CD studies on the conformation of oligonucleotides complexed with divalent metal ions: interaction of Zn2+ with guanine favours syn conformation

N2-functionalized blue luminescent guanosines by 2,2'-dipyridylamino and 2-(2'-pyridyl)benzimidazolyl chelate groups and their interactions with Zn(II) ions

The syntheses of new blue luminescent N(2)-modified guanosine derivatives with chromophores p-4,4'-biphenyl-NPh2 (1a), p-4,4'-biphenyl-N(2-py)2 (1b), and p-4,4'-biphenyl-2-(2'-pyridyl)benzimidazolyl (1c), respectively, have been achieved. These new N(2)-guanosines are moderate blue emitters with lambda(max) = 395 nm (1a), 370 nm (1b), and 403 nm (1c) and Phi = 0.13, 0.07, and 0.10 in tetrahydrofuran, respectively. Spectroscopic studies and density-functional theory calculations established that the guanine moiety and the new chromophore in all three molecules are involved in the luminescent process. We have also established that guanosines 1a-1c can interact with metal ions such as Zn(II). The interactions of Zn(II) ions with the three guanosines were examined via absorption, fluorescence, circular dichroism (CD), and NMR spectroscopic analyses. We have found that these guanosines display a distinct fluorescent response toward Zn(II) ions which can be attributed to the presence of the chelate chromophore N(2-py)2 in 1b and 2-py-benzimidazolyl in 1c. For 1a and 1b, the addition of Zn(II) ions causes straight fluorescent quenching while for 1c the addition of Zn(II) ions causes quenching initially, which is followed by a distinct spectral red shift and the intensity enhancement of the new emission peak. NMR and CD studies demonstrated that the Zn(II) ions bind preferentially to the guanine moiety in 1a and 1b but to the 2-(2'-py)benzimidazolyl chelate site in 1c. Moreover, the anion-dependent CD response of 1a-1c toward Zn(II) salts points to the possible involvement of intramolecular hydrogen bonding between the acetate bound to the Zn(II) ion and the hydroxyl groups of the guanosine.

Conformational changes induced in the human protein translin and in the single-stranded oligodeoxynucleotides d(GT)(12) and d(TTAGGG)(5) upon binding of these oligodeoxynucleotides by translin

Translin is a human single-stranded DNA and RNA binding protein that has been highly conserved in eukaryotic evolution. It consists of eight subunits having a highly helical secondary structure that assemble into a ring. The DNA and the RNA are bound inside the ring. Recently, some of us demonstrated that the human translin specifically binds the single-stranded microsatellite repeats, d(GT)(n), the human telomeric repeats, d(TTAGGG)(n), and the Tetrahymena telomeric repeats, d(GGGGTT)(n). These data suggested that translin might be involved in recombination at d(GT)(n).d(AC)(n) microsatellites and in telomere metabolism. Other data indicated that translin might stimulate binding of telomerase to single-stranded telomeric overhangs by unwinding secondary structures formed by the telomeric repeats. Here we present a circular dichroism (CD) analysis of complexes formed between the human translin and the microsatellite and telomeric oligodeoxynucleotides d(GT)(12) and d(TTAGGG)(5). We report that conformational changes occur in both the translin and the oligodeoxynucleotides upon formation of the complexes. In translin octamers bound to the oligodeoxynucleotide d(GT)(12), the fraction of alpha-helices decreases from approximately 67% to approximately 50%, while the fraction of turns and of the unordered structure increases from approximately 11% to approximately 17% and from approximately 19% to approximately 24%, respectively. In the bound oligodeoxynucleotide d(GT)(12), we observed CD shifts which are consistent with a decrease of base stacking and a putative anti-syn switch of some guanines. The oligodeoxynucleotide d(TTAGGG)(5) formed intramolecular quadruplexes under the conditions of our assays and translin was found to unfold the quadruplexes into structures consisting of a single hairpin and three unwound single-stranded d(TTAGGG) repeats. We suggest that such unfolding could account for the stimulation of telomerase activity by translin mentioned above.

The effect of magnesium and manganese ions on the structure and template activity for reverse transcriptase of polyribocytidylate and its 2'-0-methyl derivative

The secondary structure of the hydrogen bonded hybrids polycytidylate-oligodeoxguanylate (poly(rC)-(dG)12-18 and poly (2'-oMe) cytidylate-oligodeoxyguanylate (poly (rCm)-(dG)12-18 was studied at several magnesium and manganese ion concentrations. These hybrids are effective template-primer complexes for the synthesis of poly(dG) by avian myeloblastosis virus (AMV) DNA polymerase under disparate ionic conditions. Circular dichroism spectra and thermal melting data were obtained as a function of ion concentration, including conditions that allow optimum rates of poly (dG) synthesis by each complex. These studies demonstrate that both hybrids can change conformation and stability depending on their ionic environment. Comparison of enzyme activity and physical data suggest that the polymerase recognizes particular secondary structure features. Changes in the activity of the AMV polymerase can be induced by varying the Mg++ and Mn++ concentrations alone and in combination. These variations in enzyme activity are correlated with observed changes in the base-stacking alignment of the synthetic template primers. The ions, therefore, seem to affect enzyme activity by altering the conformation of the polnucleotide complexes.