a hydrogen atmosphere. After 3 h, TLC showed completion of the
reaction, and the mixture was filtered through Celite and washed
with 5:1 CH2Cl2/MeOH to afford compound 4 as a tan solid (2.73
g, 97%): 1H NMR (300 MHz, DMSO-d6) δ (ppm) 10.69 (br, 1H),
7.59 (s, 1H), 7.42 (d, J ) 7.5 Hz, 2H), 7.35-7.17 (m, 7H), 6.88
(dd, J ) 8.7, 1.6 Hz, 4H), 6.48 (br, 2H), 5.40 (d, J ) 4.0 Hz, 1H),
4.11-3.90 (m, 3H), 3.74 (s, 6H), 2.98 (dd, J ) 8.6, 3.7 Hz, 1H),
2.90 (dd, J ) 8.6, 3.4 Hz, 1H); 13C NMR (75 MHz, DMSO-d6) δ
(ppm) 158.0, 156.9, 153.4, 151.3, 144.9, 138.0, 135.6, 129.7, 127.7,
126.6, 116.4, 113.1, 85.3, 68.0, 65.7, 55.0, 46.3; IR (film) ν (cm-1
)
) 3412 (br), 3127, 2949, 2832, 1699, 1607, 1578, 1541, 1508,
1481, 1462, 1443, 1412, 1379, 1302, 1250, 1173, 1152, 1113, 1074,
1024, 986, 899, 828, 789, 777, 752, 725, 692, 629; HRMS calcd
for C29H29N5O5Na (M + Na)+ 550.2061, found (M + Na)+
550.2061.
FIGURE 3. Crude HPLC trace of the 13-mer GNA strand 3′-
CATGTCGTGCGTA-2′ after synthesis and deprotection. The solid
support for the 2′-end A nucleotide was synthesized from compound 8
as previously described.8 The strand was eluted (1 mL/min) over a
Waters XTerra column (MS C18, 4.6 × 50 mm, 2.5 µm) at 60 °C with
aqueous triethylammonium acetate buffer (50 mM, pH ) 7.0) and a
linear gradient of 2-8% acetonitrile over 30 min. See the Supporting
Information for a MALDI-TOF spectrum of this crude GNA strand.
(S)-9-(3-(4,4′-Dimethoxytrityloxy)-2-hydroxypropyl)-N2-[(dim-
ethylamino)methylene]guanine (5). To a solution of 4 (2.63 g,
4.99 mmol) in anhydrous DMF (16.0 mL) was added dimethyl-
formamide dimethyl acetal (2.35 mL, 17.4 mmol) and the mixture
heated to 60 °C for 1 h. After cooling and removal of the DMF,
the residue was redissolved in methylene chloride, washed once
with saturated aqueous NaHCO3, dried over Na2SO4, and finally
concentrated. The product was purified via column chromatography
starting with 100:1 EtOAc/Et3N then eluting with 40:3:0.01 EtOAc/
MeOH/Et3N to afford compound 5 as a white foam (2.50 g, 86%):
1H NMR (300 MHz, CDCl3) δ (ppm) 9.21 (br, 1H), 8.48 (s, 1H),
7.51-7.45 (m, 3H), 7.39-7.15 (m, 7H), 6.83 (dd, J ) 9.0, 2.3 Hz,
4H), 4.44 (m, 2H), 4.01 (dd, J ) 14.4, 8.2 Hz, 1H), 3.78 (s, 6H),
3.36 (dd, J ) 9.5, 4.8 Hz, 1H), 3.08 (dd, J ) 9.4, 7.3 Hz, 1H),
3.01 (s, 3H), 2.89 (s, 3H); 13C NMR (75 MHz, CDCl3) δ (ppm)
158.7, 158.2, 157.5, 156.5, 150.3, 145.1, 139.5, 136.2, 136.1, 130.1,
128.2, 128.0, 126.9, 120.0, 113.33, 113.30, 86.4, 69.3, 65.0, 55.4,
48.6, 41.3, 35.2; IR (solid) ν (cm-1) ) 2929, 2836, 1630, 1558,
1506, 1444, 1416, 1399, 1345, 1326, 1300, 1245, 1174, 1110, 1066,
1024, 981, 827, 755, 726, 701, 644, 581; HRMS calcd for
C32H34N6O5Na (M + Na)+ 605.2483, found (M + Na)+ 605.2477.
Phosphoramidite G*. To a solution of 5 (1.80 g, 3.09 mmol)
in 15.5 mL of anhydrous methylene chloride under nitrogen was
added a 1 M solution of dicyanoimidazole (2.20 mL in acetonitrile).
2-Cyanoethyl N,N,N′,N′-tetraisopropylphosphordiamidite (1.03 mL,
3.24 mmol) was then added dropwise and the solution stirred at
room temperature. After 2 h, the reaction mixture was diluted with
methylene chloride, washed twice with saturated aqueous NaHCO3,
dried over Na2SO4, and then concentrated. The product was purified
via column chromatography starting with 1:1:0.01 hexanes/acetone/
Et3N,then eluting with 1:2:0.01 hexanes/acetone/Et3N to afford
compound G* as a white foam (1.85 g, 76%): 31P NMR (162 MHz,
CDCl3) δ (ppm) 150.3, 150.0; HRMS calcd for C41H52N8O6P (M
+ H)+ 783.3742, found (M + H)+ 783.3736.
This improved deprotection and workup procedure represents
a saving of at least 12 h for the removal of the protection groups
and one HPLC purification compared to the conventional
procedure previously reported for GNA oligonucleotides.8 The
crude HPLC trace of a representative oligonucleotide solution
obtained according to this protocol is shown in Figure 3 and
demonstrates the high quality of the crude product.
In conclusion, we have presented an improved protection
group scheme which provides a more economical route for the
synthesis of GNA phosphoramidite building blocks and also
quicker access to GNA oligonucleotides. These synthetic routes
should be applicable to the large scale synthesis of GNA
phosphoramidites and work along these lines is in progress.
Experimental Section
(S)-9-(3-(4,4′-Dimethoxytrityloxy)-2-hydroxypropyl)-O6-ben-
zylguanine (3). Compound 1 (3.10 g, 12.8 mmol) was partially
dissolved in anhydrous DMF (25.0 mL) under a nitrogen atmo-
sphere. NaH was added (105 mg, 2.63 mmol, 60% in mineral oil),
and the solution was allowed to stir under nitrogen for 1 h. In a
separate flask, compound 2 (4.60 g, 12.2 mmol) was dissolved in
26.0 mL of DMF, added to the first solution, and then heated to 90
°C overnight. The next morning, the solution was cooled, all solvent
removed, and the resulting oil coevaporated with toluene, redis-
solved in ethyl acetate, and concentrated again. The product was
purified via column chromatography starting with 2:1:0.01 hexanes/
acetone/Et3N, then eluting with 3:2:0.01 hexanes/acetone/Et3N to
afford compound 3 as a light yellow foam (3.73 g, 47%): 1H NMR
(300 MHz, CDCl3) δ (ppm) 7.53 (s, 1H), 7.51 (d, J ) 7.1 Hz,
2H), 7.42 (d, J ) 7.5 Hz, 2H), 7.35-7.25 (m, 9H), 7.21 (t, J ) 7.3
Hz, 1H), 6.82 (d, J ) 8.8 Hz, 4H), 5.52 (s, 2H), 5.20 (br, 1H),
4.85 (s, 2H), 4.28 (m, 1H), 4.16 (m, 2H), 3.78 (s, 6H), 3.21 (dd, J
) 9.5, 4.3 Hz, 1H), 3.03 (dd, J ) 9.4, 5.6 Hz, 1H); 13C NMR (125
MHz, CDCl3) δ (ppm) 161.0, 158.8, 158.7, 154.0, 144.8, 140.8,
136.5, 136.0, 135.9, 130.1, 128.5, 128.4, 128.2, 128.1, 128.0, 127.0,
(S)-9-(3-(4,4′-Dimethoxytrityloxy)-2-hydroxypropyl)-N6-[(dim-
ethylamino)methylene]adenine) (8). To a solution of 7 (1.32 g,
2.58 mmol) in 7.5 mL of anhydrous DMF was added dimethyl-
formamide dimethyl acetal (1.21 mL, 9.04 mmol) and the mixture
heated to 60 °C for 1 h. After cooling and removal of the DMF,
the residue was redissolved in methylene chloride, washed once
with saturated aqueous NaHCO3, dried over Na2SO4, and finally
concentrated. The product was purified via column chromatography
starting with 100:1 EtOAc/Et3N then eluting with 40:3:0.01 EtOAc/
MeOH/Et3N to afford compound 8 as a white foam (1.45 g, 99%):
1H NMR (300 MHz, CDCl3) δ (ppm) 8.89 (s, 1H), 8.44 (s, 1H),
7.84 (s, 1H), 7.43 (m, 2H), 7.35-7.17 (m, 7H), 6.82 (m, 4H), 4.98
(br, 1H), 4.45 (m, 1H), 4.32-4.17 (m, 2H), 3.79 (s, 6H), 3.29 (dd,
J ) 9.4, 4.7 Hz, 1H), 3.23 (s, 3H), 3.21 (s, 3H), 3.10 (dd, J ) 9.4,
5.7 Hz, 1H); 13C NMR (75 MHz, CDCl3) δ (ppm) 159.5, 158.7,
158.4, 152.1, 151.8, 144.8, 143.0, 135.91, 135.83, 130.1, 128.11,
128.00, 127.0, 125.8, 113.3, 86.5, 69.6, 64.8, 55.3, 48.7, 41.4, 35.2;
IR (solid) ν (cm-1) ) 2929, 2836, 1630, 1558, 1506, 1444, 1416,
1399, 1345, 1326, 1300, 1245, 1174, 1110, 1066, 1024, 981, 827,
115.4, 113.3, 86.4, 69.5, 68.3, 64.7, 55.3, 48.5; IR (film) ν (cm-1
)
) 3515, 1401, 3341, 3212, 3065, 3034, 2934, 2834, 1616, 1589,
1510, 1456, 1410, 1385, 1356, 1333, 1300, 1252, 1175, 1154, 1101,
1061, 1028, 907, 828, 789, 756, 727, 698, 633, 581; HRMS calcd
for C36H35N5O5Na (M + Na)+ 640.2530, found (M + Na)+
640.2529.
(S)-9-(3-(4,4′-Dimethoxytrityloxy)-2-hydroxypropyl)gua-
nine (4). Compound 3 (3.30 g, 5.3 mmol) and Pd/C (1.70 g, 10%
on carbon) were suspended in EtOAc (125 mL), and the solution
was purged with nitrogen, then hydrogen, and allowed to stir under
J. Org. Chem. Vol. 74, No. 12, 2009 4617