4494-26-2Relevant articles and documents
Nucleosides and nucleotides. 131. Synthesis and properties of oligonucleotides containing 5-formyl-2'-deoxyuridine
Ono,Okamoto,Inada,Nara,Matsuda
, p. 2231 - 2237 (1994)
Thymidine was converted into 5-formyl-2'-deoxyuridine (1), which was incorporated into oligonucleotides, 5'd(GGAGA1CTCC)3' (I-1) and 5'd(GCTGC1GCGAAAGCTG)3' (II-1). To avoid side-reactions and degradation, protection of the formyl group of 1 using a newly developed protecting group, N,N-di-(3,5-dichlorophenyl)ethylenediamine, was necessary. Compound 1 was unstable under the conditions employed for enzymatic complete digestion of oligonucleotides, so that a peak corresponding to 1 was not detected clearly by HPLC analysis of a nucleoside mixture obtained by complete hydrolysis of I-1. Therefore, the oligonucleotide I-1 was treated with cyanomethylenetriphenylphosphorane to give an oligonucleotide containing (E) and (Z)-5-(2-cyanovinyl)-2'-deoxyuridine, which was then hydrolyzed, and the newly generated nucleosides were detected by HPLC analysis. The T(m) of the self-complementary oligonucleotide I-1 (40 °C) was higher than that of the parent oligonucleotide, 5'd(GGAGATCTCC)3', (31 °C) in a buffer containing 0.01 M sodium phosphate (pH 7.0) and 0.1 M NaCl. DNA replication study on a template-primer system [primer, 5'd(32P-CAGCTTTCGC)3'; template, 3'd(GTCGAAAGCGXCGTCG)5' (X=1 or T)] showed that dATP was incorporated into the DNA strand at a site opposite to 1 by Klenow DNA polymerase, but with a reduced rate. The formyl group of 1 in the oligonucleotides reacted with amines to give Schiff base derivatives. oligonucleotide synthesis; 5-formyluracil
RETRACTED ARTICLE: Divergent synthesis of 5-substituted pyrimidine 2′-deoxynucleosides and their incorporation into oligodeoxynucleotides for the survey of uracil DNA glycosylases
Tran, Ai,Zheng, Song,White, Dawanna S.,Curry, Alyson M.,Cen, Yana
, p. 11818 - 11826 (2020/11/18)
Recent studies have indicated that 5-methylcytosine (5mC) residues in DNA can be oxidized and potentially deaminated to the corresponding thymine analogs. Some of these oxidative DNA damages have been implicated as new epigenetic markers that could have profound influences on chromatin function as well as disease pathology. In response to oxidative damage, the cells have a complex network of repair systems that recognize, remove and rebuild the lesions. However, how the modified nucleobases are detected and repaired remains elusive, largely due to the limited availability of synthetic oligodeoxynucleotides (ODNs) containing these novel DNA modifications. A concise and divergent synthetic strategy to 5mC derivatives has been developed. These derivatives were further elaborated to the corresponding phosphoramidites to enable the site-specific incorporation of modified nucleobases into ODNs using standard solid-phase DNA synthesis. The synthetic methodology, along with the panel of ODNs, is of great value to investigate the biological functions of epigenetically important nucleobases, and to elucidate the diversity in chemical lesion repair.
Sonochemical transformation of thymidine: A mass spectrometric study
Chandran, Jisha,Aravind, Usha K.,Aravindakumar
, p. 178 - 186 (2015/06/02)
Abstract Ultrasound is extensively used in medical field for a number of applications including targeted killing of cancer cells. DNA is one of the most susceptible entities in any kind of free radical induced reactions in living systems. In the present work, the transformation of thymidine (dT) induced by ultrasound (US) was investigated using high resolution mass spectrometry (LC-Q-ToF-MS). dT was subjected to sonolysis under four different frequencies (200, 350, 620 and 1000 kHz) and at three power densities (10.5, 24.5 and 42 W/mL) in aerated as well as argon saturated conditions. A total of twenty modified nucleosides including non-fully characterized dT dimeric compounds were detected by LC-Q-ToF-MS. Out of these products, seven were obtained only in the argon atmosphere and two only in the aerated conditions. Among the identified products, there were base modified products and sugar modified products. The products were formed by the reaction of hydroxyl radical and hydrogen atom. Under aerated conditions, the reactions proceed via the formation of hydroperoxides, while in argon atmosphere disproportionation and radical recombinations predominate. The study provides a complete picture of sonochemical transformation pathways of dT which has relevance in DNA damage under ultrasound exposure.
