DNA electrostatic

The first successful application of this methodology involved glassy carbon surfaces derivatized with single-stranded DNA. " Electrostatically-bound octahedral complexes of Co(lll) were used to quantitiate immobilized DNA and to monitor the binding of a complementary oligonucleotide. This work verified that electrochemical detection of target sequences was feasible. 

The high ionic strength (high salt concentration) shields the charges on the histones and DNA and enables the proteins to dissociate from the DNA. Electrostatic interactions are rendered much weaker in a high-ionic-strength environment. 

DNA redox indicators bind to DNA or are present in the solution phase. Some of them interact with DNA on the basis of electrostatic forces [21]. Cationic indicators such as metal complex cations can be attracted to the DNA by the negative charge of the DNA backbone. On the other hand, anionic indicators, for instance hexacyanoferrate (III/II) [Fe(CN)6] ", work on the principle of repulsion by the negatively charged DNA backbone. As a consequence, its voltammetric current response is lower than and anodic to the cathodic peak potential separation, higher than that observed at bare electrodes without DNA. Electrostatic indicators can also respond to differences in negative charge density between ssDNA and dsDNA [14]. 

In this section, we present a detailed discussion of methods relevant to counterion simulations of DNA. Electrostatic interactions dominate all energies involving the DNA and ions. The largest systems simulated to date typically require truncation of nonbonded interaction potentials at around ISA. Abrupt truncation of the potential has the adverse effect of creating an artificial boundary. In an MD simulation, the abrupt truncation produces a discontinuity in force because the first derivative of the interaction potential at the cutoff radius is infinity. Computer programs simply set the forces at the boundary to be zero instead of large values to represent infinity. 

The first term represents the forces due to the electrostatic field, the second describes forces that occur at the boundary between solute and solvent regime due to the change of dielectric constant, and the third term describes ionic forces due to the tendency of the ions in solution to move into regions of lower dielectric. Applications of the so-called PBSD method on small model systems and for the interaction of a stretch of DNA with a protein model have been discussed recently ([Elcock et al. 1997]). This simulation technique guarantees equilibrated solvent at each state of the simulation and may therefore avoid some of the problems mentioned in the previous section. Due to the smaller number of particles, the method may also speed up simulations potentially. Still, to be able to simulate long time scale protein motion, the method might ideally be combined with non-equilibrium techniques to enforce conformational transitions. 

They compared the PME method with equivalent simulations based on a 9 A residue-based cutoflF and found that for PME the averaged RMS deviations of the nonhydrogen atoms from the X-ray structure were considerably smaller than in the non-PME case. Also, the atomic fluctuations calculated from the PME dynamics simulation were in close agreement with those derived from the crystallographic temperature factors. In the case of DNA, which is highly charged, the application of PME electrostatics leads to more stable dynamics trajectories with geometries closer to experimental data [30]. A theoretical and numerical comparison of various particle mesh routines has been published by Desemo and Holm [31]. 

The final class of methods that we shall consider for calculating the electrostatic compone of the solvation free energy are based upon the Poisson or the Poisson-Boltzmann equatior Ihese methods have been particularly useful for investigating the electrostatic properties biological macromolecules such as proteins and DNA. The solute is treated as a body of co stant low dielectric (usually between 2 and 4), and the solvent is modelled as a continuum high dielectric. The Poisson equation relates the variation in the potential (f> within a mediu of uniform dielectric constant e to the charge density p ... 

Backbone (protein), 1028 Backside displacement. reaction and.363-364 von Baeyer, Adolf, 113 Baeyer strain theory, 113-114 Bakelile, structure of, 1218 Banana, esters in, 808 Barton, Derek, H. R., 389 Basal metabolic rate, 1169 Basal metabolism. 1169-1170 Base, Bronsted-Lowry, 49 Lewis, 57, 59-60 organic, 56-57 strengths of, 50-52 Base pair (DNA), 1103-1105 electrostatic potential maps of. 

DNA sequencing and. 1113 Electrospray ionization (ESI) mass spectrometry, 417-418 Electrostatic potential map, 37 acetaldehyde, 688 acetamide, 791,922 acetate ion. 43. 53, 56, 757 acetic acid. 53. 55 acetic acid dimer, 755 acetic anhydride, 791 acetone, 55, 56. 78 acetone anion, 56 acetyl azide, 830 acetyl chloride, 791 acetylene. 262 acetylide anion, 271 acid anhydride, 791 acid chloride, 791 acyl cation, 558 adenine, 1104 alanine, 1017 alanine zwitterion, 1017 alcohol. 75 alkene, 74, 147 alkyl halide, 75 alkyne. 74... 

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