Monovalent cation effects on intermolecular purine-purine-pyrimidine triple-helix formation

Cheng, Ann‐Joy; Dyke, Michael W. Van

doi:10.1093/nar/21.24.5630

Cited by 114 publications

(117 citation statements)

References 24 publications

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“…Additionally, the NH 4 ϩ ions were maintained when Mg 2ϩ ions attached to DNA strands; however, the NH 4 ϩ ions were replaced when Ba 2ϩ ions attached to homodimers. These results imply that the interaction sites or modes of Mg 2ϩ differ from those of Ba 2ϩ , whereas Ba 2ϩ ions occupy the same binding sites as NH 4 ϩ with higher binding affinities than NH 4 ϩ , which will be discussed in the next section. Taking Co 2ϩ as an example, mass spectra of DNA mixtures in the presence of 100 M Co 2ϩ ions are shown in Figure 3.…”

Section: Mixtures Of Metal Ions and Dnamentioning

confidence: 90%

“…For single-strand CCT, peaks corresponding to the single strand in 3-and 4-charged ions and dimer in 5-charged ions were observed in the mass spectra (Figure 2a). Besides these, NH 4 ϩ adduct ions of purine homodimers (GGA:…”

Section: Dna Motif Without Metal Ionsmentioning

confidence: 99%

“…There are two possible structures, homoduplex and quadruplex, for this homodimer, since (GGA)n and (GGT)n were found to form either homoduplex or quadruplex in the solution [24,25]. The G-quadruplex shows a tendency to embed NH 4 ϩ between two Gquartets, to stabilize its structure, and yields NH 4 ϩ adducts of G-quartets in the ESI-MS spectra [15,16]…”

Section: Dna Motif Without Metal Ionsmentioning

confidence: 99%

“…It has been proved that cations with an ionic radius in the range 1.3-1.5 Å fit well within two G-quartets and facilitate self-aggregate of G-rich oligonucleotides, and Ba 2ϩ with the ionic radius 1.34 Å assists this self-aggregate more efficiently than NH 4 ϩ (ionic radius 1.43 Å) [29]. Mg 2ϩ with an ionic radius of 0.65 Å is too small to inlay into the G-quartets, which might be the reason that NH 4 ϩ coordinated with homodimer could be replaced by Ba 2ϩ but not by Mg 2ϩ . The differential between Ba 2ϩ and Mg 2ϩ implies that the cation size is an important factor for the binding mechanism.…”

Section: Effects Of Divalent Metal Ions On Formation Of Purine-rich Tmentioning

confidence: 99%

“…The third strand containing G/A bases binds antiparallel to the purine strand of the duplex, whereas the third strand containing G/T bases binds either parallel or antiparallel to the purine strand of the duplex. For the purine motif, the triplex will be inhibited in the presence of monovalent cations, such as sodium and potassium, which serve to coordinate and stabilize the G-rich oligonucleotide dimmers and tetramers [1,4]. The stabilization of the bivalent cation to triplex is complicated-i.e., it is not a simple electrostatic phenomenon-and has been investigated using circular dichroism, UV absorption spectroscopy, footprinting techniques, electrophoresis mobility shift assay, and laser densitometry [5][6][7][8][9][10][11].…”

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confidence: 99%

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Evaluation of effects of bivalent cations on the formation of purine-rich triple-helix DNA by ESI-FT-MS

Wan

Cui

Song

et al. 2009

J. Am. Soc. Mass Spectrom.

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The GGA triplet repeats are widely dispersed throughout eukaryotic genomes. (GGA)n or (GGT)n oligonucleotides can interact with double-stranded DNA containing (GGA:CCT)n to form triple-stranded DNA. The effects of 8 divalent metal ions (3 alkaline-earth metals and 5 transition metals) on formation of these purine-rich triple-helix DNA were investigated by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FT-MS). In the absence of metal ions, no triplex but single-strand, duplex, and purine homodimer ions were observed in mass spectra. The triple-helix DNA complexes were observed only in the presence of certain divalent ions. The effects of different divalent cations on the formation of purine-rich triplexes were compared. Transition-metal ions, especially Co 2ϩ and Ni 2ϩ , significantly boost the formation of triple-helix DNA, whereas alkaline-earth metal ions have no positive effects on triplex formation. In addition, Ba 2ϩ is notably beneficial to the formation of homodimer instead of triplex. (J Am Soc Mass

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Section: Mixtures Of Metal Ions and Dnamentioning

confidence: 90%

Section: Dna Motif Without Metal Ionsmentioning

confidence: 99%

Section: Dna Motif Without Metal Ionsmentioning

confidence: 99%

Section: Effects Of Divalent Metal Ions On Formation Of Purine-rich Tmentioning

confidence: 99%

mentioning

confidence: 99%

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Evaluation of effects of bivalent cations on the formation of purine-rich triple-helix DNA by ESI-FT-MS

Wan

Cui

Song

et al. 2009

J. Am. Soc. Mass Spectrom.

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Nucleic Acid–Metal Ion Interactions

Kazakov

Hecht

2005

Encyclopedia of Inorganic Chemistry

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Nucleic acids (DNA and RNA) are actually salts (or complexes) of metal ions from a chemical point of view. It is impossible to separate the behavior of DNA and RNA from their interactions with metal ions. Metal ions are usually required to promote and stabilize functionally active or native conformations of nucleic acids, as well as to mediate nucleic acid‐protein interactions. However, certain metal ions can also cause structural transformation of nucleic acids, and induce their chemical modification and cleavage. Metal‐nucleic acid interactions are involved in nucleotide biochemistry; genetic information storage and transfer, and control of gene expression, as well as in mutagenesis and carcinogenesis. However, in most cases, it is not currently clear whether the observed effects actually result from direct metal ion‐nucleic acid interaction, since other species, such as specific proteins, may be mediators between the metal ion and the nucleic acid in these processes in vivo . Interest in metal‐nucleic acid interactions is also enhanced by studies of the mechanisms of antitumor activity of certain platinum metal compounds, finding metal ions in crystal structure of natural RNA molecules, studies of the mechanism of RNA catalysis and possible involvement of metal ions in origin of life, as well as by the use of metal ions as structural probes of nucleic acids and as biotechnology tools. This article does not attempt to be comprehensive, but rather presents selected examples to illustrate key facets of metal ion‐nucleic acid interaction. The focus is on the chemical and structural properties of both nucleic acids and metal ions relevant to their interactions. Nucleic acid‐metal interactions can be either nonspecific or dependent on the chemical nature, sequence, and structure of nucleic acids. However, the specificity of these interactions is dependent on structural and chemical properties of both the nucleic acids and the metal ions. Both nucleic acids and metal ions exhibit considerable complexity in their interactions, and such interactions could affect the chemical and biochemical properties of both species.

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Thermodynamic and kinetic characterization of the dissociation and assembly of quadruplex nucleic acids

2000

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The dissociation and assembly of quadruplex DNA structures (and a few quadruplex RNAs) have been characterized at several levels of rigor, ranging from gross descriptions of factors that govern each process, to semiquantitative comparisons of the relative abilities of these factors to induce stabilization or destabilization, to quantitative studies of binding energies (thermodynamics), transformational rates (kinetics), and analysis of their transition‐state energies and mechanisms. This survey classifies these factors, describes the trends and focuses on their interdependencies. Quadruplex assembly is induced most efficiently by added K+ and elevating the strand concentration; however, Na+, NH4+, Sr2+, and Pb2+ are also very effective stabilizers. Quadruplex dissociation is typically accomplished by thermal denaturation, “melting”; however, when the quadruplex and monovalent cation concentrations are low enough, or the temperature is sufficiently high, several divalent cations, e.g., Ca2+, Co2+, Mn2+, Zn2+, Ni2+ and Mg2+ can induce dissociation. Stabilization also depends on the type of structure adopted by the strand (or strands) in question. Variants include intramolecular, two‐ and four‐stranded quadruplexes. Other important variables include strand sequence, the size of intervening loops and pH, especially when cytosines are present, base methylation, and the replacement of backbone phosphates with phosphorothioates. Competitive equilibria can also modulate the formation of quadruplex DNAs. For example, reactions leading to Watson–Crick (WC) duplex and hairpin DNAs, triplex DNAs, and even other types of quadruplexes can compete with quadruplex association reactions for strands. Others include nonprotein catalysts, small molecules such as aromatic dyes, metalloporphyrins, and carbohydrates (osmolytes). Other nucleic acid strands have been found to drive quadruplex formation. To help reinforce the implications of each piece of information, each functional conclusion drawn from each cited piece of thermodynamic or kinetic data has been summarized briefly in a standardized table entry. © 2001 John Wiley & Sons, Inc. Biopolymers (Nucleic Acid Sci) 56: 147–194, 2001

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Monovalent cation effects on intermolecular purine-purine-pyrimidine triple-helix formation

Cited by 114 publications

References 24 publications

Evaluation of effects of bivalent cations on the formation of purine-rich triple-helix DNA by ESI-FT-MS

Evaluation of effects of bivalent cations on the formation of purine-rich triple-helix DNA by ESI-FT-MS

Nucleic Acid–Metal Ion Interactions

Thermodynamic and kinetic characterization of the dissociation and assembly of quadruplex nucleic acids

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