Nucleic acids crosslinking methods

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. 

Chemical attachment of a detectable component to an oligonucleotide forms the basis for constructing a sensitive hybridization reagent. Unfortunately, the methods developed to crosslink or label other biological molecules such as proteins do not always apply to nucleic acids. The major reactive sites on proteins involve primary amines, sulfhydryls, carboxylates, or phenolates— groups that are relatively easy to derivatize. RNA and DNA contain none of these functionalities. 

The unique properties of oligonucleotides create crosslinking options that are far different from any other biological molecule. Nucleic acids are the only major class of macromolecule that can be specifically duplicated in vitro by enzymatic means. The addition of modified nucleoside triphosphates to an existing DNA strand by the action of polymerases or transferases allows addition of spacer arms or detection components at random or discrete sites along the chain. Alternatively, chemical methods that modify nucleotides at selected functional groups can be used to produce spacer arm derivatives or activated intermediates for subsequent coupling to other molecules. 

Several research groups used another interesting column technology as an alternative to the modification of the capillary surface. This method is inherited from the field of electrophoresis of nucleic acids and involves capillaries filled with solutions of linear polymers. In contrast to the monolithic columns that will be discussed later in this review, the preparation of these pseudostationary phases need not be performed within the confines of the capillary. These materials, typically specifically designed copolymers [85-88] and modified den-drimers [89], exist as physically entangled polymer chains that effectively resemble highly swollen, chemically crosslinked gels. 

Crosslinking is an alternative method for preventing the premature dissociation of the complex between a nucleic acid drug and a cationic polymer. Of course, stabilization by covalent crosslinking must be reversible and carefully controlled because over-stabilization can prohibit the release of nucleic acid drugs fi-om the... 

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