Synthesis of DNA oligonucleotides containing C5-ethynylbenzenesulfonamide-modified nucleotides (EBNA) by polymerases towards the construction of base functionalized nucleic acids

Goubet, Astrid; Chardon, Antoine; Kumar, Pawan; Sharma, Pawan K.; Veedu, Rakesh N.

doi:10.1016/j.bmcl.2012.11.096

Cited by 15 publications

(7 citation statements)

References 10 publications

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“…The double-headed nucleotide 173 was fully accepted by KOD (kodakaraensis), Phusion, and Klenow DNA polymerases as substrate which resulted in the formation of fully extended DNA. KOD DNA polymerase was found to be the best enzyme to produce DNA containing the double-headed nucleotide 173 in good yield and Phusion DNA polymerase amplified the template containing double-headed nucleotide 173 efficiently by PCR (polymerase chain reaction) [ 82 ].…”

Section: Reviewmentioning

confidence: 99%

Double-headed nucleosides: Synthesis and applications

Verma¹,

Maity²,

Maikhuri³

et al. 2021

Beilstein J. Org. Chem.

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Section: Reviewmentioning

confidence: 99%

Double-headed nucleosides: Synthesis and applications

Verma¹,

Maity²,

Maikhuri³

et al. 2021

Beilstein J. Org. Chem.

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“…The DNA is a common molecule to all living beings throughout the evolution of life on Earth and is also responsible for carrying and transmitting the genetic information necessary for the development of absolutely all the physical and functional characteristics of a given organism. In this sense, it is expected that such a molecule would be very stable in order to guarantee its integrity and transmissibility throughout generations; however, DNA is naturally very unstable [1,2]. Moreover, this molecule is also subject to the attack of several endogenous and exogenous agents that are capable of damaging and altering its structure, contributing to the development of several human diseases and conditions.…”

Section: Introductionmentioning

confidence: 99%

Interface of DNA Repair and Metabolism

Marconi

Ranfley

Menck

et al. 2020

Curr. Tissue Microenviron. Rep.

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Purpose of Review DNA is naturally very unstable and several agents are capable of damaging and altering its structure, thus leading to several negative consequences. Therefore, this review seeks to better understand the relationship between different DNA repair mechanisms and metabolic pathways, and how such a relationship can influence the outcome of different human inflammatory diseases. Recent Findings Studies have shown that factors involved in DNA repair are also involved in the regulation of cellular metabolism in response to DNA damage. Indeed, it was demonstrated that cells deficient in DNA repair have abrupt rewiring of cell metabolism. Additionally, oxidative stress observed in several human disorders increase DNA damage that contributes in metabolic changes and diseases progression. Summary DNA molecule is daily exposed to several types of damages and, in mammal cells, the DNA damage response (DDR) is responsible to monitor and repair genotoxic stress. The activation of DDR mostly depends on the DNA damage type and involves the activation of sensors, transducers, and effector proteins. The effector protein pathways are closely linked to several cell biology processes, such as apoptosis, senescence, cell cycle control, inflammatory response, and gene transcriptions. Recently, it was demonstrated that DDR genes are involved in cell metabolism and contribute to DNA repair and cell survival. Understanding as DNA damage impacts in cell function is important to comprehend and treat several human inflammatory diseases.

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“…[48][49][50][51][52][53][54][55][56][57][58][59][60][61][62][63][64][65] Veedu et al first tested B/L nucleotide incorporation using Phusion High Fidelity DNA polymerase, 9°Nm DNA polymerase, and Pfu DNA polymerase, and observed that the first and second of these three polymerases to exhibit superior stability in human plasma and target binding affinity (t 1/2 = 53 h, EC 50 = 2.0 nM) compared with TTA1 (t 1/2 = 42 h, EC 50 = 5.8 nM). In contrast, replacement with 2'-OMe nucleotides at the same positions, which yielded TTA1.1, resulted in a more than 2-fold decrease in binding affinity, although stability was substantially improved (t 1/2 = 49 h, EC 50 = 13.7 nM).…”

Section: Enzymatic Syntheses Of Bnasmentioning

confidence: 99%

“…This knowledge is now being widely accepted among researchers engaged in relevant studies. 54,[58][59][60]62,65,[79][80][81][82][83] To date, enzymatic syntheses of various modified DNAs using KOD-related DNA polymerases have been reported. A DNA polymerase named KOD XL is commonly used (which is essentially the same as KOD Dash); KOD XL comprises a mixture of approximately 2:98 wild-type KOD DNA polymerase and KOD(exo-) DNA polymerase.…”

Section: '4'-bna/lna Aptamers Created By Selex Selectionmentioning

confidence: 99%