Nucleic data base

Significant progress in the optimization of VDW parameters was associated with the development of the OPLS force field [53]. In those efforts the approach of using Monte Carlo calculations on pure solvents to compute heats of vaporization and molecular volumes and then using that information to refine the VDW parameters was first developed and applied. Subsequently, developers of other force fields have used this same approach for optimization of biomolecular force fields [20,21]. Van der Waals parameters may also be optimized based on calculated heats of sublimation of crystals [68], as has been done for the optimization of some of the VDW parameters in the nucleic acid bases [18]. Alternative approaches to optimizing VDW parameters have been based primarily on the use of QM data. Quantum mechanical data contains detailed information on the electron distribution around a molecule, which, in principle, should be useful for the optimization of VDW... 

The development of nucleic acid-based therapeutics is not as straightforward as researchers had initially anticipated. Stability, toxicity, specificity, and delivery of the compounds continue to be challenging issues that need further optimization. In recent years, researchers have come up with intricate solutions that have greatly improved the efficacy of potential antisense, ribozyme, as well as RNAi-based therapeutics. Clinical trials for all these types of nucleic acid-based therapeutics are underway. So far, data from several trials and studies in animal models look promising, in particular, the therapies that trigger the RNAi pathway. However, history has shown that compounds that do well in phase I or phase II clinical trials may still fail in phase III. A striking example is the nonspecific suppression of angiogenesis by siRNA via toII-Iike receptor 3 (Kleinman et al. 2008). It will become clear in the near future which compounds will make it as a new class of antiviral therapeutics. 

Tipson always enjoyed and took great pride in precise scientific writing. When the Advances in Carbohydrate Chemistry series was launched in 1945 under the editorship of W. W. Pigman and M. L. Wolfrom, he wrote a comprehensive article for Volume 1 on the chemistry of the nucleic acids that is to this day a model of historical accuracy, careful and economical use of language, and clear interpretation of experimental data based on thoroughly characterized crystalline compounds. 

The contents of the nucleic acid bases in the poly-L-lysine derivatives were determined by UV spectra of the polymers after hydrolysis The polymers were hydrolyzed in 6 N-hydrochloric acid at 105°C for 24 hr, into lysine dihydrochloride and the carboxyethyl derivatives of the nucleic acid bases. The quantitative calculation was made relative to the standard sample of the carboxyethyl derivative of the nucleic acid bases. The analytical data are listed in Table 1. It was found that the thymine and uracil derivatives was completely substituted to polylysine. Low value in case of adenine base in the polymer may be attributed to the unstability of the activated ester, Ade-PNP (2), and may also be explained in terms of the steric interaction among bulky pendant groups of the polymer. When the poly-L-lysine containing about 50 mol % adenine units was again treated with Ade-PNP, the adenine unit content in the polymer increased up to 74 mol %(,] ). 

Table 1. Analytical data of nucleic acid base substituted poly-L-lysines...

Spectral data (Amax and AE, and e x 10 3) for the pyrimidine bases investigated in a few representative papers are collected in Table XXVIII. The absorption bands are denoted by the capital letters A, B, C, etc. In Table XXVIII we have listed the results of the vacuum ultraviolet measurements by Yamada and Fukutome428 (cf. also ref. 429), who measured the spectra of sublimed films of cytosine, thymine, uracil (and also of guanine and adenine) down to 120 nm at room temperature. Several remarkable absorption peaks were found below 190 nm in addition to the already known ones near 260 and 200 nm. A weak absorption at 230-240 nm in cytosine was not indicated in the sublimed films of the molecule,428 but was visible in the stretched polyvinyl alcohol film spectrum.432 Crewe et al.i3° studied the interactions of fast electrons with the five nucleic acid bases and measured the energy-loss spectra of 20 keV electrons transmitted through thin films of these bases. These last data are also listed in Table XXVIII for comparison with the other spectral findings. 

The study of nucleic acid bases by NMR has been reported in a number of monographs (/), but very little data is available on the, 3C and, 5N NMR chemical shift tensors in these compounds. The low sensitivity of NMR spectroscopy and the long relaxation times exhibited by many of these compounds have posed the main impediments for these studies. The use of sample doping with free radical relaxation reagents, to reduce the relaxation times facilitating 2D multiple pulse experiment (2, 3), enables one to measure and analyze the principal values of the chemical shift tensors in natural abundance samples. In previous papers from this laboratory we have presented, 5N NMR chemical shift principal values for adenine, guanine, cytosine, thymine and uracil (4, 5). 

PDB is one of the oldest protein data bases, founded in 1971. It has three locations, Rutgers University in New Jersey, San Diego Supercomputer Center (SDSC) at the University of California, and the National Institute of Standards and Technology (NIST) in Gaithersburg, Maryland. The PDB is a source for protein characterization and structure as well. The PDB archive contains macromolecular structure data on proteins, nucleic acids, protein-nucleic acid complexes, and viruses. Approximately 50-100 new structures are deposited each week, which are annotated and released upon the depositor s specifications. PDB data are freely available worldwide. PDB formats, annotates, validates, and releases dozens of complicated structure files each week some of them take only a couple of hours, others take weeks to process. Data processing is the main task of people at the PDB and validation is the most time-consuming part (Smith-Schmidt, 2002). 

The structure of the DNA molecule is basically determined by nucleic acid base interactions. Although the three-dimensional double helix structure of DNA is influenced by various contributions, the hydrogen bonding in DNA base pairs is of particuar importance. Because it is difficult to obtain gas phase experimental data for isolated base pair characterisation (only a limited number of experimental studies are available [21]) quantum chemical calculations can represent a useful tool to obtain reference data on the structure, properties and interactions of nucleic acid pairs. Theoretical studies can help us to understand the properties of nucleic acids and they are fundamental for verification... 

As far as quantitative chemical derivatization GC analysis is concerned, it is necessary to mention especially the work of Gehrke and his collaborators, who specified the fundamental concepts of quantitative GC analysis combined with the chemical derivatization of sample compounds and applied them to the accurate determination of the twenty natural protein amino acids and other non-protein amino acids as their N-TFA-n-butyl esters [5 ], the urinary excretion level of methylated nucleic acid bases as their TMS derivatives [6], TMS nucleosides [7] and other investigations. Further examples include a computer program for processing the quantitative GC data obtained for seventeen triglyceride fatty acids after their transesterification by 2 NKOH in n-butanol [8], a study of the kinetics of the transesterification reactions of dimethyl terephthalate with ethylene glycol [9] and the GC-MS determination of chlorophenols in spent bleach liquors after isolation of the chlorophenols by a multi-step extraction, purification of the final extract by HPLC and derivatization with diazoethane [10]. 

Since this structural data consists of atomic parameters which describe the interatomic vectors in three dimensions, the simultaneous evolvement of computer graphics has played an important role in the way the data can be used. The data base which is the particular source for the hydrogen bond data analyzed in this monograph is the Cambridge Crystallographic Structure Data Base [39, 40]. There is also a vast amount of structural information in the protein and nucleic acid data... 

In the nucleoside field, the use of calorimetric, volumetric, and structural data for describing the properties of pyrimidine nucleic acid bases and their derivatives was the subject of a specialized review <03MI155>, and pyrimidine nucleoside analogs as cancer chemotherapeutics <03MI717>... 

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