Nucleic acids mechanical methods

All the nucleic acid bases absorb UV radiation, as seen in Tables 11-1, 11-2, 11-3, 11-4, and 11-5, making them vulnerable to the UV radiation of sunlight, since the energy of the photons absorbed could lead to photochemical reactions. As already mentioned above, the excited state lifetimes of the natural nucleobases, and their nucleotides, and nucleosides are very short, indicating that ultrafast radiationless decay to the ground state takes place [6], The mechanism for nonradiative decay in all the nucleobases has been investigated with quantum mechanical methods. Below we summarize these studies for each base and make an effort to find common mechanisms if they exist. 

It has to be underlined that, in comparison to LS containing nucleic acid molecules inside the particle, the production of CLS may be performed obviously without considering the stability problems of nucleic acid molecules. In this view, some preparation procedures are not considered, such as the microemulsion technique [55] that represents a favorable method when working with substances unstable because of the high mechanical stress produced by high-pressure homogenization. 

Sofia HJ, Chen G, Hetzler BG, et al. 2001. Radical SAM, a novel protein superfanuly linking unresolved steps in familiar biosynthetic pathways with radical mechanisms functional characterization using new analysis and information visualization methods. Nucleic Acids Res 29 1097-106. 

Transfection is the process of introducing DNA or RNA into eukaryotic ceils. The use of transfection is to study the role and regulation of proteins or to understand the mechanisms of a pathway. Transfection can be transient for rapid analysis or stable , mostly for induction of expression. There are various methods of transfection which include electroporation, viral vectors, DEAE-Dextran, calcium phosphate or Lipofectamine. The choice of transfection depends on the cell type used. The most desirable technique is the one which gives high efficiency of nucleic acid transfection with less interference to the cells physiology and high reproducibility. 

The molecular mechanics method is extremely parameter dependent. A force field equation that has been empirically parameterized for calculating peptides must be used for peptides it cannot be applied to nucleic acids without being re-parameterized for that particular class of molecules. Thankfully, most small organic molecules, with molecular weights less than 800, share similar properties. Therefore, a force field that has been parameterized for one class of drug molecules can usually be transferred to another class of drug molecules. In medicinal chemistry and quantum pharmacology, a number of force fields currently enjoy widespread use. The MM2/MM3/MMX force fields are currently widely used for small molecules, while AMBER and CHARMM are used for macromolecules such as peptides and nucleic acids. 

Previous theoretical treatments of the transition between the helicel and random forms of the desoxyribose nucleic acid (DNA) molecule are extended to Include formally the explicit consideration of the dissociation into two separate chains and the consideration of the effects of the.ends of the chains, An approximate form for the fraction of the base pairs that are bonded is obtained in terms of two parameters, a stability constant for base pairing and a constant representing the interaction of adjacent base pairs. The matrix method of statistical mechanics proves to be adaptable to this problem. Some numerical examples are worked out for very long molecules, for which case it is found that the effect of concentration is small. 

N. V. Zholtovsky and V. I. Danilov, Quantum Mechanical Study of the Electronic Structure of the Nucleic Acids Bases by CNDO/2 Method. Preprint Inst. Phys. Acad. Sci. Ukr. SSR, Kiev, 1973. 

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