Read by QxMD icon Read

single-stranded DNA binding protein

Giovanni N Roviello
This article deals with the synthesis in solid phase and characterization of a nucleoamino amide, based on a phenylalaninamide moiety which was N-conjugated to a thymine nucleobase. In analogy to the natural nucleobase-amino acid conjugates, endowed with a wide range of biological properties, the nucleoamino amide interacts with single-stranded nucleic acids as verified in DNA- and RNA-binding assays conducted by CD and UV spectroscopies. These technologies were used to show also that this conjugate binds serum proteins altering significantly their secondary structure, as evidenced by CD and UV using BSA as a model...
May 15, 2018: Amino Acids
Yi-Bin Zhang, Yan-Peng Wang, Jing Liu
Aptamers are single-stranded DNA or RNA which are isolated from synthesized random oligonucleotide library in vitro via systematic evolution of ligands by exponential enrichment (SELEX) and can bind to metal ions, small molecules, carbohydrates, lipids, proteins, and others targets with high affinity and specificity. Aptamers have the advantages of simple preparation, good thermal stability, and low immunogenicity and have great potential in the medical fields such as molecular imaging, biosensing, early diagnosis of diseases, and targeted therapy...
May 2018: Zhongguo Dang Dai Er Ke za Zhi, Chinese Journal of Contemporary Pediatrics
Yen-Hua Huang, Cheng-Yang Huang
Single-stranded DNA-binding proteins (SSBs) play crucial roles in DNA replication, repair, and recombination. Unlike E. coli , which contains only one type of SSB (EcSSB), some bacteria have two paralogous SSBs, namely, SsbA and SsbB. In this study, we found the third SSB-like protein in Staphylococcus aureus , SAAV2152, which was designated as SaSsbC. SaSsbC is a protein of 131 amino acids and shares 38%, 36%, and 33% sequence identity to SaSsbB, SaSsbA, and EcSSB, respectively. Gene map analysis showed that unlike the E...
April 17, 2018: Oncotarget
Ritu Bansal, Vijendra Arya, Ramesh Sethy, Radhakrishnan Rakesh, Rohini Muthuswami
ATP-dependent chromatin remodeling proteins use the energy released from ATP hydrolysis to reposition nucleosomes in DNA-dependent processes.  These proteins are classified as SF2 helicases. SMARCAL1, a member of this protein family, is known to modulate both DNA repair and transcription by specifically recognizing DNA molecules possessing double-strand to single-strand transition regions.  Mutations in this gene cause a rare autosomal recessive disorder known as Schimke Immuno-Osseous Dysplasia (SIOD). Structural studies have shown that the ATP-dependent chromatin remodeling proteins possess two Rec A-like domains termed as Rec A-like domain 1 and Rec A-like domain 2...
May 10, 2018: Bioscience Reports
Geoffrey Hutinet, Arthur Besle, Olivier Son, Stephen McGovern, Raphaël Guerois, Marie-Agnès Petit, Françoise Ochsenbein, François Lecointe
Bacteriophages are remarkable for the wide diversity of proteins they encode to perform DNA replication and homologous recombination. Looking back at these ancestral forms of life may help understanding how similar proteins work in more sophisticated organisms. For instance, the Sak4 family is composed of proteins similar to the archaeal RadB protein, a Rad51 paralog. We have previously shown that Sak4 allowed single-strand annealing in vivo , but only weakly compared to the phage λ Redβ protein, highlighting putatively that Sak4 requires partners to be efficient...
2018: Frontiers in Microbiology
Yuchen Nan, Yan-Jin Zhang
Phosphorodiamidate morpholino oligomers (PMO) are short single-stranded DNA analogs that are built upon a backbone of morpholine rings connected by phosphorodiamidate linkages. As uncharged nucleic acid analogs, PMO bind to complementary sequences of target mRNA by Watson-Crick base pairing to block protein translation through steric blockade. PMO interference of viral protein translation operates independently of RNase H. Meanwhile, PMO are resistant to a variety of enzymes present in biologic fluids, a characteristic that makes them highly suitable for in vivo applications...
2018: Frontiers in Microbiology
Luis B P Socas, Ernesto Ambroggio
Myristoylated proteins typically develop a tight association with membranes. One example is the matrix domain (MA) of the HIV-1 Gag protein. In addition, MA is able to bind the Sel25 RNA sequence, a ligand that can act as competitor for the interaction with the membrane. These properties make HIV-1 MA an attractive molecule to understand how protein and peptide surface properties can be controlled by myristoylation and oligonucleotide interaction. In this line, we analyzed the stability, thermodynamics and the topography of Langmuir monolayers composed of the myristoylated or unmyristoylated versions of MA in the presence or the absence of a single strand DNA (ssDNASel25) analog of the Sel25 RNA sequence...
May 4, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
Samuel W Schaffter, Leopold N Green, Joanna Schneider, Hari K K Subramanian, Rebecca Schulman, Elisa Franco
The use of proteins that bind and catalyze reactions with DNA alongside DNA nanostructures has broadened the functionality of DNA devices. DNA binding proteins have been used to specifically pattern and tune structural properties of DNA nanostructures and polymerases have been employed to directly and indirectly drive structural changes in DNA structures and devices. Despite these advances, undesired and poorly understood interactions between DNA nanostructures and proteins that bind DNA continue to negatively affect the performance and stability of DNA devices used in conjunction with enzymes...
April 30, 2018: Nucleic Acids Research
Maxwell Shapiro, Stephen Meier, Thomas MacCarthy
BACKGROUND: Activation induced deaminase (AID) and apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3 (APOBEC3) are deaminases that mutate C to U on single-stranded DNA (ssDNA). AID is expressed primarily in germinal center B-cells, where it facilitates affinity maturation and class-switch recombination. APOBEC3 are a family of anti-viral proteins that act as part of the intrinsic immune response. In both cases, there are particular sequence motifs, also known as "mutation motifs", to which these deaminases prefer to bind and mutate...
May 2, 2018: BMC Bioinformatics
Patrick Schindele, Felix Wolter, Holger Puchta
Currently, biology is revolutionized by ever growing applications of the CRISPR/Cas system. As discussed in this Review, new avenues have opened up for plant research and breeding by the use of the sequence-specific DNases Cas9 and Cas12 (formerly named Cpf1) and, more recently, the RNase Cas13 (formerly named C2c2). Although double strand break-induced gene editing based on error-prone non-homologous end joining has been applied to obtain new traits, such as powdery mildew resistance in wheat or improved pathogen resistance and increased yield in tomato, improved technologies based on CRISPR/Cas for programmed change of plant genomes via homologous recombination have recently been developed...
April 30, 2018: FEBS Letters
Shiladitya Sengupta, Chunying Yang, Muralidhar L Hegde, Pavana M Hegde, Joy Mitra, Arvind Pandey, Arijit Dutta, Abdul Tayyeb Datarwala, Kishor K Bhakat, Sankar Mitra
Posttranslational modifications of DNA repair proteins have been linked to their function. However, it is not clear if posttranslational acetylation affects subcellular localization of these enzymes. Here, we show that the human DNA glycosylase NEIL1, which is involved in repair of both endo- and exogenously generated oxidized bases via the base excision repair (BER) pathway, is acetylated by histone acetyltransferase p300. Acetylation occurs predominantly at Lys residues 296, 297 and 298 located in NEIL1's disordered C-terminal domain...
April 17, 2018: DNA Repair
Qing Yuan, Ran Tian, Haiying Zhao, Lijuan Li, Xiaolin Bi
Mre11 is a key player for DNA double strand break repair. Previous studies have shown that mammalian Mre11 is methylated at multiple arginines in its C-terminal Glycine-Arginine-Rich motif (GAR) by protein arginine methyltransferase PRMT1. Here, we found that the Drosophila Mre11 is methylated at arginines 559, 563, 565, and 569 in the GAR motif by DART1, the Drosophila homolog of PRMT1. Mre11 interacts with DART1 in S2 cells, and this interaction does not require the GAR motif. Arginines methylated Mre11 localizes exclusively in the nucleus as soluble nuclear protein or chromatin-binding protein...
April 25, 2018: G3: Genes—Genomes—Genetics
Xiaoting Ji, Haoyuan Lv, Jiayi Guo, Caifeng Ding, Xiliang Luo
A biocomplex of DNA nanotube-peptide, consisting of six concatenated DNA strands, three lock DNA strands and a cell-penetrating peptide was developed herein. The barrel structured DNA nanotube-peptide was successfully applied as a co-drug delivery system for targeting cancer therapy. The mucin 1 proteins (MUC-1) aptamer which is part of DNA nanotube can specially recognize MUC-1 protein on the surface of MCF-7 cells. Cyclo (Arg-Gly-Asp-D-phe-Lys) (cRGD), as a cell-penetrating peptide, facilitates recruitment and uptake of targeting drugs by binding to integrin receptors (αvβ3) of cytomembrane surface...
April 25, 2018: Chemistry: a European Journal
Neil R Lloyd, Deborah S Wuttke
Pot1 is the shelterin component responsible for the protection of the single-stranded DNA (ssDNA) overhang at telomeres in nearly all eukaryotic organisms. The C-terminal domain of the DNA-binding domain, Pot1pC, exhibits non-specific ssDNA recognition, achieved through thermodynamically equivalent alternative binding conformations. Given this flexibility, it is unclear how specificity for ssDNA over RNA, an activity required for biological function, is achieved. Examination of the ribose-position specificity of Pot1pC shows that ssDNA specificity is additive but not uniformly distributed across the ligand...
April 18, 2018: Structure
Jessica J Evans, Patrick E Gygli, Julienne McCaskill, Linda C DeVeaux
The haloarchaea are unusual in possessing genes for multiple homologs to the ubiquitous single-stranded DNA binding protein (SSB or replication protein A, RPA) found in all three domains of life. Halobacterium salinarum contains five homologs: two are eukaryotic in organization, two are prokaryotic and are encoded on the minichromosomes, and one is uniquely euryarchaeal. Radiation-resistant mutants previously isolated show upregulation of one of the eukaryotic-type RPA genes. Here, we have created deletions in the five RPA operons...
April 20, 2018: Genes
Mina Lee, Soochul Shin, Heesoo Uhm, Heesun Hong, Jaewon Kirk, Kwangbeom Hyun, Tomasz Kulikowicz, Jaehoon Kim, Byungchan Ahn, Vilhelm A Bohr, Sungchul Hohng
RPA is known to stimulate the helicase activity of Werner syndrome protein (WRN), but the exact stimulation mechanism is not understood. We use single-molecule FRET and magnetic tweezers to investigate the helicase activity of WRN and its stimulation by RPA. We show that WRN alone is a weak helicase which repetitively unwind just a few tens of base pairs, but that binding of multiple RPAs to the enzyme converts WRN into a superhelicase that unidirectionally unwinds double-stranded DNA more than 1 kb. Our study provides a good case in which the activity and biological functions of the enzyme may be fundamentally altered by the binding of cofactors...
April 14, 2018: Nucleic Acids Research
Ana-Maria Chiorcea-Paquim, Ramon Eritja, Ana Maria Oliveira-Brett
Guanine-rich DNA sequences are able to form G-quadruplexes, being involved in important biological processes and representing smart self-assembling nanomaterials that are increasingly used in DNA nanotechnology and biosensor technology. G-quadruplex electrochemical biosensors have received particular attention, since the electrochemical response is particularly sensitive to the DNA structural changes from single-stranded, double-stranded, or hairpin into a G-quadruplex configuration. Furthermore, the development of an increased number of G-quadruplex aptamers that combine the G-quadruplex stiffness and self-assembling versatility with the aptamer high specificity of binding to a variety of molecular targets allowed the construction of biosensors with increased selectivity and sensitivity...
2018: Journal of Nucleic Acids
Sujoy Ghosh, Niazul I Khan, John G Tsavalas, Edward Song
Selective and rapid detection of biomarkers is of utmost importance in modern day health care for early stage diagnosis to prevent fatal diseases and infections. Among several protein biomarkers, the role of lysozyme has been found to be especially important in human immune system to prevent several bacterial infections and other chronic disease such as bronchopulmonary dysplasia. Thus, real-time monitoring of lysozyme concentration in a human body can pave a facile route for early warning for potential bacterial infections...
2018: Frontiers in Bioengineering and Biotechnology
Aakash Basu, Matthew Hobson, Paul Lebel, Louis E Fernandes, Elsa M Tretter, James M Berger, Zev Bryant
Gyrase is an essential bacterial molecular motor that supercoils DNA using a conformational cycle in which chiral wrapping of > 100 base pairs confers directionality on topoisomerization. To understand the mechanism of this nucleoprotein machine, global structural transitions must be mapped onto the nucleotide cycle of ATP binding, hydrolysis and product release. Here we investigate coupling mechanisms using single-molecule tracking of DNA rotation and contraction during Escherichia coli gyrase activity under varying nucleotide conditions...
April 16, 2018: Nature Chemical Biology
Piotr M Skowron, Andrew M Kropinski, Joanna Zebrowska, Lukasz Janus, Kasjan Szemiako, Edyta Czajkowska, Natalia Maciejewska, Malgorzata Skowron, Joanna Łoś, Marcin Łoś, Agnieszka Zylicz-Stachula
Bacteriophage TP-84 is a well-characterized bacteriophage of historical interest. It is a member of the Siphoviridae, and infects a number of thermophilic Geobacillus (Bacillus) stearothermophilus strains. Its' 47.7-kbp double-stranded DNA genome revealed the presence of 81 coding sequences (CDSs) coding for polypeptides of 4 kDa or larger. Interestingly, all CDSs are oriented in the same direction, pointing to a dominant transcription direction of one DNA strand. Based on a homology search, a hypothetical function could be assigned to 31 CDSs...
2018: PloS One
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"