Perylene diimide-oligonucleotide conjugates constructed by click chemistry

Article abstract of DOI:10.1080/15257770701490936

Oligonucleotide conjugates were prepared by copper-catalyzed cycloaddition of acetylene-modified oligonucleotides to diazido derivative of perylene 3,4,9,10-tetracarboxylic acid diimide. Copyright Taylor & Francis Group, LLC.

Full text of DOI:10.1080/15257770701490936

This article was downloaded by: [Brown University]
On: 15 January 2013, At: 19:05
Publisher: Taylor & Francis
Informa Ltd Registered in England and Wales Registered Number: 1072954 Registered
office: Mortimer House, 37-41 Mortimer Street, London W1T 3JH, UK
Nucleosides, Nucleotides and Nucleic
Acids
Publication details, including instructions for authors and
subscription information:
http://www.tandfonline.com/loi/lncn20
Perylene Diimide–Oligonucleotide
Conjugates Constructed by Click
Chemistry
Alexey V. Ustinov a , Veronika V. Dubnyakova a & Vladimir A. Korshun
a
a Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian
Academy of Sciences, Moscow, Russia
Version of record first published: 10 Dec 2007.
To cite this article: Alexey V. Ustinov , Veronika V. Dubnyakova & Vladimir A. Korshun (2007):
Perylene Diimide–Oligonucleotide Conjugates Constructed by Click Chemistry, Nucleosides,
Nucleotides and Nucleic Acids, 26:6-7, 751-754
To link to this article: http://dx.doi.org/10.1080/15257770701490936
PLEASE SCROLL DOWN FOR ARTICLE
Full terms and conditions of use: http://www.tandfonline.com/page/terms-and-conditions
This article may be used for research, teaching, and private study purposes. Any
substantial or systematic reproduction, redistribution, reselling, loan, sub-licensing,
systematic supply, or distribution in any form to anyone is expressly forbidden.
The publisher does not give any warranty express or implied or make any representation
that the contents will be complete or accurate or up to date. The accuracy of any
instructions, formulae, and drug doses should be independently verified with primary
sources. The publisher shall not be liable for any loss, actions, claims, proceedings,
demand, or costs or damages whatsoever or howsoever caused arising directly or
indirectly in connection with or arising out of the use of this material.

Nucleosides, Nucleotides, and Nucleic Acids, 26:751–754, 2007
Copyright ꢀ Taylor & Francis Group, LLC
C
ISSN: 1525-7770 print / 1532-2335 online
DOI: 10.1080/15257770701490936
PERYLENE DIIMIDE–OLIGONUCLEOTIDE CONJUGATES
CONSTRUCTED BY CLICK CHEMISTRY
Alexey V. Ustinov, Veronika V. Dubnyakova, and Vladimir A. Korshun
2
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences,
Moscow, Russia
Oligonucleotide conjugates were prepared by copper-catalyzed cycloaddition of acetylene-modified
2
oligonucleotides to diazido derivative of perylene 3,4,9,10-tetracarboxylic acid diimide.
Keywords Oligonucleotides; conjugates; click chemistry; perylene diimide; [3+2]
cycloaddition
The copper-catalyzed cycloaddition reaction of azides to alkynes[1,2]
(Scheme 1) is a remarkable representative of so-called “click-chemistry”[3]
reactions that are useful for bioconjugate synthesis. The process is being
carried out regioselectively in mild conditions, tolerated by a majority of
functional groups, affords great opportunities for the preparation of modi-
fied oligonucleotides,[4,5] and oligonucleotide immobilization.[6]
Conjugates of oligonucleotides with photostable perylene diimide
dyes were extensively studied because of their interesting ability to self-
assembly.[7−9] The perylene diimide moiety located in the middle of
an oligonucleotide strand is known to increase its propensity to triplex
formation.[10,11]
Although phosphoramidite reagents[9,10] were used to introduce pery-
lene diimide into the strand, the preparation of conjugates with two strands
of the same polarity flanking a single dye is not straightforward. Herein we
would like to report a click chemistry approach to these products.
An introduction of reactive group into an oligonucleotide is required
for conjugation to take place. Since the azido group is incompatible with
This research was supported by grants from the Russian Foundation for Basic Research (projects
06-04-81019 and 06-03-32426). We thank Vadim V. Shmanai, Sergey V. Gontarev, and Maksim V. Kvach
for oligonucleotide synthesis; Andrei D. Malakhov, Igor A. Prokhorenko, and Mikhail V. Skorobogatyi
for helpful discussions; and Larisa V. Grusintseva for technical assistance.
Address correspondence to Alexey V. Ustinov, Shemyakin-Ovchinnikov Institute of Bioorganic
Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia. E-mail:
austinov@mail.ibch.ru
751

752
A. V. Ustinov et al.
SCHEME 1 Copper-catalyzed cycloaddition of azides to alkynes.
SCHEME 2 Synthesis of acetylenic oligonucleotides
phosphoramidite synthesis because of Staudinger reaction,[12] we de-
cided to introduce a terminal alkyne using a dihydroxybutyramide[13]
reagent 1 prepared from propargylamine and (R)-2-hydroxybutyrolactone
(Scheme 2).
Oligonucleotides (Table 1) were prepared from reagent 1 and solid sup-
port 2 by means of standard oligonucleotide synthesis.
Perylene diimide-derived diazide 3 prepared from perylenetetracar-
boxylic acid dianhydride in two steps (Scheme 3) was then coupled to
oligonucleotides to give corresponding conjugates (Table 2). The reaction
SCHEME 3 Synthesis of perylene diimide-oligonucleotide conjugates.

Perylene Diimide–Oligonucleotide Conjugates
753
TABLE 1 Oligonucleotides
containing terminal alkyne (X =
residue of 1)
#
Sequence, 5ꢁ → 3ꢁ
ON1
ON2
XCA-TTA-CAT-CCA-GAC
XGT-CTG-GAT-GTA-ATG
TABLE 2 Yields of conjugates of acetylenic oligonucleotides with diazide 3
Productsa
Monoadduct
Diadduct
MALDIb
Starting
oligonucleotide
Oligonucleotide/azide
Yield
MALDIb
Yield
ON1
ON1
ON2
ON2
1:1
2:1
1:1
2:1
36%
—
35%
—
5029.8/5028.5
42%
41%
35%
59%
9444.7/9439.4
9729.2/9723.6
5171.1/5170.6
a
Isolated yield (PAGE), determined by UV absorbance
MALDI-TOF mass (M+H), found/calculated
b
was carried out in aq. DMSO under argon. Tris[(1-benzyltriazol-4-
yl)methyl]amine[14] was used as a ligand for Cu(I) species to decrease
copper oxidation accompanied by free hydroxyl radical (·OH) formation
leading to oligonucleotide cleavage. Heating (95o C to rt, overnight) was
required to facilitate dissolution of azide and increase overall yield of
conjugation.
The conjugates can be isolated either by PAGE or by HPLC. It is possible
to prepare diadducts of oligonucleotides ON1 and ON2 selectively using 2
equiv. of oligonucleotide.
We are planning to study the fluorescent properties of these conjugates
as well as their use for assembly of DNA-nanostructures.[15]
REFERENCES
1. Tornøe, C.W.; Christensen, C.; Meldal, M. Peptidotriazoles on solid phase: [1,2,3]-triazoles by re-
giospecific copper(I)-catalyzed 1,3-dipolar cycloadditions of terminal alkynes to azides. J. Org. Chem.
2002, 67(9), 3057–3064.
2. Rostovtsev, V.V.; Green, L.G.; Fokin, V.V.; Sharpless, K.B. A stepwise Huisgen cycloaddition process:
Copper(I)-catalyzed regioselective ligation of azides and terminal alkynes. Angew. Chem. Int. Ed.
2002, 41(14), 2596–2599.
3. Kolb, H.C.; Finn, M.G.; Sharpless, K.B. Click chemistry: Diverse chemical function from a few good
reactions. Angew. Chem. Int. Ed. 2001, 40(11), 2004–2021.
4. Gartner, Z.J.; Grubina, R.; Calderone, C.T.; Liu, D.R. Two enabling architectures for DNA-templated
organic synthesis. Angew. Chem. Int. Ed, 2003, 42(12), 1370–1375.
5. Ustinov, A.V.; Korshun, V.A. Oligonucleotides containing arylacetylene residues: Synthesis and post-
synthetic modification via [3+2] cycloaddition. Russ. Chem. Bull. 2006, 55(7), 1268–1274.

754
A. V. Ustinov et al.
6. Devaraj, N.K.; Miller, G.P.; Ebina, W.; Kakaradov, B.; Collman, J.P.; Kool, E.T.; Chidsey, C.E.D.
Chemoselective covalent coupling of oligonucleotide probes to self-assembled monolayers. J. Am.
Chem. Soc. 2005, 127(24), 8600–8601.
7. Abdalla, M.A.; Bayer, J.; Ra¨dler, J.O.; Mu¨llen, K. Synthesis and self-assembly of perylenediimide-
oligonucleotide conjugates.Angew. Chem. Int. Ed. 2004, 43(30), 3967–3970.
8. Zheng, Y.; Long, H.; Schatz, G.C.; Lewis, F.D. Duplex and hairpin dimer structures for perylene
diimide-oligonucleotide conjugates. Chem. Comm. 2005, 4795–4797.
9. Wagner, C.; Wagenknecht, H.-A. Perylene-3,4:9,10-tetracarboxylic acid diimide dye as an artificial
DNA base surrogate. Org. Lett. 2006, 8(19), 4191–4194.
10. Bevers, S.; OꢁDea, T.P.; McLaughlin, L.W. Perylene- and naphthalene-based linkers for duplex and
triplex stabilization. J. Am. Chem. Soc. 1998, 120(42), 11004–11005.
11. Bevers, S.; Schutte, S.; McLaughlin, L.W. Naphthalene- and perylene-based linkers for the stabiliza-
tion of hairpin triplexes. J. Am. Chem. Soc. 2002, 122(25), 5905–5915.
12. Bra¨se, S.; Gil, C.; Knepper, K.; Zimmermann, V. Organic azides: An exploding diversity of a unique
class of compounds. Angew. Chem. Int. Ed. 2005, 44(33), 5188–5240.
13. Dioubankova, N.N.; Malakhov, A.D.; Stetsenko, D.A.; Gait, M.J.; Korshun, V.A. Phosphoramidites
and solid supports based on N-substituted 2,4-dihydroxybutyramides: universal reagents for synthe-
sis of modified oligonucleotides. Tetrahedron, 2006, 62(29), 6762–6773.
14. Chan, T.R.; Hilgraf, R.; Sharpless, K.B.; Fokin, V.V. Polytriazoles as copper(I)-stabilizing ligands in
catalysis. Org. Lett. 2004, 6(17), 2853–2855.
15. Detailed procedures and compound characterization will be reported elsewhere.