The synthesis of 3'- and 5'-iminodiacetic acid derivatives of thymidine and their incorporation into synthetic oligonucleotides

Article abstract of DOI:10.1016/S0040-4039(00)00583-9

The syntheses of thymidines modified with iminodiacetic acid (IDA) at the 3' (1) or 5' (2) positions have been accomplished. These modified nucleotides have been incorporated into synthetic oligonucleotides. (C) 2000 Elsevier Science Ltd.

Full text of DOI:10.1016/S0040-4039(00)00583-9

TETRAHEDRON
LETTERS
Pergamon
Tetrahedron Letters 41 (2000) 4035–4037
The synthesis of 30- and 50-iminodiacetic acid derivatives of
thymidine and their incorporation into synthetic oligonucleotides
M. Devan Jonklaas and Robert R. Kane ∗
Department of Chemistry and Biochemistry and Center for Drug Discovery, Baylor University, Waco, Texas 76798-7348, USA
Received 18 February 2000; revised 20 March 2000; accepted 23 March 2000
Abstract
The syntheses of thymidines modified with iminodiacetic acid (IDA) at the 30 (1) or 50 (2) positions have been
accomplished. These modified nucleotides have been incorporated into synthetic oligonucleotides. © 2000 Elsevier
Science Ltd. All rights reserved.
Metal ions play important structural and functional roles in oligonucleotide chemistry and biology due
to the myriad complex interactions between various metal ions and the nucleobases or anionic phospho-
diester backbone.1–7 The tools of organic synthesis have played a significant role in the study of such
interactions, especially by facilitating the construction and modification of designed ion/oligonucleotide
complexes via the introduction of unnatural metal binding sites into predetermined sites within synthetic
oligonucleotides.8–11
Our group’s interest in this area is focused upon developing methods to utilize multiple ligands,
predictably organized in space, to bind metal ions in precise locations. This work is inspired by reports
from the groups of Ghadiri12,13 and Hopkins,14 who demonstrated that multipoint metal ion binding
could be used to stabilize secondary structure in small peptides. We have taken a complimentary
approach, in that we intend to use the secondary structure of small synthetic oligonucleotides to
template the formation of metal-binding sites. We have chosen to introduce the metal-binding residues
into synthetic oligonucleotides during their solid-phase synthesis as novel phosphoramidite monomers.
Accordingly, we herein report the synthesis of iminodiacetic acid modified thymidines, their conversion
∗
Corresponding author.
0040-4039/00/$ - see front matter © 2000 Elsevier Science Ltd. All rights reserved.
PII: S0040-4039(00)00583-9
tetl 16862

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to phosphoramidites suitable for use in solid-phase DNA synthesis, and their incorporation into small
synthetic oligonucleotides.
Both syntheses are straightforward, beginning with the known 30 or 50-azido thymidines (3 or
4, respectively; Scheme 1), which were cleanly reduced to the corresponding amino nucleosides by
treatment with 1,3-propanedithiol.15 Dialkylation of these amines with ethyl bromoacetate provided the
penultimate esters 5 and 6. These esters were prepared for incorporation into synthetic oligonucleotides
by reaction of the free hydroxyl groups (50 or 30, respectively), with 2-cyanoethyl diisopropylchlorophos-
phoramidite, thereby converting them to phosphoramidites 7 and 8 (Scheme 2).
Scheme 1. Synthesis of iminodiesters 5 and 6
Scheme 2. Synthesis of free acids 9 and 10 and phosphoramidites 7 and 8
These phosphoramidites are efficiently installed as the terminal residue during oligonucleotide synthe-
sis, and the free iminodiacetate ligand is revealed by a careful two-step saponification/oligo deprotection
protocol.9 In order to preserve the natural 30-50 linkages, the 50-IDA amidite 7 was added in the final
step of a reverse-orientation 50-30 oligonucleotide synthesis (Scheme 3). Oligonucleotide compositions
were verified using MALDI mass spectrometry, and the oligo purities were evaluated using capillary
gel electrophoresis. Diesters 5 and 6 were also directly hydrolyzed to afford the monomeric nucleoside
ligands 9 and 10.
With oligonucleotides fitted with the iminodiaceticacid ligands in hand, we are presently evaluating
the ability of these macromoleculecules to preorganize high affinity metal ion binding sites. Results from
these studies will be reported elsewhere.
Acknowledgements
Financial support from the Robert A. Welch Foundation (Grant #AA-1355) is gratefully acknowled-
ged. Supporting information (NMR’s, HPLC’s, detailed experimental procedures, etc.) are available
directly from the authors.

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Scheme 3. Synthesis of iminodiacetic acid substituted oligonucleotides
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