nucleoside triphosphates
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2021 ◽  
Author(s):  
Huacan Lin ◽  
Eddy I. Jiménez ◽  
Joshua T. Arriola ◽  
Ulrich F. Müller ◽  
Ramanarayanan Krishnamurthy

2021 ◽  
Author(s):  
Huacan Lin ◽  
Eddy I. Jiménez ◽  
Joshua T. Arriola ◽  
Ulrich F. Müller ◽  
Ramanarayanan Krishnamurthy

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Taylor B Updegrove ◽  
Jailynn Harke ◽  
Vivek Anantharaman ◽  
Jin Yang ◽  
Nikhil Gopalan ◽  
...  

Hydrolysis of nucleoside triphosphates releases similar amounts of energy. However, ATP hydrolysis is typically used for energy-intensive reactions, whereas GTP hydrolysis typically functions as a switch. SpoIVA is a bacterial cytoskeletal protein that hydrolyzes ATP to polymerize irreversibly during Bacillus subtilis sporulation. SpoIVA evolved from a TRAFAC class of P-loop GTPases, but the evolutionary pressure that drove this change in nucleotide specificity is unclear. We therefore reengineered the nucleotide-binding pocket of SpoIVA to mimic its ancestral GTPase activity. SpoIVAGTPase functioned properly as a GTPase but failed to polymerize because it did not form an NDP-bound intermediate that we report is required for polymerization. Further, incubation of SpoIVAGTPase with limiting ATP did not promote efficient polymerization. This approach revealed that the nucleotide base, in addition to the energy released from hydrolysis, can be critical in specific biological functions. We also present data suggesting that increased levels of ATP relative to GTP at the end of sporulation was the evolutionary pressure that drove the change in nucleotide preference in SpoIVA.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Alexander V. Chudinov ◽  
Vadim A. Vasiliskov ◽  
Viktoriya E. Kuznetsova ◽  
Sergey A. Lapa ◽  
Natalia A. Kolganova ◽  
...  

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.


Author(s):  
Jan Matyasovsky ◽  
Laure Tack ◽  
Attila Palagyi ◽  
Miroslav Kuba ◽  
Radek Pohl ◽  
...  

We designed and synthesized nucleosides bearing aminophenyl- or aminonaphthyl-3-methoxychromone fluorophores attached at position 5 of cytosine or thymine and converted them to nucleoside triphosphates. The fluorophores exerted solvatochromic fluorescence with...


2020 ◽  
Vol 59 (49) ◽  
pp. 22063-22071 ◽  
Author(s):  
Chenglong Zhao ◽  
Stefan Weber ◽  
Dominique Schols ◽  
Jan Balzarini ◽  
Chris Meier

2020 ◽  
Vol 132 (49) ◽  
pp. 22247-22255
Author(s):  
Chenglong Zhao ◽  
Stefan Weber ◽  
Dominique Schols ◽  
Jan Balzarini ◽  
Chris Meier

2020 ◽  
Vol 29 (8) ◽  
pp. 1463-1477
Author(s):  
Nataraj Sekhar Pagadala ◽  
Rakesh Bhat ◽  
Jagadeesh Kumar D ◽  
Abdolamir Landi

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