Nucleic Acids Research, Vol 25, Issue 6 1272-1280, Copyright © 1997 by Oxford University Press
RK Kumar and DR Davis
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].
ARTICLES
Synthesis and studies on the effect of 2-thiouridine and 4-thiouridine on sugar conformation and RNA duplex stability
Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah 84112, USA.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  K. Sipa, E. Sochacka, J. Kazmierczak-Baranska, M. Maszewska, M. Janicka, G. Nowak, and B. Nawrot Effect of base modifications on structure, thermodynamic stability, and gene silencing activity of short interfering RNA RNA, August 1, 2007; 13(8): 1301 - 1316. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. R. Bjork, B. Huang, O. P. Persson, and A. S. Bystrom A conserved modified wobble nucleoside (mcm5s2U) in lysyl-tRNA is required for viability in yeast RNA, August 1, 2007; 13(8): 1245 - 1255. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. Diop-Frimpong, T. P. Prakash, K. G. Rajeev, M. Manoharan, and M. Egli Stabilizing contributions of sulfur-modified nucleotides: crystal structure of a DNA duplex with 2'-O-[2-(methoxy)ethyl]-2-thiothymidines Nucleic Acids Res., September 16, 2005; 33(16): 5297 - 5307. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. B. GAMPER JR., K. ARAR, A. GEWIRTZ, and Y.-M. HOU Unrestricted accessibility of short oligonucleotides to RNA RNA, September 1, 2005; 11(9): 1441 - 1447. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. K. VAISH, V. R. JADHAV, K. KOSSEN, C. PASKO, L. E. ANDREWS, J. A. MCSWIGGEN, B. POLISKY, and S. D. SEIWERT Zeptomole detection of a viral nucleic acid using a target-activated ribozyme RNA, September 1, 2003; 9(9): 1058 - 1072. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. M. Nair, D. G. Myszka, and D. R. Davis Surface plasmon resonance kinetic studies of the HIV TAR RNA kissing hairpin complex and its stabilization by 2-thiouridine modification Nucleic Acids Res., May 1, 2000; 28(9): 1935 - 1940. [Abstract] [Full Text] [PDF]
|
|