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 Snapshots of a modified nucleotide moving through the confines of a DNA polymerase

2018 ◽  
Vol 115 (40) ◽  
pp. 9992-9997 ◽  
Author(s):  
Heike Maria Kropp ◽  
Simon Leonard Dürr ◽  
Christine Peter ◽  
Kay Diederichs ◽  
Andreas Marx
Keyword(s):  
Dna Polymerase ◽  
Dna Polymerases ◽  
Ternary Complexes ◽  
Structural Basis ◽  
Modified Nucleotides ◽  
Molecular Mechanics Calculations ◽  
Modified Dna ◽  
Substrate Properties ◽  
Dna Strand ◽  
Dna Substrate

DNA polymerases have evolved to process the four canonical nucleotides accurately. Nevertheless, these enzymes are also known to process modified nucleotides, which is the key to numerous core biotechnology applications. Processing of modified nucleotides includes incorporation of the modified nucleotide and postincorporation elongation to proceed with the synthesis of the nascent DNA strand. The structural basis for postincorporation elongation is currently unknown. We addressed this issue and successfully crystallized KlenTaq DNA polymerase in six closed ternary complexes containing the enzyme, the modified DNA substrate, and the incoming nucleotide. Each structure shows a high-resolution snapshot of the elongation of a modified primer, where the modification “moves” from the 3′-primer terminus upstream to the sixth nucleotide in the primer strand. Combining these data with quantum mechanics/molecular mechanics calculations and biochemical studies elucidates how the enzyme and the modified substrate mutually modulate their conformations without compromising the enzyme’s activity significantly. The study highlights the plasticity of the system as origin of the broad substrate properties of DNA polymerases and facilitates the design of improved systems.

Pyrophosphoryl Derivatives of 1-(2-Deoxy-3-O-Phosphonomethyl-β-and-α-D-Erythro-Pentofuranosyl)Thymine: Synthesis and Substrate Properties Towards Some DNA Polymerases

2000 ◽  
Vol 19 (10-12) ◽  
pp. 1885-1909 ◽  
Author(s):  
Igor A. Mikhailopulo ◽  
Tamara I. Kulak ◽  
Olga V. Tkachenko ◽  
Svetlana L. Sentyureva ◽  
Lyubov S. Victorova ◽  
...  
Keyword(s):  
Dna Polymerases ◽  
Substrate Properties ◽  
Derivatives Of

Substrate properties of C5-Substituted pyrimidine 2′-Deoxynucleoside 5′-Triphosphates for thermostable DNA polymerases during PCR

2003 ◽  
Vol 13 (21) ◽  
pp. 3735-3738 ◽  
Author(s):  
Masayasu Kuwahara ◽  
Yumi Takahata ◽  
Atsushi Shoji ◽  
Akiko N. Ozaki ◽  
Hiroaki Ozaki ◽  
...  
Keyword(s):  
Dna Polymerases ◽  
Substrate Properties

dNTP Modified at Triphosphate Residues: Substrate Properties Towards DNA Polymerases and Stability in Human Serum

1998 ◽  
Vol 17 (1) ◽  
pp. 681-693 ◽  
Author(s):  
Alexander Krayevsky ◽  
Andrey Arzumanov ◽  
Elena Shirokova ◽  
Natalya Dyatkina ◽  
Lyubov Victorova ◽  
...  
Keyword(s):  
Human Serum ◽  
Dna Polymerases ◽  
Substrate Properties

Synthesis and Incorporation of Pyrrole Carboxamide Nucleoside Triphosphates by DNA Polymerases

2000 ◽  
Vol 19 (10-12) ◽  
pp. 1599-1614 ◽  
Author(s):  
D. Loakes ◽  
M. J. Guo ◽  
D. M. Brown ◽  
S. A. Salisbury ◽  
C. L. Smith ◽  
...  
Keyword(s):  
Dna Polymerases ◽  
Nucleoside Triphosphates

scholarly journals Synthesis of Polyanionic C5-Modified 2′-Deoxyuridine and 2′-Deoxycytidine-5′-Triphosphates and Their Properties as Substrates for DNA Polymerases

Molecules ◽  
2021 ◽  
Vol 26 (8) ◽  
pp. 2250
Author(s):  
Claire Dutson ◽  
Esther Allen ◽  
Mark J. Thompson ◽  
Joseph H. Hedley ◽  
Heather E. Murton ◽  
...  
Keyword(s):  
Dna Polymerases ◽  
Ether Linkage ◽  
Essential Requirement ◽  
Si Nanowire ◽  
Detection Systems ◽  
Substrate Properties ◽  
Varying Length ◽  
Diagnostic Applications ◽  
Mode Of Attachment ◽  
Reporter Group

Modified 2′-deoxyribonucleotide triphosphates (dNTPs) have widespread applications in both existing and emerging biomolecular technologies. For such applications it is an essential requirement that the modified dNTPs be substrates for DNA polymerases. To date very few examples of C5-modified dNTPs bearing negatively charged functionality have been described, despite the fact that such nucleotides might potentially be valuable in diagnostic applications using Si-nanowire-based detection systems. Herein we have synthesised C5-modified dUTP and dCTP nucleotides each of which are labelled with an dianionic reporter group. The reporter group is tethered to the nucleobase via a polyethylene glycol (PEG)-based linkers of varying length. The substrate properties of these modified dNTPs with a variety of DNA polymerases have been investigated to study the effects of varying the length and mode of attachment of the PEG linker to the nucleobase. In general, nucleotides containing the PEG linker tethered to the nucleobase via an amide rather than an ether linkage proved to be the best substrates, whilst nucleotides containing PEG linkers from PEG6 to PEG24 could all be incorporated by one or more DNA polymerase. The polymerases most able to incorporate these modified nucleotides included Klentaq, Vent(exo-) and therminator, with incorporation by Klenow(exo-) generally being very poor.

Novel Open-Chain Nucleotides Imitating 2',3'-Dideoxy-2',3'-Didehydronucleotides: Synthesis and Substrate Properties Toward DNA Polymerases

1995 ◽  
Vol 14 (3) ◽  
pp. 749-751
Author(s):  
E. A. Shirokova ◽  
N. B. Tarussova ◽  
A. V. Shipitsin ◽  
D. G. Semizarov ◽  
M. Hieber ◽  
...  
Keyword(s):  
Dna Polymerases ◽  
Open Chain ◽  
Substrate Properties

ChemInform Abstract: dNTP Modified at Triphosphate Residues: Substrate Properties Towards DNA Polymerases and Stability in Human Serum

ChemInform ◽  
2010 ◽  
Vol 29 (27) ◽  
pp. no-no
Author(s):  
A. KRAYEVSKY ◽  
A. ARZUMANOV ◽  
E. SHIROKOVA ◽  
N. DYATKINA ◽  
L. VICTOROVA ◽  
...  
Keyword(s):  
Human Serum ◽  
Dna Polymerases ◽  
Substrate Properties
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