Sequence-Selective Metal Ion Binding to DNA Oligomers.

Steinkopf, Signe; Garoufis, Achilleas; Nerdal, Willy; Sletten, Einar; Pawlak, Dorota A.; Pniewska, B.; Rasała, Danuta; Gawinecki, Ryszard

doi:10.3891/acta.chem.scand.49-0495

Cited by 20 publications

(7 citation statements)

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“…All interactions between nickel and DNA were in fast exchange as expected from previous results on simple metal salts of Mn 2+ , Co 2+ , Ni 2+ , and Zn 2+ (23,39). In contrast, palladium (40) and platinum (41) complexes often bind to DNA in slow exchange.…”

Section: Discussionsupporting

confidence: 82%

Selective Association between a Macrocyclic Nickel Complex and Extrahelical Guanine Residues

1999

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Nickel-dependent recognition and oxidation of guanine have been linked in part through the paramagnetic effects of nickel on the NMR of model oligonucleotide duplexes. Direct interaction between nickel and guanine N7 had originally been postulated from correlations between the efficiency of guanine oxidation and the environment surrounding its N7 position. (1)H and (31)P NMR spectra of DNA containing a single, isolated extrahelical guanine are consistent with selective binding of nickel to the N7 of this unique base over a background of nonspecific association to the phosphate backbone. The presence of a macrocyclic complex or simple salt of nickel did not detectably alter the structure of the duplex or extrahelical residue. Accordingly, nickel appeared to bind the extrahelical guanine N7 within the major groove as indicated by paramagnetic effects on the proton signals of nucleotides on the 5' but not 3' side of the nickel binding site. Similar (1)H NMR analysis of DNA containing a dynamic equilibrium of extrahelical guanine residues also suggested that the nickel complex did not affect the native distribution of structures. Oxidation of these sites by a nickel-mediated pathway consequently reflected their solvent accessibility in a general and metal-independent manner. The close proximity of the extrahelical guanines produced a composite of paramagnetic effects on each adjacent nucleotide resulting from both direct and proximal coordination of nickel.

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Section: Discussionsupporting

confidence: 82%

Selective Association between a Macrocyclic Nickel Complex and Extrahelical Guanine Residues

1999

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“…First, A-tracts also exhibit minor groove divalent cation binding sites which are distinct from those reported here for monovalent cations (Hud & Feigon, 1997). Secondly, some of the short sequence elements in the DNAs studied (which intersperse A-tracts in order to allow proper helical phasing) contain the dinucleotide steps GpG, GpA and GpT known to be major groove divalent cation binding sites (Froystein et al, 1993;Steinkopf et al, 1996). These could bind cations in the major groove and cause bending towards that groove (Rouzina & Bloom®eld, 1998).…”

Section: Divalent Cation Binding Sites and Dna Bendingmentioning

confidence: 63%

Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending 1 1Edited by I. Tinoco

Hud

Sklenář

Feigon

1999

Journal of Molecular Biology

208

189

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“…The binding of metal ions to DNA is also known to be sequence selective. [42][43][44][45] The order of the preference for Co(II) binding determined by line broadening of G-H8 by 1 H NMR is GG > GA > GT . GC.…”

Section: Discussionmentioning

confidence: 99%

Selective Intercalation of Charge Neutral Intercalators into GG and CG Steps: Implication of HOMO-LUMO Interaction for Sequence-Selective Drug Intercalation into DNA

et al. 2001

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We have synthesized naphthopyranone epoxide 4 from D-isoascorbic acid together with its three diastereoisomers. DNA alkylation of ODNs containing 5'XGT3' and 5'TGY3' by 4 (11R, 13R), where X and Y are any nucleotide bases, occurred at all G residues except at G of the 5'TGC3' sequence. In contrast, the three other diastereoisomers of 4 showed only weak G alkylation activity. Differential (1)H NMR NOE of the 4-G adduct confirmed the G-N7 alkylation at the epoxide carbon of 4 with concomitant S(N)2 ring opening of the epoxide. Quantitative HPLC analysis of G alkylation efficiency for 4 showed the order of G alkylation susceptibility as TGGT approximately CGT >> TGA > AGT > TGT >> TGC. The order was fully consistent with those reported for aflatoxin B(1) oxide and kapurimycin A(3), suggesting that the sequence selectivity observed for these DNA alkylating agents is not structure dependent but most likely due to the intrinsic property of DNA sequences. We found that the order of G alkylation susceptibility obtained for 4 completely matched the calculated HOMO energy level of G-containing sequences. These results underscore that 4 is a unique molecular probe for ranking the HOMO level of G-containing sequences by well-known G alkylation chemistry and suggests that the intercalation of charge neutral intercalators is a HOMO-controlled process.

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Sequence-Selective Metal Ion Binding to DNA Oligomers.

Cited by 20 publications

References 0 publications

Selective Association between a Macrocyclic Nickel Complex and Extrahelical Guanine Residues

Selective Association between a Macrocyclic Nickel Complex and Extrahelical Guanine Residues

Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending 1 1Edited by I. Tinoco

Selective Intercalation of Charge Neutral Intercalators into GG and CG Steps: Implication of HOMO-LUMO Interaction for Sequence-Selective Drug Intercalation into DNA

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