Orientation of the DNA molecule

Linear Dichroism. In this technique, the DNA molecules are aligned either by an applied electric field pulse or in a flow gradient. The orientation of the aromatic residues of the metabolite model compounds bound to the DNA (either covalently or non-covalently) relative to the orientation of the DNA bases is probed utilizing linearly polarized light. The linear dichroism A A can be either negative or positive, and is defined as... 

Only a single strand of the DNA molecule is normally transcribed into RNA over any given region. Because of the antiparallel nature of the DNA helix, transcription from one strand proceeds clockwise and transcription from the other counterclockwise (the r strand is conventionally taken as the one that is transcribed in the clockwise direction when the chromosome is oriented as in the drawing). 

Oligonulceotides modified to carry an amino group or proteins through their lysine residues can be covalently attached to aldehyde- and epoxy-derivatized surfaces. Other reactive surfaces used to covalently link both DNA and proteins include N-hydroxy succinimide [20] and maleimide [24]. Proteins expressed with polyhistidine and biotin tags have been attached to surfaces coated with nickel chelate and streptavidin, respectively [25,26]. This strategy is likely to result in the proper orientation of the displayed molecules on the surface, thereby improving their functionality and stability. 

The BRM is a natural generalization of the original reptation model where the motion of the primitive chain in its "tube is considered to become biased when an electric field is applied. The electrophoretic properties of the DNA molecules are related in the BRM to the effect of the field on the conformation of the reptation tube since this conformation tends to orient in the field direction when the primitive chain creates new tube sections, the electrophoretic velocity becomes a nonlinear function of the electric field. This tube alignment also reduces the effectiveness of the entanglements in opposing the electrophoretic drift, with the consequence that, except for transient effects or very small molecules, the mobility becomes molecular-size independent in continuous fields. 

The mass of histone in the chromosomes is larger than that necessary purely for structures of this type, as shown in Fig. 85. Considering the total mass of histone in the chromosomes, these workers conclude from the absence of orientation of the diffraction spectrum and the absence of dichroism of infrared absorption of histone that the polypeptide chain of histones is not all arranged in the same way, along or perpendicular to the length of the DNA molecules. 

Macromolecules, especially DNA, that are difficult to dissolve in stretched polymer sheets or nematic liquid crystals have often successfully been aligned in a flow. Flow LD is measured in a solution between a stationary and a fast-rotating cylinder using a Couette or Maxwell cell. It has proved very useful for the study of the interaction between mac-romolecules and smaller molecules, for example the attachment of carcinogenics to DNA. The long axis of the DNA molecules, the helix axis, becomes the orientation axis. So far such studies have primarily been performed in the UV-visible region. The two... 

The DNA molecules in each cell of an organism contain all the genetic information necessary to ensure the normal development and function of that organism. This genetic information is encoded in the precise linear sequence of the nucleotide bases from which the DNA is built. DNA is a linear molecule while its diameter is only about 20 A, if stretched out its length can reach many millimeters. This means that concentrated solutions of DNA can be pulled into fibers in which the long thin DNA molecules are oriented with their long axes parallel. 

For the analysis of the dynamical properties of the water and ions, the simulation cell is divided into eight subshells of thickness 3.0A and of height equal to the height of one turn of DNA. The dynamical properties, such as diffusion coefficients and velocity autocorrelation functions, of the water molecules and the ions are computed in various shells. From the study of the dipole orientational correlation function... 

Fig. 13 Results from the quantum calculations on the duplex sequence 5 -GAGG-3. In a, the sodium ions and their solvating water molecules are located at positions near the phosphate anions of the DNA backbone. In b, one sodium ion is moved from near a phosphate anion to N-7 of a guanine, which molecular dynamics calculations show to be a preferred site. The balloons represent the hole density on the GAGG sequences with the two different sodium ion orientations. The radical cation clearly changes its average location with movement of the sodium ion...

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