Conditions for the stability of the B, C, and Z structural forms of poly(dG-dC) in the presence of lithium, potassium, magnesium, calcium, and zinc cations

Loprete, D. M.; Hartman, K.A.

doi:10.1021/bi00066a032

Cited by 133 publications

(93 citation statements)

References 24 publications

(62 reference statements)

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“…Evidence for this comes from the lack of major spectral changes (intensity or shifting) of the prominent DNA in-plane vibrations (21)(22)(23)(24)(25)(26)(27)(28) (Figs. 1B and 2).…”

Section: Resultsmentioning

confidence: 99%

“…In a B to A transition, the DNA infrared marker bands at 836 and 1717 cm Ϫ1 were shifted toward lower frequencies at 810 and 1700 cm Ϫ1 , respectively, whereas the backbone PO 2 asymmetric stretching at 1222 cm Ϫ1 shifted toward a higher frequency at 1240 cm Ϫ1 (24,28,36). In a B to Z transition, the marker infrared bands at 1717 and 836 cm Ϫ1 were observed at 1690 and 800 cm Ϫ1 , respectively, whereas the PO 2 band at 1222 cm Ϫ1 was displaced toward a lower frequency at 1215 cm Ϫ1 (24,28,36). Such spectral changes did not occur for DNA marker bands in the presence of Cr(III) and Cr(VI) cations.…”

mentioning

confidence: 95%

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A Comparative Study of Calf Thymus DNA Binding to Cr(III) and Cr(VI) Ions

Arakawa¹,

Ahmad

Naoui

et al. 2000

Journal of Biological Chemistry

257

118

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Chromium(VI) salts are well known to be mutagens and carcinogens and to easily cross the cell membranes. Because they are powerful oxidizing agents, Cr(VI) reacts with intracellular materials to reduce to trivalent form, which binds DNA. This study was designed to investigate the interaction of calf thymus DNA with Cr(VI) and Cr(III) in aqueous solution at pH 6.5-7.5, using Cr(VI)/DNA(P) molar ratios (r) of 1:20 to 2:1 and Cr(III)/ DNA(P) molar ratios (r) of 1:80 to 1:2. UV-visible and Fourier transform infrared (FTIR) difference spectroscopic methods were used to determine the metal ionbinding sites, binding constants, and the effect of cation complexation on DNA secondary structure. Spectroscopic results showed no interaction of Cr(VI) with DNA at low anion concentrations (r ‫؍‬ 1:20 to 1:1), whereas some perturbations of DNA bases and backbone phosphate were observed at very high Cr ( Chromium(VI) salts are well known to be mutagens and carcinogens and to easily invade the insides of cells (1). Cr(VI) produced DNA cross-links in rat tissues in vivo (2) and in cultured cells in vitro (3, 4). Although Cr(VI) damaged nuclear DNA in whole cells, no reaction of Cr(VI) with isolated DNA occurred in vitro at physiological pH in the absence of a metabolizing system (5). The Cr(VI) that is taken up is considered to be reduced by glutathione, cysteine, or ascorbic acid into Cr(III) (6), and the resulting cation reacts with DNA to form Cr(III)-DNA adducts. Because Cr(III) is a final form of chromium within the cell, the interaction of Cr(III) with DNA may play crucial role in the carcinogenetic action of Cr(VI) salts.The conversion of B form into Z form in the purine-pyrimidine sequence of DNA has been considered to be a factor in the transcriptional activity of genes (7). Cr(III) is found to interact with the poly(dG-dC) at low concentration and change B form to Z form in the presence of ethanol (8). However, Cr(III) at high concentration causes DNA condensation, inhibiting the alteration of B to Z structure (8). Moreover, the study on the effect of Cr(III) on DNA replication with single-stranded DNA template and micromolar concentration of Cr(III) revealed that Cr(III) bound in a dose-dependent manner to the template DNA and prevents DNA replication (9). However, if the unbound chromium was removed from the system by gel filtration, the rate of DNA replication by polymerase I (Klenow fragment) on the chromium-bound template increased more than 6-fold relative to control. This increase was paralleled by as much as a 4-fold increase in processivity and a 2-fold decrease in replication fidelity. When the concentration of Cr(III) increased further, DNA-DNA cross-links occurred to inhibit the polymerase activity. Trivalent chromium can bind purified DNA and form lesions capable of obstructing DNA replication in vitro (10, 11). It has also been observed that intact Novikoff ascites hepatoma cells exposed to potassium chromate formed cross-linking of nuclear proteins to DNA (12). Recently, Cr(III) was shown to cause mutation...

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“…Evidence for this comes from the lack of major spectral changes (intensity or shifting) of the prominent DNA in-plane vibrations (21)(22)(23)(24)(25)(26)(27)(28) (Figs. 1B and 2).…”

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 95%

A Comparative Study of Calf Thymus DNA Binding to Cr(III) and Cr(VI) Ions

Arakawa¹,

Ahmad

Naoui

et al. 2000

Journal of Biological Chemistry

257

118

View full text Add to dashboard Cite

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“…When a complete B 3 A transition occurs the DNA marker bands such as 836 cm Ϫ1 appears at about 820 -810 cm Ϫ1 , the PO 2 Ϫ stretching vibration at 1222 cm Ϫ1 shifts toward a higher frequency at 1230 -1240 cm Ϫ1 , and the guanine band at 1717 cm Ϫ1 appears at 1710 -1700 cm Ϫ1 (64,77). In the B 3 Z transition, the guanine band at 1717 cm Ϫ1 shifts to 1690 cm Ϫ1 and the phosphate vibration at 1222 cm Ϫ1 appears at 1216 cm Ϫ1 , whereas the sugar-phosphate band at 836 cm Ϫ1 displaces toward a lower frequency at 800 -790 cm Ϫ1 (64).…”

Section: Polyamines-dna Complexes Studied By Ftir Spectroscopy-mentioning

confidence: 99%

Structural Analysis of DNA Interactions with Biogenic Polyamines and Cobalt(III)hexamine Studied by Fourier Transform Infrared and Capillary Electrophoresis

Ouameur

Tajmir-Riahi

2004

Journal of Biological Chemistry

283

234

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Biogenic polyamines, such as putrescine, spermidine, and spermine are small organic polycations involved in numerous diverse biological processes. These compounds play an important role in nucleic acid function due to their binding to DNA and RNA. It has been shown that biogenic polyamines cause DNA condensation and aggregation similar to that of inorganic cobalt(III)hexamine cation, which has the ability to induce DNA conformational changes. However, the nature of the polyamine⅐DNA binding at the molecular level is not clearly established and is the subject of much controversy. In the present study the effects of spermine, spermidine, putrescine, and cobalt(III)hexamine on the solution structure of calf-thymus DNA were investigated using affinity capillary electrophoresis, Fourier transform infrared, and circular dichroism spectroscopic methods. At low polycation concentrations, putrescine binds preferentially through the minor and major grooves of double strand DNA, whereas spermine, spermidine, and cobalt(III)hexamine bind to the major groove. At high polycation concentrations, putrescine interaction with the bases is weak, whereas strong base binding occurred for spermidine in the major and minor grooves of DNA duplex. However, major groove binding is preferred by spermine and cobalt(III)hexamine cations. Electrostatic attractions between polycation and the backbone phosphate group were also observed. No major alterations of B-DNA were observed for biogenic polyamines, whereas cobalt(III)hexamine induced a partial B 3 A transition. DNA condensation was also observed for cobalt(III)hexamine cation, whereas organic polyamines induced duplex stabilization. The binding constants calculated for biogenic polyamines are K Spm ‫؍‬ 2.3 ؋ 10 5 M ؊1 , K Spd ‫؍‬ 1.4 ؋ 10 5 M ؊1 , and K Put ‫؍‬ 1.02 ؋ 10 5 M ؊1 . Two binding constants have been found for cobalt(III)hexamine with K 1 ‫؍‬ 1.8 ؋ 10 5 M ؊1 and K 2 ‫؍‬ 9.2 ؋ 10 4 M ؊1 . The Hill coefficients indicate a positive cooperativity binding for biogenic polyamines and a negative cooperativity for cobalt(III)hexamine.The biogenic polyamines putrescine [NH 2 (CH 2 ) 4 NH 2 ], spermidine [NH 2 (CH 2 ) 4 NH(CH 2 ) 3 NH 2 ], and spermine [NH 2 (C-H 2 ) 3 NH(CH 2 ) 4 NH(CH 2 ) 3 NH 2 ] (Structure 1) are the most prevalent polyamines in mammalian cells. They are small aliphatic polycations involved in numerous diverse biological processes, such as the ability to modulate gene expression and enzyme activities, activation of DNA synthesis, cell proliferation and differentiation, and others (1-8). Other functions of polyamines have been related to DNA protection from external agents (9, 10) and against radiation damage (11, 12). In general, spermidine and spermine are present in millimolar concentrations in vivo, whereas putrescine levels are slightly lower (13-15). However, the most important characteristic of polyamines within the cells is to bind nucleic acids and DNA in particular (1, 6).Polyamines also have the ability to induce DNA conformational transitions. Their bindi...

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“…For example, poly[d(G-C)] 2 DNA has been shown to change from B form and stabilise in Z form 245 when the chloride salts of Mg 2+ , Ca 2+ , Cd 2+ , Hg 2+ or Zn 2+ are added, even in relatively low concentrations. 22 Available x-ray data suggests that these ions bind in the major groove of B-DNA and cause the major groove to disappear, the minor groove to deepen and the helix to become left-250 handed.…”

Section: Metal Ionsmentioning

confidence: 99%

Synthetic metallomolecules as agents for the control of DNA structure

2007

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DNA is often referred to as the molecule of life, since it contains the instructions for making the required proteins. However, it is not simply a (genetic) code to be read; its structure has an important role in determining when and how much of a particular 5 protein is made at any point in time. Furthermore, there are a range of special DNA structures, e.g. Holliday junctions, which play essential roles for the existence of life as we know it or as it will become. In this tutorial review the normal B-DNA structure is summarised and metallomolecule binding modes discussed then used as a basis for examining DNA structures which can be induced by molecules containing metallic cations. The effects of aquated metal ions, cobalt ammine and ruthenium octahedral metal complexes, metallo helicates and platinum complexes such as cis-platin are discussed alongside techniques such as NMR, 10 X-ray crystallography, gel electrophoresis, circular dichroism, linear dichroism and molecular dynamics.

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Conditions for the stability of the B, C, and Z structural forms of poly(dG-dC) in the presence of lithium, potassium, magnesium, calcium, and zinc cations

Cited by 133 publications

References 24 publications

A Comparative Study of Calf Thymus DNA Binding to Cr(III) and Cr(VI) Ions

A Comparative Study of Calf Thymus DNA Binding to Cr(III) and Cr(VI) Ions

Structural Analysis of DNA Interactions with Biogenic Polyamines and Cobalt(III)hexamine Studied by Fourier Transform Infrared and Capillary Electrophoresis

Synthetic metallomolecules as agents for the control of DNA structure

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