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4 protocols using calf thymus dna

1

Purification and Characterization of Biomolecules

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Tnz was purchased
from Sigma-Aldrich
and purified by re-crystallization from methanol. Copper(II) chloride
(CuCl2·2H2O), copper(II) acetate [Cu(OAc)2·H2O], NaCl, NaNO3, trichloroacetic
acid (TCA), glacial acetic acid, sodium dihydrogen phosphate, disodium
hydrogen phosphate, anthrone as reagent, Folin-Ciocalteu as reagent,
congo red, cetyltrimethylammonium bromide (CTAB), chitin flakes, Tris–HCl,
β-mercaptoethanol, phenylmethylsulfonyl fluoride (PMSF), and
KCl (all AR grade) were purchased from E. Merck, India. Thymine, cytosine,
and adenine were purchased from TCI, Japan, and calf thymus DNA, crystal
violet (CV), ethyl acetate, hydroxyl amine, NaOH, and ferric chloride
were procured from Sisco Research Laboratories, India. Calf thymus
DNA was dissolved in triple distilled water in the presence of 120
mM NaCl, 35 mM KCl, and 5 mM MgCl2. Its concentration was
determined using a molar extinction coefficient of 6600 M–1 cm–1 at 260 nm. Absorbance of the DNA solution
was also measured at 280 nm; A260/A280 was determined. The value found in the range
1.8–1.9 was considered ready for use, not requiring further
purification. Quality of calf thymus DNA was verified using circular
dichroism (CD), recording its response at 260 nm on a CD spectropolarimeter
(J815—JASCO, Japan). Aqueous solutions of all other substances
were prepared in triple distilled water.
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2

Alizarin-Manganese(II) Complex Characterization

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Alizarin was procured from Sigma and purified by re-crystallization using ethanol. The MnII complex of Alizarin [MnII(alz)2(H2O)2] (Figure 1) was prepared and characterized earlier [55 ]. KCl (AR), purchased from Merck India, was used as an electrolyte for electrochemical experiments in aqueous medium. Nucleobases uracil, thymine and adenine were obtained from Sisco Research Laboratories, India; cytosine was obtained from Sigma. Calf thymus DNA was obtained from Sisco Research Laboratories, India. Tetrabutyl ammonium bromide (TBAB) (AR) and Ethidium bromide (EtBr) were purchased from Merck, India. Triple distilled water was used for preparing solutions. Phosphate buffer (pH ~ 7.4) was prepared in triple distilled water using sodium dihydrogen phosphate (AR) and disodium hydrogen phosphate (AR) procured from Merck, Germany.

Structure of (A) Alizarin, (B) [MnII(alz)2(H2O)2] and (C) an anthracycline anticancer drug.

Figure 1
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3

Topoisomerase-DNA Interaction Assay

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THAQ was purchased
from BDH, England, and purified by re-crystallization from the alcohol–water
mixture. Hydroxy-9,10-anthraquinone, which is sensitive to light and
oxygen, solutions were prepared just before use or stored in dark
bottles under deaerated condition. CoCl2·6H2O [Merck, India] was dissolved in deionized triple-distilled water.
Calf thymus DNA, purchased from Sisco Research Laboratories, India,
was dissolved in phosphate buffer and kept for a minimum of 24 h.
Its concentration was determined in terms of nucleotide at 260 nm
considering ε260 to be 6600 M–1 cm–1. Absorbance at 260 and 280 nm was used to
calculate the ratio [1.8 < A260/A280 > 1.9] that indicates DNA to be sufficiently
free of protein. Quality of the Calf thymus DNA used was also checked
from the characteristic circular dichroism band at 260 nm. Phosphate
buffer containing 120 mM NaCl, 3.5 mM KCl, 1 mM CaCl2,
and 0.5 mM MgCl2 was prepared to maintain pH in the physiological
pH range (6.8–8.2) during titration of the complex with DNA.
Recombinant human DNA topoisomerase I and human DNA topoisomerase
II alpha were purchased from TopoGENInc (Port Orange, Florida, USA).
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4

DNA-Copper(II) Complex Characterization

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Onz
was purchased from
TCI, Japan. Copper(II) chloride (CuCl2·2H2O), zinc(II) chloride (ZnCl2), NaCl, NaNO3,
and MgCl2 (AR grade) were purchased from E. Merck, India.
Nucleic acid bases cytosine and thymine were purchased from Sisco
Research Laboratories, India, while adenine was procured from TCI,
Japan. Calf thymus DNA and ethidium bromide were purchased from Sisco
Research Laboratories, India. DNA was dissolved in phosphate buffer
(pH ∼ 7.4) containing NaCl, KCl, and MgCl2 as electrolytes.
Concentration of DNA in terms of nucleotide was determined considering
ε260 = 6600 mol–1 dm3 cm–1. Phosphate buffer (pH ∼ 7.4) was prepared
using sodium dihydrogen phosphate and disodium hydrogen phosphate
(AR, Merck, Germany) in triple-distilled water.
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