Nucleic acids aqueous solutions

The pulse radiolysis technique has been used to measure absolute rate constants for reactions of some nucleic acid constituents with Clf radicals (the species produced by reaction of OH radicals with chloride ions in acid aqueous solution). The rate of disappearance of the Cl2 absorption spectrum was measured in the absence and presence of the various solutes. Rate constants for the corresponding OH radical reactions are found to be 20 to 200 times greater than the rate constants for the Clf radical reactions. Steady state radiolysis showed that in some cases the radicals produced by reaction of these compounds with Clf radicals differ in their subsequent reaction from the corresponding OH radical adduct. 

It has also been demonstrated that the distribntion of nucleoside anomers produced in acidic aqueous solutions is kinetically controlled on short time scales, but will reach an equilibrium distribution that minimizes steiic interactions between the base and sugar, which for aldopentoses results in the predominance of the a- and P-pyranosyl forms (25,27-29). Therefore, it would not have been the selective production of p-fiiranosyl nucleosides that influenced their incorporation into piebiotic nucleic adds. 

Liquid Crystalline Structures. In certain ceUular organeUes, deoxyribonucleic acid (DNA) occurs in a concentrated form. Striking similarities between the optical properties derived from the underlying supramolecular organization of the concentrated DNA phases and those observed in chiral nematic textures have been described (36). Concentrated aqueous solutions of nucleic acids exhibit a chiral nematic texture in vitro (29,37). 

Sephadex. Other carbohydrate matrices such as Sephadex (based on dextran) have more uniform particle sizes. Their advantages over the celluloses include faster and more reproducible flow rates and they can be used directly without removal of fines . Sephadex, which can also be obtained in a variety of ion-exchange forms (see Table 15) consists of beads of a cross-linked dextran gel which swells in water and aqueous salt solutions. The smaller the bead size, the higher the resolution that is possible but the slower the flow rate. Typical applications of Sephadex gels are the fractionation of mixtures of polypeptides, proteins, nucleic acids, polysaccharides and for desalting solutions. 

Solute-solvent interactions in aqueous solutions of pyrimidine nucleic acid bases 99PAC1286. 

The two strands of the nucleic acid DNA are held together by four organic bases. The structure of one of these bases, thymine, is shown below, (a) How many protons can this base accept (b) Draw the structure of each conjugate acid that can be formed, (c) Mark with an asterisk any structure that can show amphiprotic behavior in aqueous solution. 

Mossbauer spectroscopic titration of [Me2Sn(IV)] and [MesSnflV)] hydroxides with ligands mimicking nucleic acid phosphate sites and with native DNA was the aim of work by Barbieri et al. A series of aqueous solutions of each system, formed by the organotin(IV) hydroxides and the phosphate ligands used... 

Daniels M, Hauswirth W (1971) Fluorescence of the purine and pyrimidine bases of the nucleic acids in neutral aqueous solution at 300 K. Science 171 675... 

Cieplak, P., Caldwell, J. W., Kollman, P. A., Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation aqueous solution free energies of methanol and IV-methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases, J. Comput. Chem. 2001, 22, 1048-1057... 

Nucleic acids, DNA and RNA, are attractive biopolymers that can be used for biomedical applications [175,176], nanostructure fabrication [177,178], computing [179,180], and materials for electron-conduction [181,182]. Immobilization of DNA and RNA in well-defined nanostructures would be one of the most unique subjects in current nanotechnology. Unfortunately, a silica surface cannot usually adsorb duplex DNA in aqueous solution due to the electrostatic repulsion between the silica surface and polyanionic DNA. However, Fujiwara et al. recently found that duplex DNA in protonated phosphoric acid form can adsorb on mesoporous silicates, even in low-salt aqueous solution [183]. The DNA adsorption behavior depended much on the pore size of the mesoporous silica. Plausible models of DNA accommodation in mesopore silica channels are depicted in Figure 4.20. Inclusion of duplex DNA in mesoporous silicates with larger pores, around 3.8 nm diameter, would be accompanied by the formation of four water monolayers on the silica surface of the mesoporous inner channel (Figure 4.20A), where sufficient quantities of Si—OH groups remained after solvent extraction of the template (not by calcination). 

The formation of the CLS/nucleic acid complex was performed by mixing an aqueous suspension of CLS with a solution containing the nucleic acids [19,50,56],... 

Delayed action cytotoxins that inhibit the synthesis of nucleic acids. They are obtained from various molds/fungi (Aspergillus flavus, Aspergillus parasiticus). They are colorless to pale-yellow crystalline materials melting above 450°F. The "B" toxins fluoresce blue in the presence of UV light while the "G" toxins fluoresce green. They are only slightly soluble in water, but are soluble in methanol, acetone, and chloroform. Aqueous solutions are "probably stable" and "probably tolerant" to chlorine at purification concentrations. 

Gel electrophoresis is widely used in the routine analysis and separation of many well-known biopolymers such as proteins or nucleic acids. Little has been reported concerning the use of this methodology for the analysis of synthetic polymers, undoubtedly since in many cases these polymers are not soluble in aqueous solution - a medium normally used for electrophoresis. Even for those water-soluble synthetic polymers, the broad molecular weight dispersities usually associated with traditional polymers generally preclude the use of electrophoretic methods. Dendrimers, however, especially those constructed using semi-controlled or controlled structure synthesis (Chapters 8 and 9), possess narrow molecular weight distribution and those that are sufficiently water solubile, usually are ideal analytes for electrophoretic methods. More specifically, poly(amidoamine) (PAMAM) and related dendrimers have been proven amendable to gel electrophoresis, as will be discussed in this chapter. 

CNTs can conjugate with nucleic acids via non-covalent bond. ssDNA, short double-stranded DNA and total RNA molecules can attach to the surface of CNTs and can disperse CNTs in aqueous environment. The poly(30T) has the highest dispersion efficiency (Zheng et al., 2003). For example, 1 mg DNA molecules mix with lmg CNTs in 1ml water, yield at most 4mg/ml CNT solution. DNA-CNT complexes can be purified or isolated by electronic properties such as agarose gel electrophoresis and centrifuge method (Cui et al., 2004a Karajanagi et al., 2004). 

Orotic acid readily forms dimers even when irradiated in liquid medium [582, 583]. 5-Bromouracil (5-BrU) in DNA is dehalogenated, rather than forming cyclobutane-type dimers. Such DNA derivatives are more sensitive to ultraviolet irradiation than normal DNAs [584-594], Irradiation of 5-bromo-uracil and derivatives in aqueous medium produces 5,5 -diuracil [590, 591]. However, derivatives such as 3-sbutyl-5-bromo-6-methyluracil have been reported to yield cyclobutane dimers either by irradiation of frozen aqueous solutions, or by catalysis with free radical initiators, such as aluminium chloride, ferric chloride, peroxides or azonitriles [595]. 5-Hydroxymethyluracil is reported to dimerize very slowly in frozen water at 2537 A [596]. The fundamental research in the photochemistry of the nucleic acids, the monomeric bases, and their analogues has stimulated new experiments in certain micro-organisms and approaches in such diverse fields as template coding and genetic recombination [597-616]. 

The tertiary structure of DNA is the structural level that is most relevant to 3-D reality. Traditionally, ODNs in a physiologically relevant aqueous solution are considered to be in a random-coiled ssDNA state or in the form of dsDNA helix in the presence of a complementary DNA, including the case of self-complementarity. The double helix is the dominant tertiary structure for biological DNA that can be in one of the three DNA conformations found in nature, A-DNA, B-DNA, and Z-DNA. The B-conformation described by Watson and Crick (11) is believed to predominate in cells (12). However other types of nucleic acid tertiary structures different from random or classical double-stranded helix forms can also be observed. Among them are triplexes, quadruplexes, and several other nucleic acid structures (13, 14). 

Nucleic acid derivatives are altered by exposure to ionizing radiation in aerated or oxygenated aqueous solution, but the alteration consists largely of degradation.134 Pyrimidines are more susceptible than purines but the difference is only about a factor of two (Table XIV).134 The primary product from a pyrimidine is a hydroperoxide produced according to eq. (24). 

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