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“Synthesis of oligonucleotides carrying 5’-5’ linkages using copper-catalyzed cycloaddition
reactions” Alvira, M., Eritja, R. Chem. Biodivers., 4(12), 2798-2809 (2007).
PMID: 18081090, doi: 10.1002/cbdv.200790229
Synthesis of Oligonucleotides Carrying 5’-5’ Linkages Using Copper-Catalyzed
Cycloaddition Reactions
by Margarita Alvira and Ramon Eritja*.
Institute for Research in Biomedicine-PCB, Institut de Biologia Molecular de
Barcelona-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials
and Nanomedicine, Josep Samitier 1, E-08028 Barcelona, Spain. (phone:
+34(93)4039942; fax: +34(93)2045904; e-mail : recgma@cid.csic.es)
ABSTRACT
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There is considerable interest in coupling oligonucleotides to molecules and surfaces.
Although amino- and thiol-containing oligonucleotides are being successfully used for this
purpose, cycloaddition reactions may offer greater advantages due to their higher
chemoselectivity and speed. In this study, copper-catalyzed 1,3-dipolar cycloaddition
reactions between oligonucleotides carrying azido and alkyne groups are examined. For this
purpose several protocols for the preparation of oligonucleotides carrying these two groups
are described. The non-templated chemical ligation of two oligonucleotides via copper-
catalyzed [3+2] cycloaddition is described. Using solid-phase methodology
oligonucleotides carrying 5’-5’ linkages can be obtained in good yields.
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Introduction.- Recent years have seen an increasing demand for oligonucleotide
conjugates, while the Human Genome Project has triggered a demand for oligonucleotide
chips. Oligonucleotides carrying amino and thiol groups are the most commonly used
intermediates in the preparation of oligonucleotide conjugates and DNA chips. This is due
to the special reactivity of thiol and amino groups, which allows formation of specific
covalent bonds - thiols react with maleimido and bromoacetamido groups while aliphatic
amino groups are reactive to active esters and isothiocyanates. Although these reactions are
widely used, they are not completely chemoselective in aqueous solvents and hydrolysis
occurs together with the desired coupling reaction, thereby lowering the efficiency of these
reactions.
This drawback has triggered the search for new chemoselective coupling reactions that
may be used for the coupling of biomolecules in aqueous solvents. For example the Diels-
Alder reaction has been described for the preparation of oligonucleotide conjugates [1, 2]
and for the immobilization of oligonucleotides [3, 4].
A further cycloaddition reaction of interest is the [3+2] copper-mediated cycloaddition
[5] or “Click Chemistry” [6]. This particular reaction has had a major impact on
biomolecular research, especially in peptide [7, 8] and protein chemistry [9]. In
oligonucleotide research the development of applications using Click Chemistry has been
slower. This probably reflects the difficulties involved in preparing oligonucleotides
modified with azido and alkynyl groups and the possible role of Cu(I) in producing
hydroxyl radicals that may damage DNA [10-12]. Nevertheless, Seo et al. have shown that
this reaction is useful for the immobilization of oligonucleotides on a chip as a first step for
DNA sequencing [13, 14]. In addition, the preparation of oligonucleotide-carbohydrate
conjugates [15, 16] and the synthesis of bis-nucleosides [17] using Click Chemistry have
been described. Recently, the azide-alkyne cycloaddition reaction has been used for the
template-mediated chemical ligation of two oligonucleotides and for the intramolecular
circularization of a single oligonucleotide [18]
In this paper we seek to develop efficient protocols for the preparation of azido and
alkyne groups. In addition we examine the use of the copper-catalyzed cycloaddition
reaction for the preparation of oligonucleotide derivatives carrying a non-natural 5’-5’
phosphate bond in the middle of the molecule. If the two halves of the oligonucleotide are
complementary, oligonucleotide derivatives of this type may form parallel-stranded
duplexes [19]. If half of the hairpin is a polypurine sequence and the other half is a
polypyrimidine sequence, the resulting parallel-stranded duplex will bind a polypyrimidine
sequence by triple helix formation [20-22]. Our group has been especially interested in this
type of oligonucleotides but until now the standard method for the preparation of parallel-
stranded duplexes has required the use of reversed phosphoramidites which are less
efficient and more expensive [20-22]. The present study seeks to identify the optimal
conditions for preparing parallel-stranded clamps.
Results and Discussion.- 1. Synthesis of oligonucleotides carrying alkynyl groups. A
general method for introducing functional groups at the 5’-end of oligonucleotides involves
the reaction of 5’-amino-oligonucleotides with a compound carrying the desired functional
group linked to a carboxylic acid. Using this approach, Seo et al. described the synthesis of
oligonucleotides carrying a propargyl group at the 5’-end [13]. First, we used a variant of
this method for the preparation of propargyl-oligonucleotides. Oligonucleotide 1 (T8-
5’NH2) was synthesized on a 1 μmol scale. The phosphoramidite of 6-aminohexanol
protected with the monomethoxytrityl [(MeO)Tr] group was used for introducing the amino
group at the 5’-end. After removing the (MeO)Tr group, the resulting amino-
oligonucleotide-support was treated with succinimidyl N-propargyl glutariamidate [13],
followed by cleavage and ammonia deprotection. Using this method, the propargyl
oligonucleotide 2 was obtained in good yield and the mass spectrum of the purified
compound was in agreement with the expected mass.
Alternatively we used the phosphoramidite of 10-hydroxydecanoic acid N-
hydroxysuccinimide ester for the introduction of the N-hydroxysuccinimide ester group at
the 5’-end. Oligonucleotide sequences 4 (A8-5’COOH) and 6 (T8-5’COOH) were
synthesized on a 1 μmol scale. The resulting 5’-carboxy-oligonucleotide-supports were
treated with propargylamine followed by ammonia deprotection. Propargyl-
oligonucleotides 5 and 7 were obtained in good yields and they were characterized by mass
spectrometry. This method was simpler than that described above as the use of
propargylamine avoided the need to prepare succinimidyl N-propargyl glutariamidate.
As a further step in the simplification process, we prepare the phosphoramidite
derivative of an alcohol carrying a terminal alkyne. Commercially available 5-hexyn-1-ol
was reacted with chloro-N,N-diisopropylamino-O-(2-cyanoethoxy) phosphine yielding the
desired phosphoramidite. This phosphoramidite was used to introduce an alkynyl group at
the 5’-end of oligonucleotides 11 (GA-5’alkylnyl) and 12 (CT-5’alkynyl). Alkynyl-
oligonucleotides 11 and 12 were obtained in excellent yields and they were characterized
by mass spectrometry. No oxidation products resulting from the interaction of the iodine
solution used in the DNA synthesizer and the alkyne function were observed.
2. Synthesis of oligonucleotides carrying azido groups. The azido group is not
compatible with the phosphoramidite group because azido groups react with phosphites
yielding phosphoramidates (Staudinger reaction [23]). For this reason azido groups need to
be introduced in the oligonucleotide after the completion of the sequence. The preparation
of oligonucleotides carrying azidonucleosides has also shown that azido groups attached to
the nucleobases are stable to ammonia solutions only at room temperature, but not at higher
temperature [24-26].
First we used the method described by Seo et al [13] for the preparation of
oligonucleotides carrying 5-azido groups introducing some modifications. Oligonucleotide
1 (T8-5’NH2) was synthesized as described above. After the removal of the (MeO)Tr group
the resulting amino-oligonucleotide-support was treated with 5-azidopentanoic acid N-
hydroxysuccinimide ester [13]. The resulting support was treated with concentrated
ammonia at room temperature to avoid azide decomposition [24-26]. Oligonucleotide 3
carrying an azido group at the 5’-end was obtained in good yields as determined by HPLC
analysis. The purified product had the expected mass.
A second protocol based on the iodination of the 5’-end followed by azide displacement
was studied. Oligonucleotide 8 (CT) was synthesized on a 1 μmol scale and the last
dimethoxytrityl [(MeO)2Tr] group was removed. The resulting support was treated with
triphenoxymethylphosphonium iodide as described by Miller and Kool [27] to yield the
iodo-oligonucleotide 9 (CT_I) and the resulting support was treated with sodium azide [11].
Finally, the support was treated with ammonia to yield the 5’-azido-oligonucleotide 10
(CT_N3) in excellent yields as determined by HPLC analysis. The purified oligonucleotide
was characterized by mass spectrometry and enzymatic digestion using snake venom
phosphodiesterase and alkaline phosphatase followed by HPLC analysis [25] showing the
presence of 5-azido-2’,5’-dideoxycytosine.
The success of the previous method suggested the need to prepare of a
phosphoramidite to introduce the halohexyl group at the 5’-end of the oligonucleotide. We
decided to study the potential use of the bromohexyl group in DNA as an intermediate
group in the introduction of the azido group. In addition the hexyl linker would provide less
steric hindrance to the azido group than the previous 5’-azido-2’-deoxynucleoside
derivative.
Starting from commercially available 6-bromohexanol, the phosphoramidite derivative
was prepared. This phosphoramidite was introduced in the DNA synthesizer and
incorporated into the CT oligonucleotide sequence 13. The support carrying the 5’-bromo
oligonucleotide was treated with sodium azide and the resulting support was treated with
concentrated ammonia at room temperature, giving the desired 5’-azido-oligonucleotide 14
(CT_N3hexyl) in good yields. The purified oligonucleotide had the expected mass.
3. Cu-catalyzed cycloaddition of azido-oligonucleotides and alkynyl-oligonucleotides.
Next, the use of copper-catalyzed cycloaddition reactions to chemically ligate two
oligonucleotides was studied. In order to find the optimal conditions for the coupling
reaction, a small excess of T8-5’propargyl (2) was mixed with T8-5’azide (3) in the
presence of either CuSO4/ascorbic acid or CuI as catalyst. Best results were obtained when
a large excess (10-25 times excess) of copper catalyst was used (Figure 1). When the
copper catalyst was only 0.1 equivalents, yields were between 10-15%. The length of the
product of cycloaddition was confirmed by gel electrophoresis. Mass spectrometry gave a
higher mass than expected probably due to the presence of copper ions that were not
completely eliminated by HPLC purification.
In order to facilitate the purification and removal of the copper ions we studied the Cu-
catalyzed cycloaddition reactions on the solid support. The solid support carrying
oligonucleotide sequence T8-5’azide (3) was treated with 2 equivalents of T8-5’propargyl
(2) using a large excess of CuI as catalyst. The resulting support was treated with
concentrated ammonia. Analysis of the reaction by HPLC showed the formation of the
expected product 15 as the major component (data not shown).
Likewise the solid support carrying oligonucleotide sequence CT-N3hexyl (14) was
reacted with T8-5’propargyl (7) and CuI to yield oligonucleotide 17 (Figure 2). This was
also characterized by mass spectrometry and gel electrophoresis.
Tris(benzyltriazolylmethyl)amine (TBTA) has been recommended as a copper ligand to
enhance speed and prevent damage to the oligonucleotides [11, 12]. We compared the
results using TBTA and CuI as catalysts in the reaction between CT-N3hexyl (14) and T8-
5’propargyl (7) to yield oligonucleotide 16. Although the resulting chromatogram was
slightly better when using TBTA, no great differences in the yield were observed. It is
important to notice that the use of Click Chemistry in the oligonucleotide field is strongly
influenced from the negative results described by Kanan et al [12]. These authors treated 17
pmols of an oligonucleotide with a large excess of copper sulphate/ ascorbic acid (more
than 2000 time molar excess) and found approximately 50% degradation of the
oligonucleotide after 10 min at room temperature [12]. These conditions are far away from
the preparative work such as the study described here (150-300 nmols of oligonucleotide in
the presence of 10-20 molar excess of copper). In our conditions we found only a slight
degradation after 2-3 days of treatment as seen by the fast eluting peaks in front of the
desired compound (Figure 2).
Next, the solid support carrying oligonucleotide sequence T8-5’azide (3) was treated
with A8-5’propargyl (5) and CuI (3 mg) as described above. After the reaction, the support
was extensively washed to eliminate the copper ions. The desired oligonucleotide 17 was
obtained in good yield. The purified oligonucleotide 17 was characterized by UV, mass
spectrometry, gel electrophoresis and enzymatic digestion. CD spectra of the purified 17
show the presence of a parallel duplex structure as expected (Figure 3).
When cycloaddition reactions were performed using oligonucleotides 11 and 12
carrying alkynyl groups the cycloaddition reaction resulted in low yields and the final
product could not be isolated (data not shown). Nevertheless, reaction of 5-hexyn-1-ol with
5’-azidothymidine and oligonucleotides 11 and 12 with benzylazide gave the expected
cycloaddition products (Figure 4). Most probably the 5-hexynyl group is not reactive
enough to link two large molecules such as the oligonucleotides, but it may be used for
linking small organic molecules to oligonucleotides. This result is in agreement with Click
reactions involving alkynes without a neighbouring electron-withdrawing group [28, 29].
Conclusions. The synthesis of oligonucleotides carrying alkynyl and the synthesis of
oligonucleotides carrying azido groups were carried out using three methods. We have
demonstrated that the 5’-ends of two oligonucleotides can be chemically linked using a Cu-
catalyzed cycloaddition reaction with the following observations: A) An excess of copper
ions is required. B) CuI is a more efficient catalyst than CuSO4/ascorbic acid. C) The use of
the azido-oligonucleotide anchored still in the solid phase allows the efficient removal of
the excess of copper ions. D) 5-Hexynyl groups are not reactive enough to produce the
cycloaddition products between oligonucleotides.
Oligonucleotides with a parallel duplex structure with 5’-5’ linkages are of interest for
their triplex-forming properties [19-22]. The synthesis of these compounds by the linking
of two parts is a considerable challenge. Previously we sought to link these two parts using
thiol and maleimido groups but our attempts were unsuccessful. Using Click Chemistry,
however, this synthesis has been possible. We believe that the power of this reaction will
enable a large number of oligonucleotide conjugates to be synthesized.
Acknowledgement.
This study was supported by the Institute for Research in Biomedicine (IRB Barcelona), the
Spanish Ministry of Education (NAN2004-09415-C05-03 and BFU2004-02048), the
Generalitat de Catalunya (2005/SGR/00693), the Fundació La Caixa (BM04-52-0), the
Instituto de Salud Carlos III (CIBER-BNN, CB06_01_0019) and the European
communities (Nano-3D NMP4-CT2005-014006). M.A. thanks the Spanish Ministry of
Education for a predoctoral fellowship.
Experimental Part
General. Phosphoramidites and ancillary reagents used during oligonucleotide synthesis
were from Applied Biosystems (PE Biosystems Hispania S.A., Spain), Link technologies
(Link Technologies Ltd, Scotland) and Glen Research (Glen Research Inc., USA). The rest
of the chemicals were purchased from Aldrich, Sigma or Fluka (Sigma-Aldrich Química
S.A., Spain). Solvents were from S.D.S. (S.D.S., France).
Instrumentation. 1H-NMR spectra were measured at 300 MHz on a Varian spectrometer
and 13C NMR spectra were measured at 75 MHz. 31P NMR spectra were recorded at 121
MHz and were externally referenced to 85% phosphoric acid. UV spectra were recorded on
an UV-2301PC Shimadzu spectrophotometers. Mass spectra (electrospray or matrix-
assisted laser desorption ionization time-of-flight, MALDI-TOF) were done at the Mass
spectrometry service at the University of Barcelona. CD spectra were recorded on a Jasco
J-810 spectropolarimeter.
2-Cyanoethyl hex-5-ynyl- N,N-Diisopropylphosphoramidite. 5-hexyn-1-ol (0.54 ml, 5
mmol) was dissolved in dry acetonitrile (6 ml) under argon and N,N-diisopropylethylamine
(2.6 ml, 15 mmol) was added with exclusion of moisture. The solution was cooled on ice
and 2-cyanoethoxy-N,N- diisopropylaminochlorophosphine (1.7 ml, 7.5 mmol) was added
dropwise. The solution was stirred at room temperature for 2 hours. The solvent was then
removed in vacuo and the residue dissolved in dichloromethane with 1 % triethylamine.
The solution was washed with H2O and brine solution, dried over Na2SO4, and evaporated.
The crude product was purified by silica gel column chromatography (1:9 ethyl
acetate/hexane with 4 % triethylamine) to give the desired phosphoramidite (670 mg) as a
pale yellow oil in 46 % yield. 1H NMR (CDCl3) δH: 3.90-3.55 (m, 6H), 2.64 (t, J = 5.4 Hz,
2H), 2.23 (t, J = 6.9 Hz, 2H), 1.95 (t, J = 2.7 Hz, 1H), 1.78-1.57 (m, 4H), 1.18 (d, J = 6.9
Hz, 12H); 13C NMR (CDCl3) δC (two diastereoisomers): 117.6, 84.2, 68.5, 63.2 and 63.0,
58.4 and 58.2, 43.1 and 42.9, 30.2 and 30.1, 24.7 and 24.6, 20.4 and 20.3, 18.1; 31P NMR
(CDCl3) δP: 147.76; MS(CI) Found 299.5 [M + H+] (expected for C15H27N2O2P 298.4).
2-Cyanoethyl-6-bromohexyl-N,N-Diisopropylphosphoramidite. 6-bromohexanol (0.26 ml,
2 mmol) was dissolved in dry acetonitrile (4 ml) under argon and N,N-
diisopropylethylamine (1 ml, 6 mmol) was added with exclusion of moisture. The solution
was cooled on ice and 2-cyanoethoxy-N,N- diisopropylaminochlorophosphine (0.7 ml, 3
mmol) was added dropwise. The solution was stirred at room temperature for 2.5 hours.
The solvent was then removed in vacuo and the residue dissolved in dichloromethane with
1 % triethylamine. The solution was washed with H2O and brine solution, dried over
Na2SO4, and evaporated. The crude product was purified by silica gel column
chromatography (1:9 ethyl acetate/hexane with 4 % triethylamine) to give the desired
phosphoramidite (360 mg) as a pale yellow oil in 47 % yield. 1H NMR (CDCl3) δH: 3.9-
3.76 (m, 2H), 3.7-3.52 (m, 4H), 3.41 (t, J = 6.9 Hz, 2H, -CH2Br), 2.64 (t, J = 6.6 Hz, 2H),
1.92-1.82 (m, 2H), 1.67-1.59 (m, 2H), 1.50-1.36 (m, 4H), 2.35 (d, J = 6.6 Hz, 12H); 13C
NMR (CDCl3) δC (two diastereoisomers): 117.6, 63.6 and 63.4, 58.4 and 58.2, 43.1 and
42.9, 33.8, 32.7, 31.0 and 30.9, 27.8, 25.2, 24.7 and 24.6 and 24.5 (4 -CH3), 20.4 and 20.3;
31P NMR (CDCl3) δP: 147.73; MS(ES) Found 381.3 [M + H+] (expected for
C15H30BrN2O2P 381.3).
Oligonucleotide synthesis. Oligonucleotides sequences were prepared using solid-phase
methodology and 2-cyanoethyl phosphoramidites as monomers. The syntheses were
performed on an Applied Biosystems Model 3400 DNA synthesizer using 0.2 and 1 μmol
scales. After the assembly of sequences, ammonia deprotection was performed overnight at
55 ºC. Oligonucleotides were purified by reverse-phase HPLC. HPLC solutions are as
follows. Solvent A: 5% ACN in 100 mM triethylammonium acetate (pH 6.5) and solvent
B: 70% ACN in 100 mM triethylammonium acetate pH 6.5. Columns: Nucleosil 120C18
(10 μm), 200 x 10 mm. Flow rate: 3 ml/min. Conditions A: 20 min linear gradient from 15-
80% B. Conditions B: 20 min linear gradient from 0-50% B. Conditions C: 20 min linear
gradient from 5-35% B.
Synthesis of oligonucleotides carrying alkynyl groups.
Method 1. Synthesis of oligonucleotides carrying a propargyl group at the 5’-end using the
5’-amino-oligonucleotides. Oligonucleotide 1 (T8-5’NH2, Table 1) was synthesized on 1
μmol scale. The phosphoramidite of 6-(4-monomethoxytrityl [(MeO)Tr])-aminohexanol
was used for the introduction of the amino group at the 5’-end. After the removal of the
(MeO)Tr group the resulting amino-oligonucleotide-support was treated with 20 times
excess of succinimidyl N-propargyl glutariamidate [13] in dioxane for 1 hr at room
temperature. The resulting support was washed and treated with concentrated ammonia at
room temperature for 2 hours. Oligonucleotide 2 was purified by reverse-phase HPLC
(Conditions B). The desired oligonucleotide 2 eluted at 12.5 min (starting T8-5’NH2 eluted
at 11 min). Mass spectrometry (electrospray): Found 2760 (M+ 3Na+); expected for
C94H128N18O59P8, 2701.6.
Method 2. Synthesis of oligonucleotides carrying a propargyl group at the 5’-end using the
5’-carboxy-oligonucleotides. Oligonucleotides 4 (A8-5’COOH) and 6 (T8-5’COOH) were
synthesized on 1 μmol scale. The phosphoramidite of 10-hydroxydecanoic acid N-
hydroxysuccinimide ester (5’carboxy modifier C10, Glen Research) was used for the
introduction of the N-hydroxysuccinimide ester group at the 5’-end. The resulting 5’-
carboxy-oligonucleotide-supports were treated with 10 times excess of propargylamine in
dichloromethane carrying 10% triethylamine for 4 hours at room temperature. The resulting
supports were washed and treated with concentrated ammonia at 55 ºC for 3 hours.
Oligonucleotides 5 and 7 were purified by reverse-phase HPLC. Oligonucleotide 5 eluted at
10.8 min (conditions B). Mass spectrometry found 2728 (M-H); expected for
C93H119N41O42P8, 2730.6. Oligonucleotide 7 eluted at 14.8 min (conditions C). Mass
spectrometry: Found 2657.4 (M-H); expected for C93H127N17O58P8, 2658.4.
Method 3. Synthesis of oligonucleotides carrying an alkynyl group at the 5’-end using the
phosphoramidite derivative of 5-hexyn-1-ol. The 5-hexyn-1-ol phosphoramidite was used
for the introduction of an alkynyl group at the 5’-end of oligonucleotides 11 (GA-
5’alkylnyl) and 12 (CT-5’alkynyl). After ammonia deprotection, the resulting
oligonucleotide were purified by reverse-phase HPLC. Oligonucleotide 11 eluted at 10.3
min (conditions B). Mass spectrometry (MALDI): Found 3636.3 (M-H); expected for
C116H142N55O62P11, 3638.9. Oligonucleotide 12 eluted at 9.7 min (conditions B). Mass
spectrometry (MALDI): Found 3351 (M-H); expected for C110H147N28O72P11, 3353.8.
Synthesis of oligonucleotides carrying azido groups
Method 1. Synthesis of oligonucleotides carrying an azido group at the 5’-end using the 5’-
amino-oligonucleotides. Oligonucleotide 1 (T8-5’NH2) was synthesized on 1 μmol scale as
described above. After the removal of the (MeO)Tr group the resulting amino-
oligonucleotide-support was treated with 20 times excess of succinimidyl 5-azido valerate
[12] in dioxane for 1 hr at room temperature. The resulting support was washed and treated
with concentrated ammonia at room temperature for 2 hours. Oligonucleotide 3 was
purified by reverse-phase HPLC as described above (Conditions B). The desired
oligonucleotide 3 eluted at 13.2 min (starting T8-5’NH2 eluted at 11 min). Mass
spectrometry (electrospray): Found 2716 (M+ 2Na+); expected for C91H126N20O58P8,
2675.5.
Method 2. Synthesis of oligonucleotides carrying a propargyl group at the 5’-end using the
iodination followed by azide displacement. Oligonucleotide 8 (CT) was synthesized on 1
μmol scale and the last DMT group was removed. An aliquot of this support was treated
with concentrated ammonia to yield oligonucleotide 8 (CT) which was purified by HPLC
(retention time, conditions B, 9.7 min) and characterized by mass spectrometry
(electrospray, found 3194.7 expected for C104H138N28O69P10, 3193.7). The resulting support
was treated with triphenoxymethylphosphonium iodide (68 mg, 1 mmol) [24] in DMF (1
ml) to yield the iodo-oligonucleotide 9 (CT_I). An aliquot of this support was treated with
concentrated ammonia to yield oligonucleotide 9 (CT_I) which was purified by HPLC
(retention time, conditions B, 10.9 min) and characterized by mass spectrometry (MALDI,
found 3302.2 (M-H) expected for C104H137N28O68P10I, 3303.6). Finally the support carrying
the 5’-iodo oligonucleotide was treated with sodium azide in DMF overnight at room
temperature. The resulting support was treated with concentrated ammonia at room
temperature for 3 hours yielding the desired 5’-azido-oligonucleotide 10 (CT_N3).
Oligonucleotide 10 was purified by reverse-phase HPLC (Conditions B) eluting at 10.4
min. Mass spectrometry (MALDI) found 3216.9 (M-H) expected for C104H137N31O68P10,
3218.7). The presence of 5-azido-2’,5’-dideoxycytosine at the 5’-end was also confirmed
by enzymatic digestion of the purified 5’azido-oligonucleotide using snake venom
phosphodiesterase and alkaline phosphatase followed by HPLC analysis of the resulting
nucleosides [25].
Method 3. Synthesis of oligonucleotides carrying a propargyl group at the 5’-end using the
phosphoramidite derivative of 6-bromohexanol. The phosphoramidite of 6-bromohexanol
was introduced in the DNA synthesizer and incorporated into the CT oligonucleotide
sequence 13. The support carrying the 5’-bromo oligonucleotide was treated with sodium
azide in DMF overnight at room temperature. The resulting support was treated with
concentrated ammonia at room temperature for 3 hours yielding the desired 5’-azido-
oligonucleotide 14 (CT_N3hexyl). Oligonucleotide 14 was purified by reverse-phase HPLC
(conditions C) eluting at 12 min. Mass spectrometry (MALDI): Found 3397.8 (M-H)
expected for C110H150N31O72P11, 3398.8.
Cu-catalyzed cycloaddition of azido-oligonucleotides and alkynyl-oligonucleotides.
T8-5’propargyl (2) and T8-5’azide (3) to yield oligonucleotide 15 (solution phase). In order
to find the optimal conditions for the coupling reaction a small excess of T8-5’propargyl (2)
was mixed with T8-5’azide (3) in the presence of either CuSO4/ ascorbic acid or CuI as
catalyst. In all cases we used T8-5’propargyl (2, 19.5 nmol), and T8-5’azide (3, 15 nmol).
Four conditions were tested:
1) CuSO4/ ascorbic in low amounts: 2 nmol (0.1 eq) of CuSO4 and 10 nmol (0.5 eq) of
ascorbic acid in 0.35 ml of water / 0.15 ml tert-butanol, room temperature under argon
atmosphere, 48 hours.
2) CuSO4/ ascorbic in low amounts, longer time: 2 nmol (0.1 eq) of CuSO4 and 10 nmol
(0.5 eq) of ascorbic acid in 0.05 ml of water / 0.025 ml tert-butanol, room temperature
under argon atmosphere, 72 hours.
3) CuSO4/ ascorbic in excess: 200 nmol (10 eq) of CuSO4 and 1000 nmol (50 eq) of
ascorbic acid in 0.05 ml of water / 0.025 ml tert-butanol, room temperature under argon
atmosphere, 72 hours with stirring.
4) CuI in excess: 500 nmol (25 eq) of CuI and 6 μmols of DIPEA in 0.03 ml of water / 0.03
ml of acetonitrile, room temperature under argon atmosphere, 40 hours with stirring.
Best results were obtained in trials 3-4 where an excess of the copper catalysts was used
(75% yield). When copper catalyst was only 0.1 equivalents (trials 1-2) yields were
between 10-15%. The presence of the product of cycloaddition was confirmed by gel
electrophoresis. Mass spectrometry gave a higher than expected mass (found 6157,
expected for C185H254N38O117P16, 5377.8) probably due to the presence of copper ions that
were not completely eliminated from the reaction.
T8-5’propargyl (7) and CT-N3hexyl (14) to yield oligonucleotide 16 (solid phase). The
solid support carrying oligonucleotide sequence CT-N3hexyl (14, 100 nmol) was treated
with T8-5’propargyl (7, 500 nmols) in the presence of CuI (4 mg), 4 μl of DIPEA and 2 mg
of ascorbic acid 0.2 ml of water / acetonitrile (1:1) at room temperature, stirring for 48
hours. After the reaction, the support was extensively washed with acetonitrile, a solution
of ascorbic acid (0.02 g/ ml) in water, water, 0.1M EDTA, water and
dichloromethane/methanol (1:1). The resulting support was treated with concentrated
ammonia at 55 ºC for 6 hours. Oligonucleotide 16 was purified by reverse-phase HPLC as
described above (Figure 2). The desired compound was obtained in a 38% yield. The
purified compound was further analyzed by gel electrophoresis. Mass spectrometry
(MALDI): Found 6051.5 (M -H) expected for C203H277N48O130P19, 6056). A similar
experiment was performed but adding 4 mg of TBTA in the mixture. The HPLC profile of
the final product was similar to the experiment without TBTA. The desired compound was
obtained in a 41% yield.
A8-5’propargyl (5) and T8-5’azide (3) to yield oligonucleotide 17 (solid phase). The solid
support carrying oligonucleotide sequence T8-5’azide (3, 150 nmol) was treated with A8-
5’propargyl (5, 300 nmols) in the presence of CuI (3 mg) and 5 μl of DIPEA, as described
above. After the reaction, the support was extensively washed with acetonitrile,
dimethylformamide (DMF), a solution of ascorbic acid (0.02 g/ ml) in DMF/ pyridine 6:5,
DMF, water 0.1M EDTA, water, DMF and dichloromethane/ methanol (1:1). The resulting
support was treated with concentrated ammonia at 55 ºC for 6 hours. Oligonucleotide 17
was purified by reverse-phase HPLC as described above (Conditions C). The desired
oligonucleotide 17 eluted at 14.3 min and was obtained in a 40% yield. Mass spectrometry
(MALDI) found 5501 (M + Cu2+ + Na+) expected for C184H245N61O100P16, 5415.9).
The desired compound was characterized by UV and enzymatic digestion. CD spectra show
the presence of a parallel duplex structure as expected (Figure 3).
CT-5’alkynyl (12) and benzyl azide (solid phase). The solid support carrying
oligonucleotide sequence CT-5’alkynyl (12, 1.6 mg, 50 nmols) was treated with benzyl
azide (2 μl) in the presence of CuI (4 mg), 4 μl of DIPEA and 2 mg of ascorbic acid at
room temperature, in 0.15 ml of water/acetonitrile (1:1) stirring for 17 hours. After the
reaction, the support was extensively washed with acetonitrile, a solution of ascorbic acid
(0.02 g/ ml) in water, water, 0.1M EDTA, water and dichloromethane/methanol (1:1). The
desired compound was obtained as a major product (Figure 4). Mass spectrometry
(MALDI): Found 3489.5, expected 3484.2).
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Table 1: Sequences of Oligonucleotides Prepared.
Number Oligonucleotide Sequencea
1 T8-5’NH2 5’-NH2-(CH2)6-TTTTTTTT-3’
2 T8-5’propargyl 5’-CHC-CH2NHCO(CH2)3CONH-(CH2)6-TTTTTTTT-3’
3 T8-5’azido 5’-N3-(CH2)4CONH-(CH2)6-TTTTTTTT-3’
4 A8-5’COOH 5’-SUOOC-(CH2)9-AAAAAAAA-3’
5 A8-5’propargyl 5’-CHC-CH2NHCO-(CH2)9-AAAAAAAA-3’
6 T8-5’COOH 5’-SUOOC-(CH2)9-TTTTTTTT-3’
7 T8-5’propargyl 5’-CHC-CH2NHCO-(CH2)9-TTTTTTTT-3’
8 CT 5’-CTTCCTCCTCT-3’
9 CT_I 5’-I-CTTCCTCCTCT-3’
10 CT_N3 5’-N3- CTTCCTCCTCT-3’
11 GA-5’alkynyl 5’-CHC-(CH2)4-GAAGGAGGAGA-3’
12 CT-5’alkynyl 5’-CHC-(CH2)4- CTTCCTCCTCT -3’
13 CT_Br 5’-Br-(CH2)6- CTTCCTCCTCT -3’
14 CT_N3hexyl 5’-N3-(CH2)6- CTTCCTCCTCT -3’
15 T8-5’-5’-T8 3’-TTTTTTTT-5’-(CH2)6-NHCO(CH2)4-tri-
CH2NHCO(CH2)3CONH-(CH2)6-TTTTTTTT-3’
16 CT-5’-5’T8 3’-TCTCCTCCTTC-5’-(CH2)6-NHCO(CH2)4-tri-
CH2NHCO-(CH2)9-TTTTTTTT-3’
17 T8-5’-5’-A8 3’-TTTTTTTT-5’-(CH2)6-NHCO(CH2)4-tri-CH2NHCO-
(CH2)9-AAAAAAAA-3’
a SU: N-hydroxysuccinimide ester, tri: 1,2,3-triazol.
LEGENDS
Scheme 1. Copper-Catalyzed [3+2] Cycloaddition or Click Chemistry Between
Oligonucleotides Carrying Azido and Alkynyl Groups.
Scheme 2. Protocols for the Synthesis of Oligonucleotides Carrying Alkynyl Groups at the
5’-end: A) using 5’-amino-oligonucleotides, B) using 5’-carboxy-oligonucleotides and C)
using the phosphoramidite derivative of 5-hexyn-1-ol.
Scheme 3. Protocols for the Synthesis of Oligonucleotides Carrying Azido Groups at the 5’-
end: A) using 5’-amino-oligonucleotides, B) via 5’-iodo-oligonucleotides, and C) using the
phosphoramidite derivative of 6-bromohexanol.
Figure 1. HPLC profile of Cu-catalyzed cycloaddition between T8-5’propargyl (2) and T8-
5’azido (3) to yield oligonucleotide 15 (solution phase) using 19 eq of CuSO4/ascorbic acid
(trial 3).
Figure 2. HPLC profile Cu-catalyzed cycloaddition between T8-5’propargyl (7) and CT-N3hexyl
(14) to yield oligonucleotide 16 (solid phase) using CuI.
Figure 3. CD spectra of oligonucleotide 17 and T8-5’azido 3 (1M NaCl, 50 mM sodium
phosphate/ citric acid pH 7.0). The CD spectrum of oligonucleotide 17 contains a strong
maximum at 217 nm and a strong minimum at 248 nm as described for parallel reversed Watson-
Crick [15].
Figure 4. HPLC profile of Cu-catalyzed cycloaddition between CT-5’alkynyl (12) and benzyl
azide.
Scheme 1
OLIGONUCLEOTIDE
3' 5'
N
N
+
N
–
OLIGONUCLEOTIDE
5' 3'
N
N
N
OLIGONUCLEOTIDE
3' 5'
OLIGONUCLEOTIDE
5' 3'
Scheme 2
OLIGONUCLEOTIDE
3' 5'
(CH
2
)
6
-NH
2
OLIGONUCLEOTIDE
3' 5'
(CH
2
)
6
-NH H
N
O
O
A)
OLIGONUCLEOTIDE
3' 5'
(CH
2
)
9
-COO
OLIGONUCLEOTIDE
3' 5'
(CH
2
)
9
H
N
O
B)
N
O
O
OLIGONUCLEOTIDE
3' 5'
OH
OLIGONUCLEOTIDE
3' 5'
OPO
3
C)
Scheme 3
OLIGONUCLEOTIDE
3' 5'
(CH
2
)
6
-NH
2
OLIGONUCLEOTIDE
3' 5'
(CH
2
)
6
-NH N
3
O
A)
OLIGONUCLEOTIDE
3' 5'
OH
OLIGONUCLEOTIDE
3' 5'
OPO
3
C)
Br
OLIGONUCLEOTIDE
3' 5'
OPO
3
N
3
OLIGONUCLEOTIDE
3' 5'
OH
B)
OLIGONUCLEOTIDE
3' 5'
I
OLIGONUCLEOTIDE
3' 5'
N
3
Figure 1
Figure 2
0
0,1
0,2
0,3
0,4
0,5
0,6
0 5 10 15 20
Figure 3
-20
-15
-10
-5
0
5
10
15
20
25
30
200 220 240 260 280 300 320 340 360
Wavelength [nm]
CD [mdeg]
3
17
Figure 4
0
0,01
0,02
0,03
0,04
0,05
0,06
0,07
0,08
0,09
0 5 10 15 20
Graphical illustration for the table of contents
OLIGONUCLEOTIDE
3' 5'
N3
N
NN
CCH OLIGONUCLEOTIDE
3' 5'
OLIGONUCLEOTIDE
3'5'
OLIGONUCLEOTIDE
3' 5'
