scholarly journals Pyridone-based nucleotide analogues accepted for DNA biosynthesis

Biologija ◽  
2017 ◽  
Vol 63 (1) ◽  
Author(s):  
Algirdas Mikalkėnas ◽  
Bazilė Ravoitytė ◽  
Daiva Tauraitė ◽  
Saulius Serva
Keyword(s):  
Dna Synthesis ◽  
Dna Polymerases ◽  
Primer Extension ◽  
Nucleotide Analogues ◽  
Dna Biosynthesis ◽  
Nucleoside Triphosphates

Novel pyridone-based nucleotides were investigated for maintenance of DNA synthesis, carried on by representatives of different classes of polymerases. Five different nucleoside triphosphates of similar structure were addressed, demonstrating involvement in primer extension. The  nucleotides containing 4-chloro- and 4-bromo-2-pyridone as a nucleobase were preferred by all DNA polymerases tested. These nucleotides were incorporated up to several instances in a  row and unexpectedly failed to ensure DNA primer termination. Temporary polymerase stalling obeys kinetic constrain and is alleviated by availability of nucleotides readily acquired by the polymerase. Lack of inhibitory properties of 2-pyridone nucleobase confirms the processivity of DNA polymerases challenged by incorporated nucleotides.

Translesion DNA synthesis across double-base lesions derived from cross-links of an antitumor trinuclear platinum compound: primer extension, conformational and thermodynamic studies

Metallomics ◽  
2018 ◽  
Vol 10 (1) ◽  
pp. 132-144 ◽  
Author(s):  
O. Novakova ◽  
N. P. Farrell ◽  
V. Brabec
Keyword(s):  
Dna Synthesis ◽  
Dna Polymerases ◽  
Primer Extension ◽  
Platinum Compound ◽  
Thermodynamic Studies ◽  
Translesion Dna Synthesis ◽  
Cross Links ◽  
Translesion Dna ◽  
Compound Primer ◽  
Double Base

The central linker of antitumor polynuclear Triplatin represents an important factor responsible for the lowered tolerance of its DNA double-base adducts by DNA polymerases.

scholarly journals Mononucleotide repeat expansions with non-natural polymerase substrates

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Alexander V. Chudinov ◽  
Vadim A. Vasiliskov ◽  
Viktoriya E. Kuznetsova ◽  
Sergey A. Lapa ◽  
Natalia A. Kolganova ◽  
...  
Keyword(s):  
Primer Extension ◽  
Current Paper ◽  
Mononucleotide Repeat ◽  
Biological Phenomenon ◽  
Primer Extension Reaction ◽  
Nucleotide Analogues ◽  
Full Size ◽  
Nucleoside Triphosphates ◽  
Repeat Expansions ◽  
Incorporation Efficiency

AbstractReplicative strand slippage is a biological phenomenon, ubiquitous among different organisms. However, slippage events are also relevant to non-natural replication models utilizing synthetic polymerase substrates. Strand slippage may notably affect the outcome of the primer extension reaction with repetitive templates in the presence of non-natural nucleoside triphosphates. In the current paper, we studied the ability of Taq, Vent (exo-), and Deep Vent (exo-) polymerases to produce truncated, full size, or expanded modified strands utilizing non-natural 2′-deoxyuridine nucleotide analogues and different variants of the homopolymer template. Our data suggest that the slippage of the primer strand is dependent on the duplex fluttering, incorporation efficiency for a particular polymerase-dNTP pair, rate of non-templated base addition, and presence of competing nucleotides.

New nucleoside triphosphates modified at 5'-position, synthesis and substrate properties towards DNA polymerases

1993 ◽  
Vol 58 (s1) ◽  
pp. 120-121
Author(s):  
E. Shirokova ◽  
A. Shipitsin ◽  
E. Kusnetsova ◽  
L. Victorova ◽  
A. Krayevsky
Keyword(s):  
Dna Polymerases ◽  
Nucleoside Triphosphates ◽  
Substrate Properties ◽  
Position Synthesis

scholarly journals CRISPR-Associated Primase-Polymerases are implicated in prokaryotic CRISPR-Cas adaptation

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Katerina Zabrady ◽  
Matej Zabrady ◽  
Peter Kolesar ◽  
Arthur W. H. Li ◽  
Aidan J. Doherty
Keyword(s):  
Dna Repair ◽  
Dna Synthesis ◽  
Genome Stability ◽  
Dna Polymerases ◽  
Acquired Immunity ◽  
Strand Displacement ◽  
Genetic Studies ◽  
Type Iiia ◽  
Maintain Genome Stability ◽  
Cas Proteins

AbstractCRISPR-Cas pathways provide prokaryotes with acquired “immunity” against foreign genetic elements, including phages and plasmids. Although many of the proteins associated with CRISPR-Cas mechanisms are characterized, some requisite enzymes remain elusive. Genetic studies have implicated host DNA polymerases in some CRISPR-Cas systems but CRISPR-specific replicases have not yet been discovered. We have identified and characterised a family of CRISPR-Associated Primase-Polymerases (CAPPs) in a range of prokaryotes that are operonically associated with Cas1 and Cas2. CAPPs belong to the Primase-Polymerase (Prim-Pol) superfamily of replicases that operate in various DNA repair and replication pathways that maintain genome stability. Here, we characterise the DNA synthesis activities of bacterial CAPP homologues from Type IIIA and IIIB CRISPR-Cas systems and establish that they possess a range of replicase activities including DNA priming, polymerisation and strand-displacement. We demonstrate that CAPPs operonically-associated partners, Cas1 and Cas2, form a complex that possesses spacer integration activity. We show that CAPPs physically associate with the Cas proteins to form bespoke CRISPR-Cas complexes. Finally, we propose how CAPPs activities, in conjunction with their partners, may function to undertake key roles in CRISPR-Cas adaptation.

Effects of Polyamines on In Vitro DNA Synthesis by DNA Polymerases from Calf Thymus

1976 ◽  
Vol 79 (5) ◽  
pp. 895-901 ◽  
Author(s):  
Shonen YOSHIDA ◽  
Shigeo MASAKI ◽  
Teruo ANDO
Keyword(s):  
Dna Synthesis ◽  
Dna Polymerases ◽  
Calf Thymus

Cytoplasmic control of DNA synthesis by myocardial nuclei

1980 ◽  
Vol 238 (1) ◽  
pp. H66-H72
Author(s):  
C. J. Limas
Keyword(s):  
Dna Synthesis ◽  
Dna Polymerases ◽  
Postnatal Growth ◽  
Neonatal Rats ◽  
Cytoplasmic Factor ◽  
Age Dependent ◽  
Rat Myocytes ◽  
Old Rats ◽  
Isolated Rat

In vitro DNA synthesis by isolated myocardial nuclei declines rapidly during postnatal growth. To study the mechanism(s) responsible for this decline, cytoplasmic extracts (CE) were prepared from isolated rat myocytes at different times after birth. CE from 2-day-old rats stimulated in vitro DNA synthesis by myocardial nuclei from adult (6 mo old) rats (55 +/- 6 pmol[3H]dTMP . mg DNA-1 . 15 min-1 vs. 32 +/- 4 pmol [3H]dTMP . mg DNA-1 . 15 min-1 in untreated controls, P less than 0.01). The ability of cytoplasmic extracts of stimulate DNA synthesis decreased with age, from 73 +/- 9% over controls at age 2 days to 18 +/- 6 at 28 days; adult myocytes were essentially ineffective. Pulse-chase experiments demonstrated that CE-directed DNA synthesis was replicative and discontinuous. CE stimulatory activity was heat-labile, nondialyzable, trypsin-sensitive, and distinct from DNA polymerases. The results indicate that a) adult myocyte nuclei can be induced to synthesize DNA by cytoplasmic extracts from neonatal rats, and b) that absence of regulatory cytoplasmic factor(s) may, in part, explain the age-dependent decline in myocardial DNA synthesis.

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