Synthesis and base pairing properties of 9-deazapurine N7-nucleosides in oligonucleotide duplexes and triplexes

Article abstract of DOI:10.1081/NCN-100002536

The 9-deazaguanine N⁷-2′-deoxyribofuranoside (3) as well as the bromo and iodo derivatives 4a,b were synthesized and incorporated in oligonculeotide duplexes and triplexes. Their base pairing properties were investigated and compared with those

Full text of DOI:10.1081/NCN-100002536

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SYNTHESIS AND BASE PAIRING PROPERTIES OF 9-
DEAZAPURINE N7-NUCLEOSIDES IN OLIGONUCLEOTIDE
DUPLEXES AND TRIPLEXES
P. Leonard a , T. Wiglenda a & F. Seela b
a Institut für Chemie, Universität Osnabrück, Laboratorium für Organische und
Bioorganische Chemie, Germany
b Institut für Chemie, Universität Osnabrück, Laboratorium für Organische und
Bioorganische Chemie, Germany
Version of record first published: 07 Feb 2007.
To cite this article: P. Leonard , T. Wiglenda & F. Seela (2001): SYNTHESIS AND BASE PAIRING PROPERTIES OF 9-
DEAZAPURINE N7-NUCLEOSIDES IN OLIGONUCLEOTIDE DUPLEXES AND TRIPLEXES, Nucleosides, Nucleotides and Nucleic
Acids, 20:4-7, 1279-1282
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NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS, 20(4–7), 1279–1282 (2001)
SYNTHESIS AND BASE PAIRING PROPERTIES
OF 9-DEAZAPURINE N7-NUCLEOSIDES IN
OLIGONUCLEOTIDE DUPLEXES AND TRIPLEXES
P. Leonard, T. Wiglenda, and F. Seela∗
Laboratorium fu¨r Organische und Bioorganische Chemie,
Institut fu¨r Chemie, Universita¨t Osnabru¨ck, Germany
ABSTRACT
The 9-deazaguanine N7-2ꢀ-deoxyribofuranoside (3) as well as the bromo and
iodo derivatives 4a,b were synthesized and incorporated in oligonculeotide
duplexes and triplexes. Their base pairing properties were investigated and
compared with those of the parent purine N7-2ꢀ-deoxyribofuanosides.
INTRODUCTION
Several reports have communicated on the base pairing properties of nucleo-
sides linked via nitrogen-7 or position-8 to the nucleobase (1–3). The nucleosides
1 and 2 with the unusual N7-glycosylation site form stable base pairs in duplex and
triplex DNA (1,2,4). Now, we report on the synthesis and base pairing properties of
the 9-deazaguanine N7-nucleosides 3 and 4a,b which are remarkably stable analogs
of the purine nucleosides. The pyrrolo[3,2-d]pyrimidine nucleosides were incor-
porated in oligonucleotide duplexes as well as in triplex-DNA. Their base pairing
properties were compared with compound 2.
∗ Corresponding author.
1279
ꢁ
C
Copyright 2001 by Marcel Dekker, Inc.
www.dekker.com

ORDER
REPRINTS
1280
LEONARD, WIGLENDA, AND SEELA
Scheme 1.
Scheme 2.
Scheme 3.

ORDER
REPRINTS
9-DEAZAPURINE N7-NUCLEOSIDES
Table 1. Antiparallel Duplexes with N7Gd-iCd and c9N7Gd-iCd Base Pairsa)
1281
aps-Duplexes
Tm [◦C]
aps-Duplexes
Tm [◦C]
5ꢀ-d(TAGGTCAATACT)
3ꢀ-d(ATCCAGTTATGA)
5ꢀ-d(TAiCiCTCAATA CT)
3ꢀ-d(AT 2 2 AGTTATGA)
5ꢀ-d(TA 3 3 T CAATACT)
3ꢀ-d(ATiCiC A GTTATGA) 17
14
15
5ꢀ-d(TA4a4aT CAATA CT) 16
3ꢀ-d(ATiCiC A GTTATGA) 17
5ꢀ-d(TA4b4bTCAATA CT) 20
3ꢀ-d(ATiCiC A GTTATGA) 17
47
40
40
18
19
40
38
21
a)Measured at 260 nm in 0.1M NaCl, 10 mM MgCl2, and 10 mM Na-cacodylate (pH 7.0) at
5 µM of single strand concentration. iCd = 5-methyldeoxyisocytidine.
RESULTS AND DISCUSSION
The synthesis of the nucleosides 3 (5) and 4a,b utilized the nucleobases 5a (6)
and 5b–c as precursors. Compounds 5b,c were obtained from 5a by regioselective
halogenation. The stereoselective nucleobase-anion glycosylation of 5a–c with the
halogenose 6 furnished the N7-β-D-nucleosides 7a–c. Deblocking of 7a–c (0.01M
NaOMe) resulted in a selective detoluoylation (→9a–c), while treatment of 7a–c
with 0.1M NaOMe cleaved the pivaloyloxymethyl group (→8a–c). Treatment of
7a–c with conc. aq. NH3 furnished the nucleosides 3 and 4.
Next, formamidine protecting groups were introduced. The half-life values of
depotection were 8 min for 8a, 12 min (8b) and 17 min (8c) (25% aq. NH3, 40◦C).
The protected nucleosides 8a,b as well as 9a–c were tritylated (→ 10a–c and
11a–c) and were converted in building blocks for solid-phase synthesis (12a,b and
13a–c).
The base-pairing properties of the nucleosides 3 and 4a,b were investigated
on duplexes with antiparallel chain orientation. According to Table 1 compounds
3 and 4a,b form base pairs with 5-methyl-2ꢀ-deoxyisocytidine (iCd) in aps-duplexes
(16·17, 20·17 and 21·17). This is in line with observations made on the base pairing
properties of the purine N7-nucleoside 2 (2) (see duplex 18·19). In this case a strong
base pair with iCd was formed. Furthermore, the bulky bromo and iodo substituents
Scheme 4.

ORDER
REPRINTS
1282
LEONARD, WIGLENDA, AND SEELA
Table 2. Oligonucleotides Forming the Base Triplets 3:dG-dC and dC:dG-dCa)
5ꢀ-d(TTTXTTTTXTXTXTT
5ꢀ-d(TTTXTTTTXXXXXTT
5ꢀ-d(GCGCGAAAGAAAAGAGAGAACCCGG)
3ꢀ-d(CGCGCTTTCTTTTCTCTCTTGGGCC)
5ꢀ-d(GCGCGAAAGAAAAGGGGGAACCCGG)
3ꢀ-d(CGCGCTTTCTTTTCCCCCTTGGGCC)
X
Tm [◦C] pH 6.5
Tm [◦C] pH 8.0
X
Tm [◦C] pH 6.5
Tm [◦C] pH 8.0
3
C
45/72
45/72
44/72
16/72
3
C
53/74
24/74
52/74
n.t./74
a)Measured at 260 nm in 10 mM HEPES, 50 mM NaCl, 10 mM MgCl2 and 0.5 mM spermine at
1 µM of single strand concentration. N.t.: no transition.
introduced in position-9 of the heterocycle (4a,b) are well accommodated in the
duplex structure.
The results of Table 1 raise the question about the structure of the base pairs.
Several base pair motives were considered. Due to the almost identical Tm-values
of the duplexes containing 2,3 and 4a,b and the fact that the tridentate base pairs
(II and III) are similar to the tridentate WC-base pair of I, the motifs II and III are
the most likely ones.
Earlier, the triplex formation of oligomers containing N7Gd(2) as well as of
an acyclic derivative of 2 recognizing a dG-dC pair of a duplex DNA was described
(4,7). Now, compound 3 was introduced into the third strand of a triplex (Table 2).
Sigmoidal melting curves with a biphasic profile were obtained in all cases. The
higher Tm-values are assigned to the duplex melting while the lower ones describe
the triplex dissociation.
Table 2 shows that triplex melting is independent from the pH-value, when
compound 3 is a constituent of the base triplet. The triplexes containing dC-residues
at that position require protonation before triplex formation. As the sugar phosphate
backbone of the pyrimidine-rich third strand becomes distorted by the incorporation
of 3, the stability of the triplex is higher when the 3-residues are in a consecutive
order instead of being dispersed. The advantage of compound 3 compared to 2 is
its remarkable glycosylic bond stability and the possibility to introduce reporter
groups at the 9-position (4a,b).
REFERENCES
1. Seela, F.; Winter, H. ‘10th International Roundtable 1992’, Park City, USA.
2. Seela, F.; Leonard, P. Helv. Chim. Acta, 1996, 79, 477–485.
3. Seela, F.; Zulauf, M.; Debelak, H. Helv. Chim. Acta, 2000, 83, 1437–1453.
4. Hunziker, J.; Priestley, E. S.; Brunar, H.; Dervan, P. B. J. Am. Chem. Soc., 1995, 117,
2661–2662.
5. Girgis, N. S.; Cottam, H. B.; Larson, S. B.; Robins, R. K. J. Heterocycl. Chem., 1987,
24, 821–827.
6. Taylor, E. C.; Young, W. B.; Ward, C. C. Tetrahedron Lett., 1993, 34, 4595–4598.
7. St.Clair, A.; Xiang, G. X.; McLaughlin, L. W. Nucleosides Nucleotides, 1998, 925–
937.

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