Synthesis of Novel Phosphoramidite Building Blocks from Pentaerythritol

Article abstract of DOI:10.1055/s-2003-41406

The synthesis of four types of phosphoramidites containing various protecting groups (DMTr, TBDMS, Lev) has been achieved starting from pentaerythritol. The protecting groups can be deprotected selectively in an orthogonal manner.

Full text of DOI:10.1055/s-2003-41406

1838
LETTER
Synthesis of Novel Phosphoramidite Building Blocks from Pentaerythritol
P
hosphoramid
u
ite Building Block
J
s
eong Kim, Eun-Kyoung Bang, Byeang Hyean Kim*
National Research Laboratory, Department of Chemistry, Division of Molecular and Life Sciences, Pohang University of Science and
Technology, San 31 Hyoja Dong, Pohang 790-784, Korea
Fax +82(54)2793399; E-mail: bhkim@postech.ac.kr
Received 14 July 2003
used to protect the 2¢-hydroxyl group of RNA phospho-
Abstract: The synthesis of four types of phosphoramidites contain-
ramidite, and here we have adapted it because we required
ing various protecting groups (DMTr, TBDMS, Lev) has been
a moiety having deprotection conditions that are different
achieved starting from pentaerythritol. The protecting groups can be
from those of the DMTr group. Finally, we selected the
Lev group because it has been used, in conjunction with
the DMTr group, for preparing asymmetric triply
branched ODNs.9 Based on these prior results, we de-
signed and synthesized various phosphoramidite mono-
mers using combinations – either the same or different –
of these three protecting groups.
deprotected selectively in an orthogonal manner.
Key words: protecting groups, chemoselectivity, alcohols, DNA,
oligonucleotides
The controllable formation of nanoscale architectures in
solution and on solid supports is a central requirement for
a range of activities in the emerging field of nanotechnol-
ogy.1 DNA molecules are well suited for these purposes
because of their unique molecular recognition features.
Linear DNA chains can be made to assemble into a range
of non-linear structures by inducing branching of double
helices through the incorporation of non-complementary
sequences in the component strands.2 More-versatile
building blocks can be designed in which DNA chains are
linked through components that take no part in double he-
lix formation. For example, dendrimers3 with arms termi-
nating in oligodeoxyribonucleotides (ODNs) of the same4
or different5 sequences have been used to build cages,
cryptands, tubes, nets, scaffolds and other more-complex
three-dimensional (3-D) structures. For the construction
of programmed nanostructures, there has been an increase
in the importance of branched ODNs, especially heterose-
quence-containing branched ODNs, as vertices of nano-
structures such as tetrahedra and cubes. For this purpose,
both triply and quadruply branched ODNs have been syn-
thesized using phosphoramidite monomers.6 In this paper,
we report not only the design and synthesis of novel sym-
metrical and unsymmetrical building blocks that are use-
ful for constructing quadruply branched ODNs, but also
the conditions for removing their several different protect-
ing groups.
Figure 1 Phosphoramidite monomers.
The four pentaerythritol-derived phosphoramidite mono-
mers were synthesized as shown in Scheme 1. Treatment
of pentaerythritol (5) with DMTr-Cl (2.5 equiv) in the
presence of DMAP in pyridine gave the mono-, bis-, and
tris-O-DMTr-protected products in 7%, 12%, and 70%
yields, respectively. The tris(DMTr)-protected compound
was reacted with chloro-(2-cyanoethyl)-N,N-diisopropyl-
aminophosphine (CEP-Cl) in the presence of DIPEA in
THF to prepare the symmetrical phosphoramidite build-
ing block 1 in 35% yield. TBDMS-Cl was reacted with the
bis(DMTr)-protected compound
7
to afford the
bis(DMTr)-mono-TBDMS-protected compound. This
compound could not, however, be made to react with
CEP-Cl because of steric hindrance by the bulky protect-
ing groups. For this reason, we chose to replace the TB-
DMS group with the Lev group, and with this change we
were able to synthesize the desired phosphoramidite prod-
uct 2 in 77% yield. When the mono-DMTr-protected
pentaerythritol was reacted with levulinic acid (1.2
equiv), both the mono- and bis(Lev)-protected products
were obtained. The bis(Lev)-protected compound 10 was
converted to the phosphoramidite 3 in 61% yield. The
mono-Lev-protected compound 11 was protected with the
TBDMS group and then converted to the phosphoramidite
4 in 50% yield.
We designed the phosphoramidite molecules7 1–4 as
branching points for ODNs (Figure 1). For the synthesis
of 1–4, we choose three protecting groups [dimethoxy-
trityl (DMTr), tert-butyldimethylsilyl (TBDMS), and le-
vulinyl (Lev)] for the hydroxyl groups of pentaerythritol
(5). Because it can be easily and virtually quantitatively
deprotected by trichloroacetic acid, the DMTr group is
used generally in ODN syntheses using the phosphora-
midite method.8 The TBDMS protecting group has been
Synlett 2003, No. 12, Print: 29 09 2003. Web: 28 08 2003.
Art Id.1437-2096,E;2003,0,12,1838,1840,ftx,en;U13503ST.pdf.
DOI: 10.1055/s-2003-41406
© Georg Thieme Verlag Stuttgart · New York

LETTER
Phosphoramidite Building Blocks
1839
Scheme 1 Reagents and conditions: (a) DMTr-Cl, DMAP, Py; (b) 6, CEP-Cl, DIPEA, THF; (c) 7, levulinic acid, EDC, DMAP, CH2Cl2; (d)
9, CEP-Cl, DIPEA, THF; (e) 8, levulinic acid, EDC, DMAP, CH2Cl2; (f) 10, CEP-Cl, DIPEA, THF; (g) 11, TBDMS-Cl, Et3N, CH2Cl2; (h) 12,
CEP-Cl, DIPEA, THF.
The DMTr, Lev, and TBDMS moieties are virtually
orthogonal protecting groups; i.e., each one is susceptible
to specific deprotection conditions. The DMTr group can
be cleanly removed using trichloroacetic acid or ZnBr2 in
CH2Cl2 solution; the Lev and TBDMS groups are quite
stable under either of these conditions. The Lev protecting
group can be deprotected selectively by using buffered
hydrazine hydrate.6c,d,9 The TBDMS protecting group can
be deprotected by using tetrabutylammonium fluoride;
Figure 2 Order of reactions for the synthesis of quadruply branched
ODNs.
unfortunately, under this deprotection condition, the Lev
group is also cleaved (Scheme 2). On the basis of these
properties, we propose that branched ODNs containing
four different base sequences should be amenable to syn- ly, we are using these compounds to prepare branched
thesis based on the order of reactions shown in Figure 2. ODNs having homo- and hetero-sequences.
Additionally, it should be possible to synthesize sym-
metrical, quadruply branched ODNs10 by using phospho-
Acknowledgment
ramidites 1–3.
We are grateful to KISTEP for financial support through the NRL
(Lab. for Modified Nucleic Acid Systems) program. S.J.K. and
E.-K.B. thank the Ministry of Education for the BK21 fellowship.
References
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2
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In summary, we have synthesized four different, non-nu-
cleoside phosphoramidite monomers based on pen-
taerythritol. These compounds should be amenable to the
preparation of a versatile range of compounds, such as
quadruply branched ODNs, dendrimers, and materials for
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Synlett 2003, No. 12, 1838–1840 © Thieme Stuttgart · New York

1840
S. J. Kim et al.
LETTER
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(m/z): [M + H]+ calcd for C61H72N2O11P, 1039.4874; found,
1039.4877. 3: Reaction of CEP-Cl (74 mL, 0.33 mmol), 10
(141 mg, 0.222 mmol), and DIPEA (77 mL, 0.445 mmol) in
THF (6 mL) for 30 min, followed by the workup described
above, provided 3 as a yellow oil (114 mg, 0.135 mmol,
61%). 1H NMR (300 MHz, CDCl3): d = 7.40–7.38 (m, 2 H),
7.29–7.26 (m, 7 H), 6.82 (d, J = 8.7 Hz, 4 H), 4.17–4.12 (m,
4 H), 3.78 (s, 6 H), 3.73–3.65 (m, 2 H), 3.61–3.51 (m, 2 H),
3.15 (s, 2 H), 2.68 (t, J = 6.5 Hz, 4 H), 2.56 (t, J = 6.3 Hz, 2
H), 2.48 (t, J = 6.5 Hz, 4 H), 2.16 (s, 6 H), 1.25 (d, J = 6.7
Hz, 2 H), 1.16 (d, J = 6.7 Hz, 6 H), 1.10 (d, J = 6.7 Hz, 6 H);
13C NMR (75.5 MHz, CDCl3): d = 205.8, 171.8, 158.0,
158.0, 144.2, 135.3, 135.0, 129.7, 127.7, 127.4, 127.3,
126.3, 117.2, 112.6, 112.5, 85.8, 85.5, 62.6, 61.6, 61.4, 60.2,
57.9, 57.7, 54.7, 46.9, 43.5, 42.7, 42.5, 37.3, 30.5, 29.3, 27.3,
24.2, 24.1, 22.1, 20.7, 19.9, 19.8; 31P NMR (121.5 MHz,
CDCl3): d = 150.7; HR-FABMS (m/z): [M + Na]+ calcd for
C45H59N2O11PNa, 857.3754; found, 857.3759. 4: Reaction
of CEP-Cl (114 mL, 0.518 mmol), 12 (134.8 mg, 0.207
mmol), and DIPEA (144 mL, 0.828 mmol) in THF (4.2 mL)
for 90 min, followed by the workup described above,
provided 4 as a yellow oil (86.2 mg, 0.101 mmol, 50%). 1H
NMR (300 MHz, CDCl3): d = 7.41–7.38 (m, 2 H), 7.29–7.17
(m, 7 H), 6.79 (d, J = 8.9 Hz, 4 H), 4.11–4.09 (m, 2 H), 3.76
(s, 6 H), 3.70–3.52 (m, 8 H), 3.12 (s, 2 H), 2.66–2.64 (m, 2
H), 2.53–2.45 (m, 4 H), 2.15 (s, 3 H), 1.14 (d, J = 6.8 Hz, 6
H), 1.08 (dd, J1 = 6.7, J2 = 1.4 Hz, 6 H), 0.08 (d, J = 1.1 Hz,
9 H), –0.03 (d, J = 2.4 Hz, 6 H); 13C NMR (75.5 MHz,
CDCl3): d = 205.9, 171.9, 157.9, 144.6, 135.7, 129.7, 127.2,
126.1, 117.2, 112.5, 85.3, 63.2, 61.0, 60.4, 57.7, 54,7, 45.0,
42.6, 42.5, 37.4, 29.4, 27.3, 25.3, 24.2, 24.1, 19.9, 19.8, 17.7,
–6.12; 31P NMR (121.5 MHz, CDCl3): d = 150.3, 150.1; HR-
FABMS (m/z): [M + Na]+ calcd for C46H67N2O9PSiNa,
873.4251; found, 873.4252.
(7) Reaction conditions and selected spectroscopic data. 1:
CEP-Cl (297 mL, 1.34 mmol) was added to a solution of 6
(560 mg, 0.537 mmol) and DIPEA (187 mL, 1.074 mmol) in
THF (6 mL). The reaction mixture was stirred at room
temperature for 80 min and then 5% NaHCO3 solution and
EtOAc were added. The organic layer was separated, dried
over MgSO4, and concentrated under reduced pressure.
Purification by flash chromatography provided 1 as a
colorless oil (236 mg, 0.190 mmol, 35%). 1H NMR (300
MHz, CDCl3): d = 7.27–7.14 (m, 27 H), 6.72–6.68 (m, 12
H), 4.11 (q, J = 6.7 Hz, 2 H), 3.75 (s, 18 H), 3.39–3.23 (m, 8
H), 2.23 (t, J = 6.3 Hz, 2 H), 2.03 (s, 2 H), 1.31–1.22 (m, 4
H), 1.09 (d, J = 6.7 Hz, 6 H), 0.95 (d, J = 6.7 Hz, 6 H); 13
C
NMR (75.5 MHz, CDCl3): d = 157.7, 144.7, 135.8, 129.7,
127.8, 127.1, 126.0, 112.5, 85.1, 62.3, 57.7, 54.7, 42.5, 24.1,
24.0, 13.7; 31P NMR (121.5 MHz, CDCl3): d = 148.9; HR-
ESIMS (m/z): [M + Na]+ calcd for C77H83N2O11PNa,
1243.5852; found, 1243.5807. 2: Reaction of CEP-Cl (166
mL, 0.74 mmol), 9 (319.7 mg, 0.37 mmol), and DIPEA (260
mL, 1.48 mmol) in THF (4 mL) for 90 min, followed by the
workup described above, provided 2 as a yellow oil (302.8
mg, 0.29 mmol, 77%). 1H NMR (300 MHz, CDCl3): d = 7.24
(d, J = 7.2 Hz, 4 H), 7.17–7.09 (m, 14 H), 6.67 (d, J = 8.4 Hz,
8 H), 4.02 (q, J = 10.7 Hz, 2 H), 3.68 (s, 12 H), 3.66–3.37 (m,
6 H), 3.17–3.14 (m, 4 H), 2.50 (t, J = 7.0 Hz, 2 H), 2.35 (t, J
= 6.3 Hz, 2 H), 2.28 (t, J = 6.7 Hz, 2 H), 2.05 (s, 3 H), 1.21
(t, J = 5.7 Hz, 4 H), 1.05 (d, J = 6.7 Hz, 6 H), 0.94 (d, J = 6.7
Hz, 6 H); 13C NMR (75.5 MHz, CDCl3): d = 172.5, 158.8,
145.2, 136.2, 130.5, 128.4, 127.9, 126.8, 117.9, 113.2, 86.0,
61.6, 60.6, 55.4, 43.3, 43.1, 38.0, 30.0, 28.0, 24.8, 24.7, 14.4;
31P NMR (121.5 MHz, CDCl3): d = 150.2; HR-FABMS
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Synlett 2003, No. 12, 1838–1840 © Thieme Stuttgart · New York