Bases Base pair

It can be seen from the figure that the electrostatic repulsive forces between the macrocations are overwhelmed, probably by hydrophobic attractive forces between their hydrophobic side groups. It should be noted that the complimentary base-base pairing is unimportant in the present case. If this is not the case, the mixtures of APVP and TPVP should show the largest hypochromicity. This, however, is not the case. The importance of the hydrophobic interactions between nucleic acid bases has been proposed by Ts o et al.I9 from thermodynamic parameters of various nucleic acid bases or nucleosides in aqueous media. 

BR0NSTED THEORY LEWIS BASE BASE PAIRING BASE STACKING... 

Keywords DNA Bases, Base Pair, Laser Desorption, REMPI, IR-UV Double Resonance... 

Solvation of DNA bases/base pairs is of fundamental importance to biological processes as they take place in aqueous media. The effect of hydration on neutral bases or base pairs has been addressed using quantum chemical methods [106-112] as well as molecular dynamics (MD) simulations [113, 114], It is known that unlike the gas phase, dipole bound anions do not exist in condensed environments because such diffuse states are destabilized in the aqueous phase [115]. The drastic change in the nature of excess electron binding in the presence of water molecules with uracil has been observed experimentally by Bowen and co-workers [95b] using negative electron photoelectron spectroscopy (PES). They observed that even with a single water molecule the dipole bound state of uracil anion in gas phase... 

The rates of copolymerization investigated in DMSO, DMF and pyridine are to those calculated with 0 = 1 (cross-termination constant) while the rates in enthanol and dioxane deviate largely from the calculated ones (Fig. 4). In the latter cases, it is assumed that the alternating propagation is accelerated by the effective formation of specific base-base pairing between uracil and adenine units. 

From the values of the monomer reactivity ratios, the relative reactivity of the monomers toward the growing free radicals derived from MAOThe, MAOA and MAOU (t, a and u, respectively) was estimated (Table 6). As for the growing radical of MAOThe (t), for example, the reactivities of MAOThe and MAOU monomer are equal but higher than that of MAOA monomer in ethanol solution while the reactivities of these monomers are nearly equal in dioxane solution. The copolymerization proceeds predominantly under the influence of base-base pairing between adenine and uracil rings. 

Water is an essential part in the biomacromolecular system, which is mainly responsible for the structure and functions of nucleic acids, proteins, and other constituents of cell [136-138]. Both proteins and DNA are generally hydrated. It is well known that the conformation of DNA is sensitive to hydration, and presence of salts and ligand molecules [112, 138]. The nucleic acids have three levels of water structure. About 12 water molecules per nucleotide are involved in the primary hydration shell [107, 112, 137, 138]. The water molecules present in the primary shell are impermeable to cations and do not form ice on freezing. The secondary level is permeable to cations and forms ice on freezing and third level is the completely disordered, so-called bulk water. Several theoretical studies have been carried out on the level of hydration on DNA bases, base pairs, base stacks, and double helical DNA [107, 121, 131, 139]. Both the experimental and molecular simulation studies have clearly brought out the importance of hydration in DNA and RNA structures [140-147]. 

Experimental studies of ground state properties of DNA bases have been carried out for many years. This includes studies of their molecular structures. Although one can conclude that the ground state of these important DNA constituents is well characterized, data concerning their excited state properties is scarce. The molecular geometry of such complex systems like DNA bases cannot be determined by experimental methods. It creates a need for theoretical studies that could shed light on the properties of DNA bases in the excited state. In the last chapter of this volume, M.K. Shukla and J. Leszczynski discuss available experimental data of DNA bases, base pairs, and their complexes with water. The discussion is enhanced by an overview of the results of recent... 

Optical Response of DNA Bases, Base Pairs, and Their Tautomers in the Gas Phase. 

Owing to the central role of DNA in biochemistry and biophysics, the computation of the electronic structure of periodic polymers constructed from nucleotide bases, base pairs, and nucleotides by applying the ab initio Hartree-Fock crystal-orbital method has attracted much... 

Recent studies on interactions between bases, base pairs, and metal cations were mainly aimed at clarifying the following items. 

Due to the central role of DNA and proteins in biochemistry and biophysics the computation of the electronic structure of periodic polymers built from nucleotide bases, base pairs, nucleotides and amino acids, respectively, had been of high interest since about twenty years. Early calculations of the band structure of DNA related periodic polymers have been performed with the crystal orbital (CO) method on the basis of different semiempirical levels (1). Recently the results of ab initio Hartree-Fock CO (2, 3) band structure calculations for the four nucleotide base stacks (4-6), the two Watson-Crick base pair stacks (6), the sugar-phosphate chain (4,5) and the three nucleotides cytidine (4,5), adenylic acid and th3nnidine (6) have been reported. These computations represent a significant progress but the following improvements are required for a more accurate description of the electronic structure of real DNA and its transport properties ... 

---