Thermodynamics of DNA binding and condensation: isothermal titration calorimetry and electrostatic mechanism 1 1Edited by I. Tinoco

Matulis, Daumantas; Rouzina, Ioulia; Bloomfield, Victor A.

doi:10.1006/jmbi.1999.3470

Cited by 233 publications

(319 citation statements)

References 31 publications

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“…Some other experiments estimated the association constant of the phosphate groups of one DNA molecule and spermidinium to be 1.4 ¥ 10 5 M -1 in the absence of DAPI. 26,27 This value is about twenty times as large as that of our results. Spermidinium prefers the minor grooves of DNA, 28 and DAPI also prefers the minor grooves as mentioned above.…”

Section: The Association Constant Of Phosphate Group Of Dna Molecule contrasting

confidence: 46%

In Situ Fluorescence Microscopic Investigation into the Dependence of Conformation and Electrophoretic Velocity of Single DNA Molecules on Acid or Spermidine Concentration

Inoshita

Tsukahara

2009

ANAL. SCI.

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A measurement cell for DNA migration was fabricated by agarose gel on a glass plate for the purpose of in situ fluorescence microscopic measurements of the electrophoretic behaviors of single giant DNA (T4GT7DNA, 165600 base pairs) molecules. The cell was connected to an original circuit that can supply a constant electric field strength to a DNAmigration-space of the cell. Conformation and electrophoretic velocity of single DNA molecules were measured at the same time as a function of acid or spermidinium concentration. As a result, the conformational change from the randomcoiled to globular states and reduced electrophoretic velocities were induced by an addition of acid or spermidinium. The change of the electrophoretic velocity was quantitatively attributable to the partial neutralization of anionic phosphate groups of DNA molecules by H + or tricationic spermidinium. The acid-dissociation constant of the conjugate acid of phosphate group of the DNA molecules (pKa) and the association constant of the phosphate groups of DNA molecule with tricationic spermidinium (Kass) were determined to be 2.0 and 5.5 ¥ 10 3 dm 3 mol -1 , respectively.

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Section: The Association Constant Of Phosphate Group Of Dna Molecule contrasting

confidence: 46%

In Situ Fluorescence Microscopic Investigation into the Dependence of Conformation and Electrophoretic Velocity of Single DNA Molecules on Acid or Spermidine Concentration

Inoshita

Tsukahara

2009

ANAL. SCI.

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“…The binding energies obtained from the explicitly hydrated models listed in Table 2 are generally lower than those predicted by the continuum and are better suit to the free energies observed in the DNA-metal binding experiments. 52,53 In both models the Cu 2+ ion binds most strongly at the N7 position, and exhibits an exceptional preference for the N7 site over O6. The Cu 2+ binding to the N3 site provided lower interaction energies (not shown) than for the N7 or O6 complexes.…”

Section: Resultsmentioning

confidence: 99%

Infrared Absorption Detection of Metal Ion-Deoxyguanosine Monophosphate Binding: Experimental and Theoretical Study

Andrushchenko

Bouř

2008

J. Phys. Chem. B

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Metal ion interactions with nucleic acids attract attention because of the environmental and biological consequences. The formation of the complex is often monitored by the vibrational spectroscopy. To identify characteristic binding patterns and marker bands on a model DNA component, infrared absorption spectra of the deoxyguanosine monophosphate complexes with Na + , Mg 2+ , Ca 2+ , Ni 2+ , Cu 2+ , Zn 2+ , and Cd 2+ cations were recorded and interpreted on the basis of density-functional computations. The aqueous environment was simulated by continuum and combined continuum-explicit solvent models. For the binding to the N7 position of the guanine base, the computation predicted a characteristic frequency upshift and splitting of the 1578 cm -1 band, which is in accord with available experimental data. Contrary to the expectation, the modeling suggests that the binding to the carbonyl group might not be detectable, as the metal causes smaller spectral changes if compared to the hydrogen-bound water molecules. The binding to the phosphate group causes significant spectral changes in the sugar-phosphate vibrating region (∼800-1200 cm -1 ), but also notable frequency shifts of the carbonyl vibrations. The Cu 2+ and Zn 2+ ions induced the largest alterations in observed vibrational absorption, which corresponds to the calculated strong interaction energies in the N7-complexes and to previous experimental experience. Additional changes in the vibrational spectra of the copper complexes were observed under high metal concentration, corresponding to the simultaneous binding to the phosphate residue. The two-step Cu 2+ binding process was also confirmed by the microcalorimetry titration curve. The computations and combination of more techniques thus help us to assign and localize spectral changes caused by the metal ion binding to nucleic acids. IntroductionComplexes of metal ions with nucleic acids participate in various biological processes, such as DNA replication and transcription, enzymatic cleavages, mutagenesis, carcinogenesis, and DNA packing in a living cell and also stabilize particular nucleic acid secondary structures. 1-6 A vast number of experimental and theoretical studies have been dedicated to metal interactions with nucleic acids and their components. [5][6][7][8][9][10] In the present work we systematically investigate interactions of some common metal ions with deoxyguanosine monophosphate (dGMP) as a model system, in order to better explain previously observed changes in infrared absorption (IR) spectra of nucleic acids upon the interaction with the metals.Being relatively simple and widely available, infrared spectroscopy provided precious information about the interaction of metal ions with nucleic acids (e.g., see refs 11-23). Detailed structural information could be obtained from the IR spectra when observed bands were assigned to particular bonds or DNA functional groups. [24][25][26][27] In practice, however, the assignment is complicated by solvent interference, overlapped and naturally bro...

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“…Overcharged complexes, and screening of the electrostatic interactions are two causes of such a behaviour, compaction usually being seen as enthalpically driven, with entropic effects opposing the existence of compact structures. Variations in this behavior are sometimes observed for low charge cationic agents [34,35], but the observations are not totally consistent (see, e.g., Ref. [36]).…”

Section: Proteinsmentioning

confidence: 97%

Cationic agents for DNA compaction

Gawęda

Morán

Pais

et al. 2008

Journal of Colloid and Interface Science

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Fluorescence microscopy was used to investigate the conformational changes of individual T4 DNA molecules induced by different compacting agents, namely the cationic surfactants, cetyltrimethylammonium bromide (CTAB) and chloride (CTAC), iron(III), lysozyme, and protamine sulfate. A protocol for establishing size estimates is suggested to obtain reproducible results. Observations show that in the presence of lysozyme and protamine sulfate, DNA molecules exhibit a conformational change from an elongated coil structure to compact globules, usually interpreted as a first-order transition. The maximum degree of compaction that is attained when iron(III) or CTAB (CTAC) are used as compacting agents is considerably smaller, and intermediate structures (less elongated coils) are visible even for high concentrations of these agents. Dynamic light scattering experiments were carried out, for some of the systems, to assess the reliability of size estimates from fluorescence microscopy.

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Thermodynamics of DNA binding and condensation: isothermal titration calorimetry and electrostatic mechanism 1 1Edited by I. Tinoco

Cited by 233 publications

References 31 publications

In Situ Fluorescence Microscopic Investigation into the Dependence of Conformation and Electrophoretic Velocity of Single DNA Molecules on Acid or Spermidine Concentration

In Situ Fluorescence Microscopic Investigation into the Dependence of Conformation and Electrophoretic Velocity of Single DNA Molecules on Acid or Spermidine Concentration

Infrared Absorption Detection of Metal Ion-Deoxyguanosine Monophosphate Binding: Experimental and Theoretical Study

Cationic agents for DNA compaction

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