Nucleic Acids Research, Vol 26, Issue 13 3127-3135, Copyright © 1998 by Oxford University Press
M Ahmadian, P Zhang and DE Bergstrom
Two series of modified oligonucleotides based on the self-complementary
dodecamer d(CGCTAATTAGCG) were synthesized. The first contained the -C
identical withCCH2R linker at C5 of deoxyuridine at position 4 (T*) of
d(CGCT*AATTAGCG) and the second contained the -SR linker. The goal of the
study was to evaluate and compare these two types of side chains for
suitability as tethers for linking reporter groups to oligonucleotides. Our
primary concern was how these tethers would effect duplex stability. The
modified nucleosides were synthesized by palladium-mediated coupling
reactions between the substituted alkyne and 5'-(4,
4'-dimethoxytrityl)-5-iodo-2'-deoxyuridine and between a disulfide and
5-chloromercurio-2'-deoxyuridine. The C5 deoxyuridine side chains evaluated
included C identical with CCH3, C identical with CCH2NHC(O)CH3, C identical
with CCH2N(CH3)2, C identical with CCH2N- HC(O)C5H4N, C identical with
CCH2NHC(O)C10H15, SCH3, SC6H5 and SCH2CH2NHC(O)CH3. The nucleosides
containing these substituents were incorporated into
oligo-deoxyribonucleotides by standard phosphoramidite methodology. Melting
studies demonstrated that the sequence containing the C identical with
CCH3side chain had the highest T m value (59.1 degrees C) in comparison
with the control sequence (T m = 55.2 degrees C) and that any additional
substituent on C3 of the propynyl group lowered the T m value relative to
propynyl. Nevertheless, even the most destabilizing substituent,
adamantylcarbamoyl, yielded an oligodeoxyribonucleotide that dissociated
with a T m of 54 degrees C, which is only 1.2 degrees C less than the
control sequence. In contrast, the thioether substituents led to lower T m
values, ranging from as low as 45.1 degrees C for SPh up to 52.2 degrees C
for SMe. Replacing the methyl of the SMe substituent with a CH2CH2NHC(O)CH3
tether led to no further reduction in melting temperature. The T m value of
the CH2CH2NHC(O)CH3-containing oligonucleotide was less than the natural
sequence by 1.6 degrees C/substituent. This is sufficiently small that it
is anticipated that the C5 thioether linkage may be as useful as the
acetylenic linkage for tethering reporter groups to oligonucleotides. More
importantly, the thioether linkage provides a means to position functional
groups to interact specifically with opposing complementary (target)
sequences.
ARTICLES
A comparative study of the thermal stability of oligodeoxyribonucleotides containing 5-substituted 2'-deoxyuridines
Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  J. A. Brazier, T. Shibata, J. Townsley, B. F. Taylor, E. Frary, N. H. Williams, and D. M. Williams Amino-functionalized DNA: the properties of C5-amino-alkyl substituted 2'-deoxyuridines and their application in DNA triplex formation Nucleic Acids Res., March 3, 2005; 33(4): 1362 - 1371. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. He and F. Seela Propynyl groups in duplex DNA: stability of base pairs incorporating 7-substituted 8-aza-7-deazapurines or 5-substituted pyrimidines Nucleic Acids Res., December 15, 2002; 30(24): 5485 - 5496. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. M. Soto, B. I. Kankia, P. Dande, B. Gold, and L. A. Marky Thermodynamic and hydration effects for the incorporation of a cationic 3-aminopropyl chain into DNA Nucleic Acids Res., July 15, 2002; 30(14): 3171 - 3180. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. A. Klewer, A. Hoskins, P. Zhang, V. J. Davisson, D. E. Bergstrom, and A. C. LiWang NMR structure of a DNA duplex containing nucleoside analog 1-(2'-deoxy-{beta}-D-ribofuranosyl)-3-nitropyrrole and the structure of the unmodified control Nucleic Acids Res., November 15, 2000; 28(22): 4514 - 4522. [Abstract] [Full Text] [PDF]
|
|