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Synthesis and base pairing properties of DNA-RNA heteroduplex containing 5-hydroxyuridine

  • Cui, Song (Department of Biochemistry, College of Natural Sciences, Kyungpook National University) ;
  • Kim, Yong-Hoon (Department of Biochemistry, College of Natural Sciences, Kyungpook National University) ;
  • Jin, Cheng-Hao (Drug Targeting Laboratory, College of Pharmacy, Sungkyunkwan University) ;
  • Kim, Sang-Kook (Department of Biochemistry, College of Natural Sciences, Kyungpook National University) ;
  • Rhee, Man-hee (Laboratory of Veterinary Physiology and Signaling, College of Veterinary Medicine, Kyungpook National University) ;
  • Kwon, Oh-Shin (Department of Biochemistry, College of Natural Sciences, Kyungpook National University) ;
  • Moon, Byung-Jo (Department of Biochemistry, College of Natural Sciences, Kyungpook National University)
  • Published : 2009.06.30

Abstract

5-Hydroxyuridine (5-OHU) is a major lesion of uridine and cytosine produced in RNA by various chemical oxidants. To elucidate its biochemical and biophysical effects on RNA replication, the site-specifically modified oligoribonucleotides containing 5-OHU were synthesized with C5-hydroxy-5'-ODMTr-2'-TBDMS-uridine phosphoramidite using automated solid phase synthesis. The base-pairing properties of nucleotides opposite 5-OHU in 24 mer oligoribonulcleotides with dNTP were studied using three reverse transcriptases (Super-$Script^{TM}II$-, AMV-, MMLV-RT) in cDNA synthesis. Adenine as well as guanine was incorporated preferentially by all reverse transcriptases. In the UV-melting temperature experiment, the results from the relative stabilities of the base pairs were A : 5-OHU > G : 5-OHU > T : 5-OHU $\approx$ C : 5-OHU. Circular Dichroism (CD) studies showed that DNA-RNA containing 5- OHU heteroduplexes exhibit a similar conformation between the A-type RNA and B-type DNA. These results suggest that 5- OHU from oxidative damage was mainly influenced by adenine mismatch.

Keywords

References

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