Literature DB >> 28074944

Synthesis and biophysical analysis of modified thymine-containing DNA oligonucleotides.

F Kawasaki1, P Murat1, Z Li1, T Santner1, S Balasubramanian2.   

Abstract

We report the synthesis of a 5-formyl-2'-deoxyuridine (5fU) phosphoramidite and the preparation of oligonucleotides comprising all known, naturally observed eukaryotic thymidine modifications. Biophysical characterization of the synthetic oligonucleotides indicates that 5fU, but not the other T-derivatives, can alter DNA structures.

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Year:  2017        PMID： 28074944      PMCID： PMC5759927          DOI： 10.1039/c6cc08670e

Source DB:  PubMed          Journal:  Chem Commun (Camb)        ISSN： 1359-7345            Impact factor:   6.222


  21 in total

1.  Oxidation of thymine to 5-formyluracil in DNA promotes misincorporation of dGMP and subsequent elongation of a mismatched primer terminus by DNA polymerase.

Authors:  A Masaoka; H Terato; M Kobayashi; Y Ohyama; H Ide
Journal:  J Biol Chem       Date:  2001-01-29       Impact factor: 5.157

2.  Nucleosides and nucleotides. 131. Synthesis and properties of oligonucleotides containing 5-formyl-2'-deoxyuridine.

Authors:  A Ono; T Okamoto; M Inada; H Nara; A Matsuda
Journal:  Chem Pharm Bull (Tokyo)       Date:  1994-11       Impact factor: 1.645

3.  Glucosylated hydroxymethyluracil, DNA base J, prevents transcriptional readthrough in Leishmania.

Authors:  Henri G A M van Luenen; Carol Farris; Sabrina Jan; Paul-Andre Genest; Pankaj Tripathi; Arno Velds; Ron M Kerkhoven; Marja Nieuwland; Andrew Haydock; Gowthaman Ramasamy; Saara Vainio; Tatjana Heidebrecht; Anastassis Perrakis; Ludo Pagie; Bas van Steensel; Peter J Myler; Piet Borst
Journal:  Cell       Date:  2012-08-31       Impact factor: 41.582

4.  DNA sequence recognition by NF kappa B p50 homodimer: strict and obscure recognition sites in the binding sequence.

Authors:  A Kittaka; H Takayama; M Kurihara; C Horii; H Tanaka; T Miyasaka; J Inoue
Journal:  Nucleosides Nucleotides Nucleic Acids       Date:  2001 Apr-Jul       Impact factor: 1.381

5.  Syntheses of two 5-hydroxymethyl-2'-deoxycytidine phosphoramidites with TBDMS as the 5-hydroxymethyl protecting group and their incorporation into DNA.

Authors:  Qing Dai; Chun-Xiao Song; Tao Pan; Chuan He
Journal:  J Org Chem       Date:  2011-04-14       Impact factor: 4.354

6.  X-ray analyses of DNA dodecamers containing 2'-deoxy-5-formyluridine.

Authors:  M Tsunoda; T Sakaue; S Naito; T Sunami; N Karino; Y Ueno; A Matsuda; A Takénaka
Journal:  Nucleic Acids Res Suppl       Date:  2001

Review 7.  Human telomeric G-quadruplex: structures of DNA and RNA sequences.

Authors:  Anh Tuân Phan
Journal:  FEBS J       Date:  2009-11-27       Impact factor: 5.542

8.  Identification of the glucosyltransferase that converts hydroxymethyluracil to base J in the trypanosomatid genome.

Authors:  Whitney Bullard; Jessica Lopes da Rosa-Spiegler; Shuo Liu; Yinsheng Wang; Robert Sabatini
Journal:  J Biol Chem       Date:  2014-06-02       Impact factor: 5.157

9.  Substrate and mispairing properties of 5-formyl-2'-deoxyuridine 5'-triphosphate assessed by in vitro DNA polymerase reactions.

Authors:  M Yoshida; K Makino; H Morita; H Terato; Y Ohyama; H Ide
Journal:  Nucleic Acids Res       Date:  1997-04-15       Impact factor: 16.971

10.  5-Formylcytosine alters the structure of the DNA double helix.

Authors:  Eun-Ang Raiber; Pierre Murat; Dimitri Y Chirgadze; Dario Beraldi; Ben F Luisi; Shankar Balasubramanian
Journal:  Nat Struct Mol Biol       Date:  2014-12-15       Impact factor: 15.369
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  6 in total

1.  Novel entry to the synthesis of (S)- and (R)-5-methoxycarbonylhydroxymethyluridines - a diastereomeric pair of wobble tRNA nucleosides.

Authors:  Robert Borowski; Agnieszka Dziergowska; Elzbieta Sochacka; Grazyna Leszczynska
Journal:  RSC Adv       Date:  2019-12-06       Impact factor: 4.036

2.  Enrichment and fluorogenic labelling of 5-formyluracil in DNA.

Authors:  Chaoxing Liu; Yafen Wang; Xiong Zhang; Fan Wu; Wei Yang; Guangrong Zou; Qian Yao; Jiaqi Wang; Yuqi Chen; Shaoru Wang; Xiang Zhou
Journal:  Chem Sci       Date:  2017-04-05       Impact factor: 9.825

3.  Highly Selective 5-Formyluracil Labeling and Genome-wide Mapping Using (2-Benzimidazolyl)Acetonitrile Probe.

Authors:  Yafen Wang; Chaoxing Liu; Fan Wu; Xiong Zhang; Sheng Liu; Zonggui Chen; Weiwu Zeng; Wei Yang; Xiaolian Zhang; Yu Zhou; Xiaocheng Weng; Zhiguo Wu; Xiang Zhou
Journal:  iScience       Date:  2018-11-02

4.  Sequencing 5-Hydroxymethyluracil at Single-Base Resolution.

Authors:  Fumiko Kawasaki; Sergio Martínez Cuesta; Dario Beraldi; Areeb Mahtey; Robyn E Hardisty; Mark Carrington; Shankar Balasubramanian
Journal:  Angew Chem Int Ed Engl       Date:  2018-07-04       Impact factor: 15.336

5.  Oxime formation coordination-directed detection of genome-wide thymine oxides with nanogram-scale sample input.

Authors:  Feng Xiao; Qi Wang; Kaiyuan Zhang; Chaoxing Liu; Guangrong Zou; Xiang Zhou
Journal:  Chem Sci       Date:  2022-07-19       Impact factor: 9.969

6.  Translesion DNA Synthesis Across Lesions Induced by Oxidative Products of Pyrimidines: An Insight into the Mechanism by Microscale Thermophoresis.

Authors:  Ondrej Hrabina; Viktor Brabec; Olga Novakova
Journal:  Int J Mol Sci       Date:  2019-10-10       Impact factor: 5.923
  6 in total

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