scholarly journals Exploring the dynamic nature of divalent metal ions involved in DNA cleavage by CRISPR-Cas12a

2022 ◽  
Author(s):  
Heyjin Son ◽  
Jaeil Park ◽  
You Hee Choi ◽  
Youngri Jung ◽  
Joong-Wook Lee ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Dna Cleavage ◽  
Metal Ion ◽  
Divalent Metal ◽  
Nucleic Acid Detection ◽  
Dependent Manner ◽  
Divalent Metal Ions ◽  
Dynamic Nature ◽  
Target Dna ◽  
Divalent Metal Ion

CRISPR-Cas12a has been widely used in genome editing and nucleic acid detection. In both of these applications, Cas12a cleaves target DNA in a divalent metal ion-dependent manner. However, when and...

On the Divalent Metal Ion Dependence of DNA Cleavage by Restriction Endonucleases of the EcoRI Family

2009 ◽  
Vol 393 (1) ◽  
pp. 140-160 ◽  
Author(s):  
Vera Pingoud ◽  
Wolfgang Wende ◽  
Peter Friedhoff ◽  
Monika Reuter ◽  
Jürgen Alves ◽  
...  
Keyword(s):  
Dna Cleavage ◽  
Metal Ion ◽  
Divalent Metal ◽  
Restriction Endonucleases ◽  
Divalent Metal Ion

scholarly journals HK97 gp74 Possesses an α-Helical Insertion in the ββα Fold That Affects Its Metal Binding, cos Site Digestion, and In Vivo Activities

2020 ◽  
Vol 202 (8) ◽  
Author(s):  
Sasha A. Weiditch ◽  
Sarah C. Bickers ◽  
Diane Bona ◽  
Karen L. Maxwell ◽  
Voula Kanelis
Keyword(s):  
Metal Binding ◽  
Metal Ion ◽  
Divalent Metal ◽  
Metal Ion Binding ◽  
Divalent Metal Ions ◽  
Nmr Studies ◽  
Phage Dna ◽  
Divalent Metal Ion ◽  
Phage Morphogenesis

ABSTRACT The last gene in the genome of the bacteriophage HK97 encodes gp74, an HNH endonuclease. HNH motifs contain two conserved His residues and an invariant Asn residue, and they adopt a ββα structure. gp74 is essential for phage head morphogenesis, likely because gp74 enhances the specific endonuclease activity of the HK97 terminase complex. Notably, the ability of gp74 to enhance the terminase-mediated cleavage of the phage cos site requires an intact HNH motif in gp74. Mutation of H82, the conserved metal-binding His residue in the HNH motif, to Ala abrogates gp74-mediated stimulation of terminase activity. Here, we present nuclear magnetic resonance (NMR) studies demonstrating that gp74 contains an α-helical insertion in the Ω-loop, which connects the two β-strands of the ββα fold, and a disordered C-terminal tail. NMR data indicate that the Ω-loop insert makes contacts to the ββα fold and influences the ability of gp74 to bind divalent metal ions. Further, the Ω-loop insert and C-terminal tail contribute to gp74-mediated DNA digestion and to gp74 activity in phage morphogenesis. The data presented here enrich our molecular-level understanding of how HNH endonucleases enhance terminase-mediated digestion of the cos site and contribute to the phage replication cycle. IMPORTANCE This study demonstrates that residues outside the canonical ββα fold, namely, the Ω-loop α-helical insert and a disordered C-terminal tail, regulate the activity of the HNH endonuclease gp74. The increased divalent metal ion binding when the Ω-loop insert is removed compared to reduced cos site digestion and phage formation indicates that the Ω-loop insert plays multiple regulatory roles. The data presented here provide insights into the molecular basis of the involvement of HNH proteins in phage DNA packing.

scholarly journals Structure of New Binary and Ternary DNA Polymerase Complexes From Bacteriophage RB69

2021 ◽  
Vol 8 ◽  
Author(s):  
Jongseo Park ◽  
Hyung-Seop Youn ◽  
Jun Yop An ◽  
Youngjin Lee ◽  
Soo Hyun Eom ◽  
...  
Keyword(s):  
Metal Ions ◽  
Dna Polymerase ◽  
Metal Ion ◽  
Ternary Complex ◽  
Critical Role ◽  
Divalent Metal ◽  
Binary Complex ◽  
Divalent Metal Ions ◽  
Divalent Metal Ion ◽  
Initial Binding

DNA polymerase plays a critical role in passing the genetic information of any living organism to its offspring. DNA polymerase from enterobacteria phage RB69 (RB69pol) has both polymerization and exonuclease activities and has been extensively studied as a model system for B-family DNA polymerases. Many binary and ternary complex structures of RB69pol are known, and they all contain a single polymerase-primer/template (P/T) DNA complex. Here, we report a crystal structure of the exonuclease-deficient RB69pol with the P/T duplex in a dimeric form at a resolution of 2.2 Å. The structure includes one new closed ternary complex with a single divalent metal ion bound and one new open binary complex in the pre-insertion state with a vacant dNTP-binding pocket. These complexes suggest that initial binding of the correct dNTP in the open state is much weaker than expected and that initial binding of the second divalent metal ion in the closed state is also much weaker than measured. Additional conformational changes are required to convert these complexes to high-affinity states. Thus, the measured affinities for the correct incoming dNTP and divalent metal ions are average values from many conformationally distinctive states. Our structure provides new insights into the order of the complex assembly involving two divalent metal ions. The biological relevance of specific interactions observed between one RB69pol and the P/T duplex bound to the second RB69pol observed within this dimeric complex is discussed.

Thermoelectric properties of Li-doped Cu0.95-xM0.05LixO (M=Mn, Ni, Zn)

2012 ◽  
Vol 1490 ◽  
pp. 69-73
Author(s):  
N. Yoshida ◽  
T. Naito ◽  
H. Fujishiro
Keyword(s):  
Thermal Conductivity ◽  
Electrical Resistivity ◽  
Thermoelectric Properties ◽  
Metal Ion ◽  
Figure Of Merit ◽  
Divalent Metal ◽  
Thermoelectric Figure Of Merit ◽  
Divalent Metal Ions ◽  
Thermoelectric Figure ◽  
Divalent Metal Ion

ABSTRACTThermoelectric properties of the Li-doped Cu0.95-xM0.05LixO (M=divalent metal ion; Mn, Ni, Zn) were investigated at the temperature up to 1273 K. In the doped divalent metal ions, Zn2+ ion was the most effective to reduce the thermal conductivity, and the Ni2+ substitution was preferable to decrease the electrical resistivity. For the Cu0.95-xNi0.05LixO sample at x=0.03, the maxima of the dimensionless thermoelectric figure of merit ZT and the power factor P at 1246 K were 4.2×10-2 and 1.6 ×10-4 W/K2m, respectively. The enhancement of the thermoelectric properties of the Li-doped Cu0.95-xM0.05LixO system was discussed.

An internal charge transfer-DNA platform for fluorescence sensing of divalent metal ions

2016 ◽  
Vol 52 (61) ◽  
pp. 9586-9588 ◽  
Author(s):  
Darian J. M. Blanchard ◽  
Richard A. Manderville
Keyword(s):  
Charge Transfer ◽  
Metal Ion ◽  
Divalent Metal ◽  
Ion Binding ◽  
Metal Ion Binding ◽  
Divalent Metal Ions ◽  
Fluorescence Sensing ◽  
Divalent Metal Ion ◽  
Internal Charge Transfer ◽  
Internal Charge

Utility of internal fluorescent guanine replacements for effective signaling of divalent metal ion binding.

Divalent metal ion-mediated assembly of spherical nucleic acids: the case study of Cu2+

2015 ◽  
Vol 17 (45) ◽  
pp. 30292-30299 ◽  
Author(s):  
Jang Ho Joo ◽  
Jae-Seung Lee
Keyword(s):  
Nucleic Acids ◽  
Metal Ions ◽  
Metal Ion ◽  
Divalent Metal ◽  
Divalent Metal Ions ◽  
New Strategy ◽  
Divalent Metal Ion ◽  
Spherical Nucleic Acids

A new strategy for reversibly assembling spherical nucleic acids (SNAs) is demonstrated based on the coordinative binding of divalent metal ions, particularly Cu2+, to nucleobases.

scholarly journals Effect of divalent metal ions on annexin-mediated aggregation of asolectin liposomes.

2000 ◽  
Vol 47 (3) ◽  
pp. 675-683 ◽  
Author(s):  
V I Mel'gunov ◽  
E I Akimova ◽  
K S Krasavchenko
Keyword(s):  
Metal Ions ◽  
Metal Ion ◽  
Relative Concentration ◽  
Toxic Metal ◽  
Transition Metal Ions ◽  
Divalent Metal ◽  
Divalent Metal Ions ◽  
Large Unilamellar Vesicles ◽  
Protein Molecules ◽  
Divalent Metal Ion

Annexins belong to a family of Ca2+- and phospholipid-binding proteins that can mediate the aggregation of granules and vesicles in the presence of Ca2+. We have studied the effects of different divalent metal ions on annexin-mediated aggregation of liposomes using annexins isolated from rabbit liver and large unilamellar vesicles prepared from soybean asolectin II-S. In the course of these studies, we have found that annexin-mediated aggregation of liposomes can be driven by various earth and transition metal ions other than Ca2+. The ability of metal ions to induce annexin-mediated aggregation decreases in the order: Cd2+ > Ba2+, Sr2+ > Ca2+ > Mn2+ > Ni2+ > Co2+. Annexin-mediated aggregation of vesicles is more selective to metal ions than the binding of annexins to membranes. We speculate that not every type of divalent metal ion can induce conformational change sufficient to promote the interaction of annexins either with two opposing membranes or with opposing protein molecules. Relative concentration ratios of metal ions in the intimate environment may be crucial for the functioning of annexins within specialized tissues and after treatment with toxic metal ions.

Structural and thermodynamic insights into a novel Mg2+–citrate-binding protein from the ABC transporter superfamily

2021 ◽  
Vol 77 (12) ◽  
Author(s):  
Suraj Kumar Mandal ◽  
Shankar Prasad Kanaujia
Keyword(s):  
Metal Ions ◽  
Abc Transporter ◽  
Metal Ion ◽  
Binding Protein ◽  
Substrate Binding ◽  
Divalent Metal ◽  
Uptake System ◽  
Divalent Metal Ions ◽  
Gram Negative ◽  
Divalent Metal Ion

More than one third of proteins require metal ions to accomplish their functions, making them obligatory for the growth and survival of microorganisms in varying environmental niches. In prokaryotes, besides their involvement in various cellular and physiological processes, metal ions stimulate the uptake of citrate molecules. Citrate is a source of carbon and energy and is reported to be transported by secondary transporters. In Gram-positive bacteria, citrate molecules are transported in complex with divalent metal ions, whereas in Gram-negative bacteria they are translocated by Na+/citrate symporters. In this study, the presence of a novel divalent-metal-ion-complexed citrate-uptake system that belongs to the primary active ABC transporter superfamily is reported. For uptake, the metal-ion-complexed citrate molecules are sequestered by substrate-binding proteins (SBPs) and transferred to transmembrane domains for their transport. This study reports crystal structures of an Mg2+–citrate-binding protein (MctA) from the Gram-negative thermophilic bacterium Thermus thermophilus HB8 in both apo and holo forms in the resolution range 1.63–2.50 Å. Despite binding various divalent metal ions, MctA possesses the coordination geometry to bind its physiological metal ion, Mg2+. The results also suggest an extended subclassification of cluster D SBPs, which are known to bind and transport divalent-metal-ion-complexed citrate molecules. Comparative assessment of the open and closed conformations of the wild-type and mutant MctA proteins suggests a gating mechanism of ligand entry following an `asymmetric domain movement' of the N-terminal domain for substrate binding.

Transfer of divalent metal ions into the organic phase of the systems water–chloroform–ZnCl2–CdCl2–HgCl2–NaOH–(NaCl)–n-alkyltri(oxyethylene)carboxylic acid

1988 ◽  
Vol 66 (10) ◽  
pp. 2640-2646 ◽  
Author(s):  
Jerzy Strzelbicki ◽  
Witold Charewicz ◽  
Jorg Beger ◽  
Lutz Hinz
Keyword(s):  
Carboxylic Acid ◽  
Aqueous Solutions ◽  
Metal Ions ◽  
Organic Phase ◽  
Metal Ion ◽  
Alkyl Chain ◽  
Divalent Metal ◽  
Divalent Metal Ions ◽  
Chemical Equilibria ◽  
Divalent Metal Ion

The influence of the length of an n-alkyl chain incorporated into the molecule of an n-alkyltri(oxyethylene) carboxylic acid of a general formula CnH(2n+1)(OCH2CH2)3OCH2CO2H(n = 6, 8, 10, and 12, respectively) on transfer of the zinc group element ions into chloroform was investigated. Metal ions were transferred from the aqueous solutions of ZnCl2, CdCl2, and HgCl2 at initial concentrations of 0.835 mM and 1.67 mM with, and without, added NaCl. From the aqueous solutions to which no NaCl was added, the selectivity of transfer of divalent metal ions into the organic phase was low.The selectivity of transfer of the divalent metal ions improved remarkably when NaCl was added to the aqueous phase due to the chemical equilibria involving complexation of the divalent metal ions by Cl−, OH−, and n-alkyltri(oxyethylene) carboxylic acid. In most systems (with NaCl added), Zn(II) was separated from Cd(II) and Hg(II). Less lipophilic n-alkyltri(oxyethylene) carboxylic acids (with a shorter n-alkyl chain incorporated) exhibited higher selectivity and efficiency as divalent metal ion carriers.

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