Sequence - Selective Binding of Transition Metal Complexes to DNA - Metal Complex-DNA Interactions - page 13

Table 1.1 Mn 2+ paramagnetic induced broadening of G-H8
resonances. The residues which show maximum broadening
are marked in bold and underlined. Restriction enzyme
recognition sequences are marked in italic

Sequence

1. 5 ′ -CGC G AATTC GCG Eco- RI

2. 5 ′ -GCC G ATATC G GC Eco- RV

3. 5 ′ -GCCGTATAC G GC AccI

4. 5 ′ -GCCA G ATCT G GC Bgl II

5. 5 ′ - G AATTTAAATTC

6. 5 ′ -CGC G TATACGCG

7. 5 ′ -GCCGTGCAC G GC

8. 5 ′ -GCCGTTAAC G GC Hpa I

9. 5 ′ -GCC T G ATCA G GC Bcl I

10. 5 ′ -CCAAGCTT G G

11. 5 ′ -GCC G AATTC G GC

12. 5 ′ -AT GG GTACCCAT

13. 5 ′ -TAT G GTACCATA

14. 5 ′ -TAT GG ATCCAAT

15. 5 ′ -TAT G GCCATA

16. 5 ′ - G GCGCC

on the 3 ′ -side according to the simple rule : 5 ′ - G G ≥ 5 ′ - G A > 5 ′ - G T >> 5 ′ - G C.

Apparently, the residue on the 5 -side is less important. At higher metal ion concen-

trations most 1 H NMR resonances undergo varying degrees of broadening. It must
be stressed, however, that only relative broadening effects for each sequence are
taken into account. For sequences 12, 13 and 14 the GGX (X = A, T, G) triplet is
placed in an almost identical environment. The effects of varying the X-residue are
clearly shown in Figure 1.7. In sequence no. 12 containing a GGG triplet, both line-
broadening and T 1 data show the following order: G 3 = G 4

′

> G 5 consistent for, not

only Mn 2+ , but also for Ni 2+ and Co 2+ (see Ni 2+ ions below).

F e 2+ Ions
In early investigations of Fe 2+ -DNA binding using NMR, the T 1 spin - spin relaxation
time technique indicated that both the base and the phosphate groups interact with
Fe 2+ ions. 38 Later on, Bertoncini et al. 39 , by using X-ray absorption near edge struc-
ture spectroscopy (XANES), demonstrated that while Fe 3+ tends to associate with
oxygen ligands, Fe 2+ prefers to form inner-sphere coordination with nitrogen ligands
on DNA. Linn and coworkers have made extensive studies on sequence-specifi c
DNA cleavage by Fe 2+ - mediated Fenton reactions. 40 - 42 Nicking of duplex DNA by
the iron-mediated Fenton reaction occurs preferentially at a limited number of
nucleotide sequences. Most notable are a purine nucleotide followed by three or
more G residues, [RGGG], and purine nucleotides fl anking a TG combination,
[TTGR]. 42 The preferred reaction sites are probably a consequence of sequence-
selective localization of the ferrous ions. Using 1 H NMR to characterize Fe 2+ binding
within the duplex CGAGTTAGGGTAGC/GCTACCCTAACTCG it was shown
that Fe 2+ binds preferentially at the GGG sequence, most strongly towards its 5 ′ -