricted to CD4+CD8+ thymocytes, an expression pattern similar to that observed for RORγ2. These observations appear to suggest that NABP1 expression is regulated either directly or indirectly by RORγ2. Confocal microscopic analysis showed that the NABP1 protein localizes to the nucleus. Analysis of nuclear proteins by size-exclusion chromatography indicated that NABP1 is part of a high molecular-mass protein complex. Since the OB-fold is frequently involved in the recognition of nucleic acids, the interaction of NABP1 with various nucleic acids was examined. Our results demonstrate that NABP1 binds single-stranded nucleic acids, but not double-stranded DNA, suggesting that it functions as a single-stranded nucleic acid binding protein.

scholarly journals Phosphoregulation provides specificity to biomolecular condensates in the cell cycle and cell polarity

2020 ◽  
Vol 219 (7) ◽  
Author(s):  
Therese M. Gerbich ◽  
Grace A. McLaughlin ◽  
Katelyn Cassidy ◽  
Scott Gerber ◽  
David Adalsteinsson ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Nucleic Acids ◽  
Cell Polarity ◽  
Filamentous Fungus ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Ashbya Gossypii ◽  
Mrna Targets ◽  
Functional Identities

Biomolecular condensation is a way of organizing cytosol in which proteins and nucleic acids coassemble into compartments. In the multinucleate filamentous fungus Ashbya gossypii, the RNA-binding protein Whi3 regulates the cell cycle and cell polarity through forming macromolecular structures that behave like condensates. Whi3 has distinct spatial localizations and mRNA targets, making it a powerful model for how, when, and where specific identities are established for condensates. We identified residues on Whi3 that are differentially phosphorylated under specific conditions and generated mutants that ablate this regulation. This yielded separation of function alleles that were functional for either cell polarity or nuclear cycling but not both. This study shows that phosphorylation of individual residues on molecules in biomolecular condensates can provide specificity that gives rise to distinct functional identities in the same cell.

Role of Tyr-22 in the Binding of Pf3 ssDNA Binding Protein to Nucleic Acids

Biochemistry ◽  
1995 ◽  
Vol 34 (16) ◽  
pp. 5635-5643 ◽  
Author(s):  
Michael D. Powell ◽  
Donald M. Gray
Keyword(s):  
Nucleic Acids ◽  
Binding Protein ◽  
Ssdna Binding ◽  
Ssdna Binding Protein
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