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2623
M.; Maher, L. J. Nucleic Acids Res. 2002, 30, 1879; (c) Gao, R.; Claeboe, Ch. D.;
Eisenhauer, B. M.; Hecht, S. M. Biochemistry 2004, 43, 6167; (d) Tian, L.;
Claeboe, Ch. D.; Hecht, S. M.; Shuman, S. Structure 2004, 12, 31; (e) Kurpiewski,
M. R.; Engler, L. E.; Wozniak, L. A.; Kobylanska, A.; Koziolkiewicz, M.; Stec, W. J.;
Jen-Jacobson, L. Structure 2004, 12, 1775; (f) Liu, J.; Déclais, A.-C.; McKinney, A.
S.; Ha, T.; Norman, D. G.; Lilley, D. M. J. Chem. Biol. 2005, 12, 217.
13. (a) Enders, D.; Saint-Dizier, A.; Lannou, M. I.; Lenzen, A. Eur. J. Org. Chem. 2006,
29; (b) Liu, X.; Hu, X. E.; Tian, X.; Mazur, A.; Ebetino, F. H. J. Organomet. Chem.
2002, 646, 212; (c) Bochwic, B.; Michalski, J. Nature 1951, 167, 1035.
14. (a) Simoni, D.; Invidiata, F. P.; Manferdini, M.; Lampronti, I.; Rondanin, R.;
Roberti, P.; Pollini, M. G. Tetrahedron Lett. 1998, 39, 7615; (b) Haynes, R. K.
Tetrahedron Lett. 1996, 37, 4729; (c) Yamashita, M.; Tamada, Y.; Iida, A.;
Oshikawa, T. Synthesis 1990, 420.
5
.
.
(a) Le s´ nikowski, Z. J.; Jaworska-Ma s´ lanka, M.; Stec, W. J. Nucleosides Nucleotides
1
1
991, 10, 733; (b) Le s´ nikowski, Z. J.; Jaworska, M.; Stec, W. J. Nucleic Acids Res.
988, 16, 11675.
Sheehan, D.; Lunstad, B.; Yamada, Ch. M.; Stell, B. G.; Caruthers, M. H.;
Dellinger, D. J. Nucleic Acids Res. 2003, 31, 4109.
15. Verkade, J. G. Top. Curr. Chem. 2003, 223, 3.
16. Al O (5 g) was added to 1 M KOH (3 g KOH in 50 mL H O), concentrated under
2 3 2
6
vacuum, washed with dry EtOH (4 times), concentrated, and dried under high
vacuum at room temperature: Semenzin, D.; Moghadam, G. M.; Albouy, D.;
Diallo, O.; Koenig, M. J. Org. Chem. 1997, 62, 2414.
7
8
.
.
Yamada, Ch. M.; Dellinger, D. J.; Caruthers J. Am. Chem. Soc. 2006, 128, 5251.
Fathi, R.; Huang, Q.; Coppola, G.; Delaney, W.; Teasdale, R.; Krieg, A. M.; Cook, A.
F. Nucleic Acids Res. 1994, 22, 5416.
17. The 1
H
NMR analysis revealed that
a
single base modification occurred
0
selectively on the 5 -thymidine to the modified internucleotide bond.
18. The absolute configurations at phosphorus were assigned based on 31P and 1
NMR (COSY) analysis.
9
.
Fathi, R.; Delaney, W.; Huang, Q.; Cook, A. F. Nucleosides Nucleotides 1995, 14,
H
1
725.
0
0
1
0 0 0 0
3
19. FAST: H NMR (500 MHz, CDCl ) 6.4(H1 ), 6.1 (H1 ), 5.2 (H3 ), 4.4 (H3 ), 4.3
1
0. The yields of the condensation between 5 -O-DMT-nucleoside 3 -O-H-
0
0
0
00
0
0
00
0
0
00
phosphonates and 3 -O-protected nucleosides, activated by adamantoyl
(H4 ), 4.2 (H5 /5 ), 4.0 (H4 ), 3.6 (H5 ), 3.4 (H5 ), 2.4 (H2 ), 2.3 (H2 ), 2.3 (H2 ),
6.8 (P-CH CH CN), 1.4 (P-CH CH CN).
20. Compounds were prepared from
31
chloride were very high (90% to quantitative, as estimated from P NMR),
however, separation of the diastereomers caused a significant decrease of the
final yields. Isomers SLOW were usually obtained in low yields (10–15%) only,
depending on the sequence and scale of purification.Compound 1 (B = Thy)
FAST): H NMR (500 MHz, CDCl
H5 ), 4.2 (4 H, 5 H), 4.0 (4 H), 3.5 (5 H), 3.3 (5 H), 2.6 (2 H), 2.4 (2 H), 2.3 (2 H,
2
2
2
2
Bz
3
(B = Cyt
)
P P
a R , S mixture of 1
(diastereomeric ratio 2:1), and separated into diastereomers after addition
0
and 3 -O-deprotection.
1
0
0
0
0
(
(
2
(
3
): 6.4 (H1 ), 6.0 (H1 ), 5.2 (3H ), 4.5 (H3 ), 4.3
21. Wozniak, L. A.; Bukowiecka-Matusiak, M.; Janicka, M. Eur. J. Org. Chem. 2005,
0
0
00
0
0
00
0
00
0
5189.
00
1
0
H), 6.89 (P–H, JP–H = 717 Hz)Compound 1 (SLOW) H NMR: 6.4 (1H ), 6.2
22. MALDI TOF spectra confirmed the constitution of both oligonucleotides: R
(found 3941.1, calcd; m/z 3943.2) and R -11 (found 3925.8, calcd; m/z 3924.2)
23. Evertsz, E. M.; Karsten, R.; Jovin, T. M. Nucleic Acids Res. 1994, 22, 3293.
P
-10
0
0
0
0
0
0
0
0
1H ), 5.3 (3H ), 4.4 (3H ), 4.3 (H 4 ), 4.2 (H 5 ), 4.1 (H 5 ), 3.9 (H 4 ), 3.5 (H 5 ),
P
00 0 00 0 00
.4 (H5 ), 2.7 (H 2 ), 2.6 (H2 ), 2.2 (H 2 ), 2.1 (H2 ), 6.9 (P–H, JP–H = 717 Hz), MS
Bz 31
3
FAB [M+1] = 927.1Compound
1
(B = Cyt ):
P
NMR (81.03 MHz CDCl
3
):
24. Oligonucleotides 10 or 11 and the corresponding templates were mixed
together in 10 mM Tris buffer, 10 mM MgCl2, and 100 mM NaCl (pH 7.4) at a
total 4.1 M concentration of duplex, heated at 60 °C for 5 min, and kept
overnight at 4 °C. Melting profiles were recorded in the range 3–90 °C, in both
directions, with a temperature gradient of 0.3 °C/min.
7
.64 ppm (FAST), 8.36 ppm (SLOW), JP–H = 720 Hz, MS FAB [M+1] = 1125.3 9
(
calcd; 1124.23)
1
1
1. Seela, F.; Kretschmer, U. J. Org. Chem 1991, 12, 3861.
2. Stawi n´ ski, J.; Strömberg, R. In Current Protocols in Nucleic Acid Chemistry;
Beaucage, S. L., Bergstrom, D. E., Herdewijn, P., Matsuda, A., Eds.; John Wiley
and Sons, 2005.