Chemistry Reference
In-Depth Information
Figure 9.15 (a) Complementary strands 21 and 22 carrying trityl-protected thio groups
were cross-linked in the presence of iodine. (b) MALDI spectra show that 21 and 22 were
sequence specifically cross-linked into 21-22 in water containing 1% THF. (c) When
placed in the same aqueous solution (water/THF ΒΌ 9/1, v/v), strands 19, 20, 21, and 22
sequence specifically cross-linked into 19-20 and 21-22.
association of the two stands, which increases the rate of disulfide bond formation by
increasing the effective molarity of the S-trityl groups. The thermodynamic mechan-
ism is based on the selective stabilization of the cross-linked product consisting of the
sequence-matched strands. To distinguish these two mechanisms, control strands 23,
24, and 25 (Fig. 9.16) were designed and prepared (Li et al. 2008).
First, to investigate whether intermolecular association of complementary
strands determines the final product distribution, the cross-linking of 19 and 20
was examined in the presence of control strand 23. Sharing the same backbone
and H bonding sequence, strands 23 and 19 should compete for H bonding or
aromatic stacking interactions with 20. The only difference between 19 and 23 is
that the latter is incapable of forming a disulfide cross-linked product with 20.If
the sequence-specific formation of 19-20 relied on the intermolecular association
of 19 and 20, the presence of 23 should interfere with such an association, which
would slow down the rate-determining step of the disulfide bond formation reaction
and compromise the sequence selectivity. Examining the mixture containing 19, 20,
and 23 (0.5 mM each) in aqueous solution in the presence of iodine using MALDI
revealed two peaks
corresponding to cross-linked 19-20 and strand 23
