Changes in poly[d(T-G).d(C-A)] chirality due to Hg(II)-binding: circular dichroism (CD) studies

Interaction of metal ions and DNA films on gold surfaces: an electrochemical impedance study

Electrochemical impedance spectroscopy (EIS) has been used to investigate the effects of a number of metal ions with DNA films on gold surfaces exploiting [Fe(CN)6](3-/4-) as a solution-based redox probe. Alkaline earth metal ions Mg2+, Ca2+, trivalent Al3+, La3+ and divalent transition metal ions Ni2+, Cu2+, Cd2+ and Hg2+ have been selected in this study and the results are compared with previous studies on the effects of Zn2+ on the EIS of DNA films. All experimental results were evaluated with the help of equivalent circuits which allowed the extraction of resistive and capacitive components. For all metal ions studied here, addition of the metal ions causes a decrease in the charge transfer resistance. The difference of charge transfer resistance (DeltaR(ct)) of ds-DNA films in the presence and absence of the various metal ions is different and particular to any given metal ion. In addition, we studied the EIS of ds-DNA films containing a single A-C mismatch in the presence and absence of Ca2+, Zn2+, Cd2+ and Hg2+. DeltaR(ct) values for ds-DNA films with a single A-C mismatch is smaller than those of fully matched ds-DNA films.

DNA-Metal Base Pairs

Recent developments show encouraging results for the use of DNA as a construction material for nanometer-sized objects. Today, however, DNA-based molecular nanoarchitectures are constructed with mainly unmodified or at best end-modified oligonucleotides, thus shifting the development of functionalized DNA structures into the limelight. One of most recent developments in this direction is the substitution of the canonical Watson-Crick base pairs by metal complexes. In this way "metal-base pairs" are created, which could potentially impart magnetic or conductive properties to DNA-based nanostructures. This review summarizes research which started almost 45 years ago with the investigation of how metal ions interact with unmodified DNA and which recently culminated in the development of artificial ligand-like nucleobases so far able to coordinate up to ten metal ions inside a single DNA duplex in a programmable fashion.

Particles of liquid-crystalline dispersions formed by (nucleic acid-rare earth element) complexes as a potential platform for neutron capture therapy

Microscopic size particles of the cholesteric double-stranded DNA (RNA) liquid-crystalline dispersions, containing the ions of the rare earth elements in their content, have been obtained for the first time. The properties of these particles differ from those of classical DNA cholesterics noticeably. The local concentration of the rare earth elements in a particle reaches 200 mg/ml. The particles of the liquid-crystalline dispersion of the (DNA-gadolinium) complex maintain the properties for a long time. The combination of the microscopic size of particles, high concentration of gadolinium in particles and their stability opens a way to practical application of this new biomaterial.

Mercury(II) Site-Selective Binding to a DNA Hairpin. Relationship of Sequence-Dependent Intra- and Interstrand Cross-Linking to the Hairpin-Duplex Conformational Transition

Hg(II) interacted site selectively with only one of three deoxyribooligonucleotides examined; these "oligos" each had a different number of unmatched T residues. Thus, Hg(II) formed an intrastrand T-Hg-T cross-link between the first and fourth T residues of the hairpin, d(GCGCTTTTGCGC) (T4). The DNA strand formed a loop around the Hg, as if the Hg atom had been lassoed. The interactions of Hg(II) with two other oligos, d(ATGGGTTCCCAT) (T2) and d(GCGCTTTGCGC) (T3), were less specific. Previously, we found that at high DNA and salt concentrations, T2 was a mixture of hairpin and duplex forms while T3 and T4 had the hairpin form; modeling studies showed that in the free T4 hairpin the two T's at the ends of the (T)(4) loop form a T.T wobble base pair. Only in T4 are the T residues positioned to form an intrastrand cross-link readily. The Hg(II)-oligo adducts formed as a function of added Hg(II) were investigated by titrations monitored by UV, CD, and (1)H NMR spectroscopy. The appearance of a new set of (1)H signals with the concomitant decay of the free oligo (1)H signals indicated that 1:1 Hg(II):T2, 1.5:1 Hg(II):T3, and 1:1 Hg(II):T4 adducts were formed with Hg(NO(3))(2). In H(2)O, these adducts all had spectra with very downfield signals for the exchangeable TN(3)H and GN(1)H groups, a characteristic of base-paired regions. All upfield N(3)H signals from the (T)(2) and (T)(3) sequences of the free oligo disappeared in the spectra of the 1:1 Hg(II):T2 and 1.5:1 Hg(II):T3 adducts. The disappearance of the NH signals, the UV spectral changes, and the stoichiometries (1:1 Hg(II):T2 and 1.5:1 Hg(II):T3) indicate that these adducts are duplexes containing two and three T-Hg-T interstrand cross-links for T2 and T3, respectively. The (1)H and (13)C signals of the 1:1 Hg(II):T4 adduct in D(2)O were nearly completely assigned by 2D NMR spectroscopy. The spectrum of the adduct in H(2)O had only two of the four original TN(3)H signals from the (T)(4) sequence present in the spectrum of T4; this result is consistent with the presence of a TN3-Hg-TN3 cross-link. The (13)C chemical shift changes upon Hg(II) binding indicated that the TN3-Hg-TN3 cross-link was between the T's at each end of the (T)(4) loop. The NOESY, CD, and UV spectra were all consistent with a hairpin conformation for the 1:1 Hg(II):T4 adduct. A hairpin conformation also appeared reasonable from molecular modeling calculations. In conclusion, the length of the central (T)(n)() sequence influenced the type of T-Hg-T cross-link formed and, in turn, the conformation of the adducts. For (T)(2) and (T)(3), interstrand T-Hg-T cross-linking favored the duplex form. In contrast, for (T)(4), intrastrand T-Hg-T cross-linking stabilized the hairpin form.

An A-form of poly[d(A-C)].poly[d(G-T)] induced by mercury (II) as studied by UV and FTIR spectroscopies

The conformational changes of poly[d(A-C)].poly[d(G-T)] induced by Hg(ClO4)2 in aqueous solution have been studied using UV absorption and fourth derivative spectrophotometries, and FTIR spectroscopy. The UV absorption and fourth derivative spectra reflect changes in the polynucleotide stacking interactions as a result of the metal-polynucleotide interaction. The fourth derivative spectra do not indicate a Z-form either at low or at high metal-to-polynucleotide ratios. Furthermore, the infrared spectrum at high metal-to-polynucleotide ratio (r = 1.2; r = [Hg(ClO4])2/[nucleotide] molar ratio) has the main features of an A-form, in contrast with previous CD studies which proposed that the polynucleotide adopts a Z-form under these conditions. The nature of a different conformation of the polynucleotide induced at low r-ratios (r < or = 0.2) is discussed.

Effect of Hg(II) on the spectroscopic properties of poly[d(A-T).d(A-T] and poly[d(A).d(T)] and their constituent subunits (deoxyadenosine and thymidine monomers and dimers)

Adding, respectively, increasing amounts of Hg(ClO4)2 (identical to Hg(II)) to poly[d(A-T).d(A-T)] (I), poly[d(A).d(T)] (II) as well as to their constituent subunits 2'-deoxyadenosine (identical to dA), thymidine (identical to dT), 2'-deoxyadenosine-5'- monophosphate (identical to dAp), thymidine-5'-monophosphate (identical to dTp), 2'-deoxyadenylyl-(3'-->5')-2'-deoxyadenosine (identical to d(ApA)), 2'-deoxyadenylyl-(3'-->5')-thymidine (identical to d(ApT)), thymidylyl- (3'-->5')-2'-deoxyadenosine (identical to d(TpA)), and thymidylyl- (3'-->5')-thymidine (identical to dTpT))--all dissolved in 0.1 M NaClO4, 5 mM cacodylic acid, pH 7--generates changes in their UV spectra that (a) progress in (I) in a pattern that is distinctly different from the one occurring in (II) and that (b) reveal a strong sequence dependence in the case of the dinucleoside phosphates. The spectroscopic parameters D (dipole strength), f (oscillator strength), and h (hypochromicity) were determined as a function of Hg(II) concentration for both polymers as well as for all dimers. Also determined were D and f of the monomers. D and f of dA, dAp, and d(ApA) display a different dependence on Hg(II) concentration than do D and f of dT, dTp, and d(TpT). The corresponding parameters of the mixed-sequence dimers d(ApT) and d(TpA) vary with Hg(II) in a 'mirror'-like fashion. Increase in base stacking subsequent to mercury binding is noted with d(TpT) and d(TpA). The opposite occurs in d(ApT). Hg(II) exerts only marginal effects on the base stacking in d(ApA). Both D and f of polymers (I) and (II) increase with increasing levels of Hg(II), i.e. Hg(II) binding decreases base stacking (loss of hypochromicity).(ABSTRACT TRUNCATED AT 250 WORDS)

The mercury(II) and high-salt-induced conformational B<==>Z transitions of poly[d(G-m5C).d(G-m5C)] as studied by non-polarized (ultraviolet) and circularly polarized (CD) ultraviolet spectroscopy

The B<==>Z transition of poly[d(G-m5C).d(G-m5C)] in buffered solution (0.002 M sodium cacodylate, pH 7) was studied by CD and ultraviolet spectroscopy as a function of the supporting electrolyte concentration (0.002-1.1 M NaClO4) in the absence of Hg(ClO4)2 [Hg(II)], and as a function of the Hg(II) concentration at a given NaClO4 level. NaClO4 alone changes the conformation of the polymer from B<==>Z at approximately 0.7 M NaClO4. The spectral changes caused by Hg(II) in the B-form polymer (e.g. at 0.002 M < or = [Na] < or = 0.7) resemble those generated by salt alone during the B<==>Z transition; the changes generated by Hg(II) in the Z-form polymer (e.g. in 1.1 M [Na]) leave principally intact the Z-form spectrum obtained at the higher levels of NaClO4 (e.g. at [Na] > 0.7 M) in the absence of Hg(II). It is concluded that particularly the long-wavelength positive-CD band, located at 274 nm, is a correct indicator of duplex DNA right<==>left-screwness inversion. According to generally accepted criteria, the NaClO4-induced left-handed form is Z DNA; Hg(II) generates a left-handed form termed here ZHg(II). This form is close to (but not identical with) the salt-induced Z-form. All Hg(II)-induced spectral changes are reversible upon removal of Hg(II) with a suitable complexing reagent (e.g. NaCN).