Nucleic crystallization

PDB files were designed for storage of crystal structures and related experimental information on biological macromolecules, primarily proteins, nucleic acids, and their complexes. Over the years the PDB file format was extended to handle results from other experimental (NM.R, cryoelectron microscopy) and theoretical methods... 

A crystal is a solid with a periodic lattice of microscopic components. This arrangement of atoms is determined primarily by X-ray structure analysis. The smallest unit, called the unit cell, defines the complete crystal, including its symmetry. Characteristic crystallographic 3D structures are available in the fields of inorganic, organic, and organometallic compounds, macromolecules, such as proteins and nucleic adds. 

The PDB contains 20 254 experimentally determined 3D structures (November, 2002) of macromolecules (nucleic adds, proteins, and viruses). In addition, it contains data on complexes of proteins with small-molecule ligands. Besides information on the structure, e.g., sequence details (primary and secondary structure information, etc.), atomic coordinates, crystallization conditions, structure factors. 

Propidium iodide (3,8-diamino-5-(3-diethylaminopropyl)-6-phenylphenantridinium iodide methiodide) [25535-16-4] M 668.4, m 210-230 (dec), pKeskd 4 (aniline NH2), pKesi(2) (EtN2). Recrystd as red crystals from H2O containing a little KI. It fluoresces strongly with nucleic acids. [Eatkins J Chem Soc 3059 7952.] TOXIC. 

To date, a number of simulation studies have been performed on nucleic acids and proteins using both AMBER and CHARMM. A direct comparison of crystal simulations of bovine pancreatic trypsin inliibitor show that the two force fields behave similarly, although differences in solvent-protein interactions are evident [24]. Side-by-side tests have also been performed on a DNA duplex, showing both force fields to be in reasonable agreement with experiment although significant, and different, problems were evident in both cases [25]. It should be noted that as of the writing of this chapter revised versions of both the AMBER and CHARMM nucleic acid force fields had become available. Several simulations of membranes have been performed with the CHARMM force field for both saturated [26] and unsaturated [27] lipids. The availability of both protein and nucleic acid parameters in AMBER and CHARMM allows for protein-nucleic acid complexes to be studied with both force fields (see Chapter 20), whereas protein-lipid (see Chapter 21) and DNA-lipid simulations can also be performed with CHARMM. 

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 removal and reduction of the nucleic acid content of various SCPs is achieved by chemical treatment with sodium hydroxide solution or high salt solution (10%). As a result, crystals of sodium urate form and are removed from the SCP solution.16,17 The quality of SCP can be upgraded by the destruction of cell walls. That may enhance the digestibility of SCP. With chemical treatment the nucleic acid content of SCP is reduced. 

Nucleic acid hybridization can be detected by means of the piezoelectric QCM (= quartz crystal microbalance) (a) Y Okahata, Y Matsunobu, K Ijiro, M Mukae, A Murakami, K Makino. J. Am. Chem. Soc. 114 8299-8300, 1992 (b) S Yamaguchi, T Shimomura. Anal. Chem. 65 1925-1927,1993 (c) KIto, KHashimoto, Y Ishimori. Anal. Chim. Acta 327 29-35,1996 ... 

Rill, RL Ramey, BA Van Winkle, DH Locke, BR, Capillary Gel Electrophoresis of Nucleic Acids in Pluronic F127 Copolymer Liquid Crystals, Chromatographia Supplement I, Vol 49, S65, 1999. 

Numerous organisms, both marine and terrestrial, produce protein toxins. These are typically relatively small, and rich in disulfide crosslinks. Since they are often difficult to crystallize, relatively few structures from this class of proteins are known. In the past five years two dimensional NMR methods have developed to the point where they can be used to determine the solution structures of small proteins and nucleic acids. We have analyzed the structures of toxins II and III of RadiarUhus paumotensis using this approach. We find that the dominant structure is )9-sheet, with the strands connected by loops of irregular structure. Most of the residues which have been determined to be important for toxicity are contained in one of the loops. The general methods used for structure analysis will be described, and the structures of the toxins RpII and RpIII will be discussed and compared with homologous toxins from other anemone species. 

Our method has evolved during many studies over the last two decades. These include studies on the effect of strong internal electric fields in crystals on optical transition dipole directions of nucleic acid bases [2, 3], QM-MM predictions of time-dependent solvatochromism on 3-methylindole (3MI) in water [4], and on tryptophan in several proteins [5-8]. More recently, the same techniques have been... 

The mechanism of carcinogenesis by PAHs is believed to involve alkylation of an informational macromolecule in a critical, but at present unknown, manner. Such an interaction with a protein has been modelled by alkylation of a peptide this showed a conformational change occurred on alkylation. It has not yet been possible to study the structure of DNA alkylated by an activated carcinogen this is because DNA is a fiber and the structural order in it is not sufficient for a crystal structure determination. However the crystal structures of some alkylated portions of nucleic acids are described, particularly some nucleosides alkylated by chloromethyl derivatives of DMBA. In crystals of these alkylation products the PAH portion of the adduct shows a tendency to lie between the bases of other nucleoside... 

Several complexes that involve intercalation of an acridine in a portion of a nucleic acid have been studied by X-ray crystallographic techniques. These include complexes of dinucleoside phosphates with ethidium bromide, 9-aminoacridine, acridine orange, proflavine and ellipticine (65-69). A representation of the geometry of an intercalated proflavine molecule is illustrated in Figure 6 (b) this is a view of the crystal structure of proflavine intercalated in a dinucleoside phosphate, cytidylyl- -S ) guano-sine (CpG) (70, TV). For comparison an example of the situation before such intercalation is also illustrated in Figure 6 (a) by three adjacent base pairs found in the crystal structure of a polynucleotide (72, 73). In this latter structure the vertical distance (parallel to the helix axis) between the bases is approximately... 

F. Caruso, E. Rodda, D.F. Furlong, K. Niikura, and Y. Okahata, Quartz crystal microbalance study of DNA immobilization and hybridization for nucleic acid sensor development. Anal. Chem. 69, 2043-2049 (1997). 

Y. Sato and F. Mizutani, Electrochemical responses of cytochrome c on gold electrodes modified with nucleic acid base derivatives - electrochemical and quartz crystal microbalance studies. Electrochim. Acta 45, 2869-2875 (2000). 

The synthesis and crystal structure of the peptide nucleic acid (PNA) monomer 25 having cyanuric acid as nucleobase have been described. Monomer 25 can be directly used for the solid phase synthesis of PNA oligomers . 

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