Single-Stranded DNA Binding Proteins Unwind the Newly Synthesized Double-Stranded DNA of Model Miniforks

Biochemistry ◽  
2011 ◽  
Vol 50 (6) ◽  
pp. 932-944 ◽  
Author(s):  
Emmanuelle Delagoutte ◽  
Amélie Heneman-Masurel ◽  
Giuseppe Baldacci
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Single Stranded Dna ◽  
Double Stranded Dna

scholarly journals PredPSD: A Gradient Tree Boosting Approach for Single-Stranded and Double-Stranded DNA Binding Protein Prediction

Molecules ◽  
2019 ◽  
Vol 25 (1) ◽  
pp. 98 ◽  
Author(s):  
Changgeng Tan ◽  
Tong Wang ◽  
Wenyi Yang ◽  
Lei Deng
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Computational Method ◽  
Sequence Information ◽  
Feature Subset ◽  
Single Stranded Dna ◽  
Cell Functions ◽  
Double Stranded Dna ◽  
Maximal Relevance

Interactions between proteins and DNAs play essential roles in many biological processes. DNA binding proteins can be classified into two categories. Double-stranded DNA-binding proteins (DSBs) bind to double-stranded DNA and are involved in a series of cell functions such as gene expression and regulation. Single-stranded DNA-binding proteins (SSBs) are necessary for DNA replication, recombination, and repair and are responsible for binding to the single-stranded DNA. Therefore, the effective classification of DNA-binding proteins is helpful for functional annotations of proteins. In this work, we propose PredPSD, a computational method based on sequence information that accurately predicts SSBs and DSBs. It introduces three novel feature extraction algorithms. In particular, we use the autocross-covariance (ACC) transformation to transform feature matrices into fixed-length vectors. Then, we put the optimal feature subset obtained by the minimal-redundancy-maximal-relevance criterion (mRMR) feature selection algorithm into the gradient tree boosting (GTB). In 10-fold cross-validation based on a benchmark dataset, PredPSD achieves promising performances with an AUC score of 0.956 and an accuracy of 0.912, which are better than those of existing methods. Moreover, our method has significantly improved the prediction accuracy in independent testing. The experimental results show that PredPSD can significantly recognize the binding specificity and differentiate DSBs and SSBs.

Mitochondrial Single-Stranded DNA-Binding Proteins: in Search for New Functions

2001 ◽  
Vol 382 (2) ◽  
Author(s):  
L'ubomír Tomáka ◽  
Jozef Nosek ◽  
Blanka Kucejová
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Single Stranded Dna

Identification of single-stranded-DNA-binding proteins that interact with muscle gene elements

1991 ◽  
Vol 11 (4) ◽  
pp. 1944-1953
Author(s):  
I M Santoro ◽  
T M Yi ◽  
K Walsh
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Regulatory Element ◽  
Dna Binding Proteins ◽  
Binding Activity ◽  
Sequence Motif ◽  
Mobility Shift ◽  
Specific Sequence ◽  
Single Stranded Dna ◽  
Muscle Gene

A sequence-specific DNA-binding protein from skeletal-muscle extracts that binds to probes of three muscle gene DNA elements is identified. This protein, referred to as muscle factor 3, forms the predominant nucleoprotein complex with the MCAT gene sequence motif in an electrophoretic mobility shift assay. This protein also binds to the skeletal actin muscle regulatory element, which contains the conserved CArG motif, and to a creatine kinase enhancer probe, which contains the E-box motif, a MyoD-binding site. Muscle factor 3 has a potent sequence-specific, single-stranded-DNA-binding activity. The specificity of this interaction was demonstrated by sequence-specific competition and by mutations that diminished or eliminated detectable complex formation. MyoD, a myogenic determination factor that is distinct from muscle factor 3, also bound to single-stranded-DNA probes in a sequence-specific manner, but other transcription factors did not. Multiple copies of the MCAT motif activated the expression of a heterologous promoter, and a mutation that eliminated expression was correlated with diminished factor binding. Muscle factor 3 and MyoD may be members of a class of DNA-binding proteins that modulate gene expression by their abilities to recognize DNA with unusual secondary structure in addition to specific sequence.

scholarly journals Identification of single-stranded-DNA-binding proteins that interact with muscle gene elements.

1991 ◽  
Vol 11 (4) ◽  
pp. 1944-1953 ◽  
Author(s):  
I M Santoro ◽  
T M Yi ◽  
K Walsh
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Regulatory Element ◽  
Dna Binding Proteins ◽  
Binding Activity ◽  
Sequence Motif ◽  
Mobility Shift ◽  
Specific Sequence ◽  
Single Stranded Dna ◽  
Muscle Gene

A sequence-specific DNA-binding protein from skeletal-muscle extracts that binds to probes of three muscle gene DNA elements is identified. This protein, referred to as muscle factor 3, forms the predominant nucleoprotein complex with the MCAT gene sequence motif in an electrophoretic mobility shift assay. This protein also binds to the skeletal actin muscle regulatory element, which contains the conserved CArG motif, and to a creatine kinase enhancer probe, which contains the E-box motif, a MyoD-binding site. Muscle factor 3 has a potent sequence-specific, single-stranded-DNA-binding activity. The specificity of this interaction was demonstrated by sequence-specific competition and by mutations that diminished or eliminated detectable complex formation. MyoD, a myogenic determination factor that is distinct from muscle factor 3, also bound to single-stranded-DNA probes in a sequence-specific manner, but other transcription factors did not. Multiple copies of the MCAT motif activated the expression of a heterologous promoter, and a mutation that eliminated expression was correlated with diminished factor binding. Muscle factor 3 and MyoD may be members of a class of DNA-binding proteins that modulate gene expression by their abilities to recognize DNA with unusual secondary structure in addition to specific sequence.

scholarly journals Cell rounding causes genomic instability by dissociation of single-stranded DNA-binding proteins

2018 ◽  
Author(s):  
Qian Guo ◽  
Xianglu Liao ◽  
Xingwu Wang ◽  
Ling Liu ◽  
Bao Song
Keyword(s):  
Stem Cell ◽  
Dna Binding ◽  
Cell Therapy ◽  
Genomic Instability ◽  
Stem Cell Therapy ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Single Stranded Dna ◽  
Cell Rounding ◽  
Wide Range

AbstractGenomic instability can cause a wide range of diseases, including cancer and cellular senescence, which is also a major challenge in stem cell therapy. However, how a single event can cause extremely high levels of genomic instability remains unclear. Using our developed method, cell in situ electrophoresis (CISE), and models of normal, cancer, and embryonic stem cells, we found that cell rounding as a catastrophic source event ubiquitously observed in vivo and in vitro might lead to large-scale DNA deprotection, genomic instability, chromosomal shattering, cell heterogeneity, and senescent crisis by dissociation of single-stranded DNA-binding proteins (SSBs). Understanding the mechanism may facilitate the development of clinical strategies for cancer therapy, improve the safety of stem cell therapy, and prevent pathological aging.

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