Chemistry Reference
In-Depth Information
by .0.2 ppm. Obviously, the exchange of single strands 3, 6, and 7 with the corre-
sponding duplex 3†6 or 3†7 was slow on the NMR timescale. This phenomenon is
consistent with the formation of H bonded 3†6 and 3†7, which have unsymmetrical
structures and relatively high kinetic stabilities.
The NOESY spectrum of 3†6 showed that one end of this pair was locked
by intermolecular H bonds, whereas the other end around the mismatched site con-
sisting of the two amide carbonyl groups at that end was open. In contrast, the
NOESY study indicated that both ends of 3†7 were locked, but no or very weak
NOEs were detected for protons close to the internal mismatched site. These
results indicated that, in spite of the presence of mismatched sites, these mutant
duplexes still formed. More detailed analysis showed five interstrand H bonds in
3†6 or 3†7, suggesting that these strands were still fully registered. However, the oli-
goamide backbones must be twisted near the mismatched sites to alleviate any unfa-
vorable interactions.
The sequence specificity in the formation of duplex 3†4 was probed in the
presence of strands 6 and 7 by
1
H-NMR. Thus, adding 1 equiv of 4 into the solution
of either 3†6 or 3†7 in CDCl
3
containing 5% dimethylsulfoxide-d
6
(DMSO-d
6
) led
to the complete replacement of the “wrong” strands 6 or 7, resulting in the appearance
of new
1
H-NMR signals corresponding to those from duplex 3†4 and the free strand
6 or 7.
The stabilities of 3†6 and 3†7 were compared to that of 3†4 by ITC (5%
DMSO in CHCl
3
). Results from ITC experiments showed that introducing one
mismatched site led to a .40-fold drop in the association constants of the mis-
matched 4†7 and 4†8 relative to that of 4†5. Like the binding of 4 to 3, the
binding of 6 or 7 to 3 was largely enthalpically driven. However, compared to
Figure 9.5 GPC studies (CHCl
3
,1mL/min) on mixtures of (a) 8†8
þ
9†9
þ
3
0
†4
0
,
(b) 3
0
†4
0
þ
11†9†9, and (c) 8†8
þ
9†9. The retention times of the individual duplexes are
identical to those shown here.
