Nucleic acid bases, base pairing

DNA arrays have been categorized into different formats based upon what is immobilized to the surface (also known as the solid phase, substrate, or chip) and what is captured from the sample solution. Definitions change depending upon the format. For the classic Southern dot blot, the sample was first spotted down on the surface, cross-linked, and then bathed with a radio-labeled oligonucleotide under hybridization (complementary nucleic acid strand base-pairing) conditions to detect the presence of a parhcular sequence within the sample. This was called probing. The oligonucleohde... 

J. P. Ritchie and A. S. Copenhaver, J. Comput. Chem., 16, 777 (1995). Comparison of Potential-Derived Charge and Atomic Multipole Models in Calculating Electrostatic Potentials and Energies of Some Nucleic Acid Bases and Pairs. 

Traditionally the phosphate ester moiety is often overlooked and viewed as a passive element of nucleic acid structure. Base pairing and other nucleic acid base oriented structural features have been assumed to control nucleic acid structure and conformation. More recently (and as discussed in this paper) we have begun to appreciate the important role played by the phosphate ester (Figure 1) in defining the structure and dynamics of nucleic acids as well as nucleic acid-drug or protein complexes. 

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. 

Santamaria, R., Charro, E., Zacarias, A., Castro, M., 1999, Vibrational Spectra of Nucleic Acid Bases and Their Watson-Crick Pair Complexes , J. Comput. Chem., 20, 511. 

Santamaria, R., and A. Vasquez. 1994. Structural and Electronic Property Changes of the Nucleic Acid Bases upon Base Pair Formation. J. Comp. Chem. 15,981. 

Tab. 6.2 Calculated principle values nucleic acid bases and base pairs and orientations of chemical shift tensors of the imino nitrogens in...

In general, the size of h2/NN couplings between imino or amino 15N donor and aromatic 15N acceptor nuclei in nucleic acid base pairs ranges between 5 and 11 Hz... 

For a pair of H-bonded histidine side chains, Ii3/Nn couplings in the range 8-11 Hz (Tab. 9.2) have been observed between a protonated 15Ne2-nucleus and an unprotonated 15Ne2 using an HNN-COSY-based technique [48]. These values are similar to the h2/NN coupling values observed for the imino and amino N-l I Nlorii ,, lc H-bonds of nucleic acid base pairs (Tab. 9.1). 

The fluorescence of 2AP is strongly quenched by nucleic acid bases [17, 18, 24-29]. Time-correlated single-photon counting studies have shown that the interactions of 2AP with different nucleic acid bases significantly decrease the 2AP fluorescence hfetime [17, 24-29]. While the fluorescence lifetime of free 2AP in aqueous solution is about 10 ns, in double-stranded DNA the 2AP hfetimes are reduced to 30-50 ps. This effect has been used extensively to study the dynamics of mismatched base pairs [19, 21, 25, 30], local changes in dynamics of DNA molecules produced by their binding to the active sites of polymerases [26, 31-33], stacking interactions at abasic... 

Scheurer and Briischweiler71 calculated 2hJ(N,N) couplings in three nucleic acid base pairs, namely, Watson-Crick uracil-adenine (U A) [4a] and cytosine-guanine (C-G) base pairs [4b] and in the Hoogsteen adenine thymine (A-T) base pair [7]. 

Relatively few simple pyrimidine monomers have been incorporated into heterocyclic polymers (70MI11100). By far the greatest efforts with this ring system have involved polymerizable derivatives of nucleic acid bases and related compounds (81MH1102). The majority of this work has involved the synthesis and free radical polymerization of suitable vinyl- and acrylic-functional monomers, e.g. (134)-(136), although epoxy and other derivatives have also been studied. A number of the polymers exhibit base-paired complex formation with natural nucleic acid polymers or synthetic analogues, have found use in... 

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