scholarly journals Kinetic Analysis of the Interaction of Nicking Endonuclease BspD6I with DNA

Biomolecules ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 1420
Author(s):  
Liudmila A. Abrosimova ◽  
Nikita A. Kuznetsov ◽  
Natalia A. Astafurova ◽  
Anastasiia R. Samsonova ◽  
Andrey S. Karpov ◽  
...  
Keyword(s):  
Specific Binding ◽  
Divalent Metal ◽  
Optimal Size ◽  
Divalent Metal Ions ◽  
Fast Kinetics ◽  
Phosphodiester Bond ◽  
Specific Complex ◽  
Dna Complex ◽  
First Time

Nicking endonucleases (NEs) are enzymes that incise only one strand of the duplex to produce a DNA molecule that is ‘nicked’ rather than cleaved in two. Since these precision tools are used in genetic engineering and genome editing, information about their mechanism of action at all stages of DNA recognition and phosphodiester bond hydrolysis is essential. For the first time, fast kinetics of the Nt.BspD6I interaction with DNA were studied by the stopped-flow technique, and changes of optical characteristics were registered for the enzyme or DNA molecules. The role of divalent metal cations was estimated at all steps of Nt.BspD6I–DNA complex formation. It was demonstrated that divalent metal ions are not required for the formation of a non-specific complex of the protein with DNA. Nt.BspD6I bound five-fold more efficiently to its recognition site in DNA than to a random DNA. DNA bending was confirmed during the specific binding of Nt.BspD6I to a substrate. The optimal size of Nt.BspD6I’s binding site in DNA as determined in this work should be taken into account in methods of detection of nucleic acid sequences and/or even various base modifications by means of NEs.

scholarly journals Rhizosphere Acidification by Iron Deficient Bean Plants: The Role of Trace Amounts of Divalent Metal Ions

1989 ◽  
Vol 90 (1) ◽  
pp. 359-364 ◽  
Author(s):  
H. Frits Bienfait ◽  
Henk J. Lubberding ◽  
Peter Heutink ◽  
L. Lindner ◽  
Jacques Visser ◽  
...  
Keyword(s):  
Metal Ions ◽  
Divalent Metal ◽  
Divalent Metal Ions ◽  
Rhizosphere Acidification ◽  
Bean Plants ◽  
Iron Deficient

scholarly journals Structure of the endonuclease IV homologue fromThermotoga maritimain the presence of active-site divalent metal ions

2010 ◽  
Vol 66 (9) ◽  
pp. 1003-1012 ◽  
Author(s):  
Stephen J. Tomanicek ◽  
Ronny C. Hughes ◽  
Joseph D. Ng ◽  
Leighton Coates
Keyword(s):  
Metal Ions ◽  
Active Site ◽  
Excision Repair ◽  
Divalent Metal ◽  
Hydroxyl Group ◽  
Divalent Metal Ions ◽  
Ap Endonuclease ◽  
Phosphodiester Bond ◽  
Dna Base ◽  
Ap Site

The most frequent lesion in DNA is at apurinic/apyrimidinic (AP) sites resulting from DNA-base losses. These AP-site lesions can stall DNA replication and lead to genome instability if left unrepaired. The AP endonucleases are an important class of enzymes that are involved in the repair of AP-site intermediates during damage-general DNA base-excision repair pathways. These enzymes hydrolytically cleave the 5′-phosphodiester bond at an AP site to generate a free 3′-hydroxyl group and a 5′-terminal sugar phosphate using their AP nuclease activity. Specifically,Thermotoga maritimaendonuclease IV is a member of the second conserved AP endonuclease family that includesEscherichia coliendonuclease IV, which is the archetype of the AP endonuclease superfamily. In order to more fully characterize the AP endonuclease family of enzymes, two X-ray crystal structures of theT. maritimaendonuclease IV homologue were determined in the presence of divalent metal ions bound in the active-site region. These structures of theT. maritimaendonuclease IV homologue further revealed the use of the TIM-barrel fold and the trinuclear metal binding site as important highly conserved structural elements that are involved in DNA-binding and AP-site repair processes in the AP endonuclease superfamily.

scholarly journals A dual role of divalent metal ions in catalysis and folding of RNase H1 from extreme halophilic archaeonHalobacteriumsp. NRC-1

FEBS Open Bio ◽  
2012 ◽  
Vol 2 (1) ◽  
pp. 345-352 ◽  
Author(s):  
Elias Tannous ◽  
Koji Yokoyama ◽  
Dong-Ju You ◽  
Yuichi Koga ◽  
Shigenori Kanaya
Keyword(s):  
Metal Ions ◽  
Divalent Metal ◽  
Dual Role ◽  
Divalent Metal Ions

Role of divalent metal ions in the hammerhead RNA cleavage reaction

Biochemistry ◽  
1991 ◽  
Vol 30 (39) ◽  
pp. 9464-9469 ◽  
Author(s):  
SueAnn C. Dahm ◽  
Olke C. Uhlenbeck
Keyword(s):  
Metal Ions ◽  
Divalent Metal ◽  
Rna Cleavage ◽  
Divalent Metal Ions ◽  
Cleavage Reaction ◽  
Hammerhead Rna

Autoantigenic Targets of B-Cell Receptors (BCR) Derived From Chronic Lymphocytic Leukemias Bind to and Induce Proliferation of Leukemic Cells.

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 2884-2884
Author(s):  
Klaus-Dieter Preuss ◽  
Gerhard Held ◽  
Natalie Fadle ◽  
Evi Regitz ◽  
Maria Kemele ◽  
...  
Keyword(s):  
B Cell ◽  
Conflicts Of Interest ◽  
Specific Binding ◽  
Cell Receptor ◽  
Convincing Evidence ◽  
Lymphocytic Leukemia ◽  
Leukemic Cells ◽  
Long Time ◽  
First Time

Abstract Abstract 2884 Background Auto-antigenic targets of the B-cell receptor (BCR) derived from malignant cells in chronic lymphocytic leukemia (CLL) might play a role in the pathogenesis of this neoplasm. Patients and Methods In order to identify autoantigenic targets of CLL-derived BCR we screened human tissue-derived protein macroarrays with Fab fragments obtained by papain treatment of CLL cells derived from 50 consecutive cases. Antigens were biochemically and molecularly characterized and recombinantly expressed. Results An autoantigenic target was identified for 12/50 (24%) of the cases, with 3 autoantigens being the target of the BCR from two patients each. CLL-BCR derived from the same stereotype subset recognized the same antigen, but differed epitopes. By flow cytometry using flag-tagged recombinantly expressed autoantigens binding of antigen to the surface of CLL was demonstrated, which was specific for the CLL cells from which the BCR used for the identification of the respective autoantigen was derived. Moreover, binding of the autoantigen to the respective leukemic cells induced specific activation as shown by increased cytoplasmic calcium concentration, induced MYC expression and proliferation of leukemic CLL cells as demonstrated by a proliferation assay (EZ4U). Conclusions Autoantigens are frequent targets of CLL-derived BCR. Their specific binding to and induction of proliferation in respective leukemic cells, which has been demonstrated for the first time, provide the most convincing evidence to date for the long-time hypothesized role of autoantigens in the pathogenesis of chronic lymphocyte leukemia. Supported by Sander-Stiftung (Munich, Germany) Disclosures: No relevant conflicts of interest to declare.

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