Cited by 152RNA and protein synthesis mechanismsDNA and Nucleic Acid ChemistryRNA modifications and cancer

Synthesis and studies on the effect of 2-thiouridine and 4-thiouridine on sugar conformation and RNA duplex stability

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Kumar, R.·1997·Nucleic Acids Research

Abstract

In order to understand the effect of 2-thiouridine (s2U) substitution on RNA structure and the potential for stabilization of tRNA codon-anticodon interactions through s2U-34 modification, a pentamer RNA sequence, Gs2UUUC, was synthesized and characterized by NMR spectroscopy. The single strand contains the UUU anticodon sequence of tRNALys with flanking GCs to increase duplex stability. Regiochemical effects of uridine thiolation were determined by comparing the structure and stability of the 2-thiouridine containing oligonucleotide with an identical sequence containing 4-thiouridine (s4U) and also the normal uridine nucleoside. Circular dichroism spectrum indicated an A-form helical conformation for Gs2UUUC which was further confirmed by 2D ROESY NMR experiments. The duplex stability of the three pentamers complexed with a 2'-O-methyl-ribonucleotide complementary strand, GmAmAmAmCm, was determined by UV thermal melting studies and by 1H NMR spectroscopy. The duplex containing s2U has a T m of 30.7 degrees C compared to 19. 0 degrees C for the unmodified control and 14.5 degrees C for the s4U containing duplex. The results from UV experiments were corroborated by imino proton NMR studies that show proton exchange rates, chemical shift differences, and NH proton linewidths indicative of the stability order s2U >U >s4U. The magnitude of the effect of s2U in our model system is comparable to the 20 degrees C stabilization observed by Grosjean and co-workers for 2-thiolation in a codon-anticodon model system composed of two tRNAs with complementary anticodon sequences [Houssier, C., Degee, P., Nicoghosian, K. and Grosjean, H. (1988) J. Biomol. Struct. Dyn., 5, 1259-1266].

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  1. Yokoyama, S., Nishimura, S. (1995) In Soll, D., RajBhandary, U.L. (ed.), tRNA. Structure, Biosynthesis, and Function. ASM Press, Washington, pp. 207-224.
  2. Agris, P. F. (1996) In Cohn, W. M., K. (ed.), Progress in Nucleic Acid Research and Molecular Biology. Academic Press, pp. 74-129.
  3. Yokoyama, S., Watanabe, T., Murao, K., Ishikura, H., Yamaizumi, Z., Nishimura, S. and Miyazawa, T. (1985) Proc. Natl. Acad. Sci. USA, 82, 4905-4909.
  4. Kumar, R. K., Davis, D.R. (1997) Nucleosides Nucleotides, in press.

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Authors
Kumar, R.
Affiliations
University of Utah (US)
Corresponding author
Kumar, R.
Venue
Nucleic Acids Research
Published
1997-03-15
Volume
25
Issue
6
Pages
1272-1280
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
OpenAlex
W2045600076
Cited by
152
References
40
Citations by year
2026: 3 · 2025: 6 · 2024: 5 · 2023: 6 · 2022: 5 · 2021: 3 · 2020: 6 · 2019: 13 · 2018: 11 · 2017: 6 · 2016: 6 · 2015: 9 · 2014: 8 · 2013: 10 · 2012: 3
FWCI
1.19
Type
journal article
Language
en
Open access
Locations
  • Nucleic Acids Research (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
  • National Institutes of Health
  • National Cancer Institute (CA42014, P30CA042014)
  • National Center for Research Resources (RR0626)
  • Division of Molecular and Cellular Biosciences
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
Keywords
2-thiouridine, 4-thiouridine, RNA duplex stability, sugar conformation, A-form helix, anticodon, 2'-O-methyl oligonucleotides, duplex melting temperature, imino proton NMR
MeSH terms
Anticodon, Codon, Indicators and Reagents, Kinetics, Magnetic Resonance Spectroscopy, Oligoribonucleotides, RNA, RNA, Transfer, Lys, Thermodynamics, Thiouridine

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