In Vitro Selection of Ligase Ribozymes Containing 2'-Amino Groups

Novel ribozymes containing 2'-amino groups in the side chains were in vitro selected to accelerate their ligation reaction rates with oligodeoxynucleotides. The ligation rate of random sequenced RNAs in the starting pool was accelerated by incorporation of 2'-amino-2'-deoxyuridine and N6-(6-aminohexyl)adenosine. The incorporation of the amino group enhanced the activity of non-selected RNAs independent of the incorporation site. In vitro selection using 2'-amino-2'-deoxyuridine instead of uridine produced more active ribozymes. In this case, the activity of ribozyme was reduced when N6-(6-aminohexyl)adenosine was incorporated into the selected RNAs instead of natural adenosine. The presence of amino groups as well as the incorporation site affected the activity of the in vitro selected ribozyme. It seems that RNAs with tertiary structures suitable for the ligation reaction were selected by the in vitro method.

In vitro selection of a photoresponsive RNA aptamer to hemin

A photoresponsive RNA aptamer to hemin was selected in vitro from a random sequence library of RNAs with azobenzene residues. The aptamer bound to hemin under visible light irradiation and was released by ultraviolet light.

A novel, modification-dependent ATP-binding aptamer selected from an RNA library incorporating a cationic functionality

An analogue of uridine triphosphate containing a cationic functional group was incorporated into a degenerate RNA library by enzymatic polymerization. In vitro selection experiments using this library yielded a novel receptor that binds ATP under physiological pH and salt conditions in a manner completely dependent on the presence of the cationic functionality. The consensus sequence and a secondary structure model for the ATP binding site were obtained by the analysis of functional sequences selected from a partially randomized pool based on the minimal parental sequence. Mutational studies of this receptor indicated that several of the modified uridines are critical for ATP binding. Analysis of the binding of ATP analogues revealed that the modified RNA receptor makes numerous contacts with ATP, including interactions with the triphosphate group. In contrast, the aptamer repeatedly isolated from natural RNA libraries does not interact with the triphosphate group of ATP. The incorporation of a cationic amine into nucleic acids clearly allows novel interactions to occur during the molecular recognition of ligands, which carries interesting implications for the RNA world hypothesis. In addition, new materials generated from such functionalized nucleic acids could be useful tools in research and diagnostics.

In vitro selection of RNA aptamers that bind to cell adhesion receptors of Trypanosoma cruzi and inhibit cell invasion

Trypanosoma cruzi causing Chagas' disease needs to invade host cells to complete its life cycle. Macromolecules on host cell surfaces such as laminin, thrombospondin, heparan sulfate, and fibronectin are believed to be important in mediating parasite-host cell adhesions and in the invasion process of the host cell by the parasite. The SELEX technique (systematic evolution of ligands by exponential enrichment) was used to evolve nuclease-resistant RNA ligands (aptamer = to fit) that bind with affinities of 40-400 nm to parasite receptors for the host cell matrix molecules laminin, fibronectin, thrombospondin, and heparan sulfate. After eight consecutive rounds of in vitro selection four classes of RNA aptamers based on structural similarities were isolated and sequenced. All members of each class shared a common sequence motif and competed with the respective host cell matrix molecule that was used for displacement during the selection procedure. RNA pools following seven and eight selection rounds as well as individual aptamers sharing consensus motifs were active in inhibiting invasion of LLC-MK(2) monkey kidney cells by T. cruzi in vitro.

Peroxidase activity of in vitro-selected 2'-amino RNAs

Peroxidase activities of RNAs containing 2'-amino groups, which were selected as aptamers binding to N-methylmesoporphyrin IX, were investigated. Some clones promoted the oxidation reaction of 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) with hydrogen peroxide (H(2)O(2)) in the presence of iron(III)-protoporphyrin (hemin), whereas others did not. Each of them had a different substrate specificity. One of the active clones promoted the oxidation of o-dianisidine and beta-nicotinamide adenine dinucleotide reduced form (NADH) with H(2)O(2) 5 and 15 times faster than hemin only, respectively. On the other hand, one clone that was inactive on oxidation of ABTS exhibited the same level of activity on oxidation of o-dianisidine as that shown by the clone active on ABTS but no activity on NADH. By in vitro selection, we can produce various types of peroxidase-like non-natural RNAs.

RNA and DNA aptamers as potential tools to prevent cell adhesion in disease

Recent research has shown that receptor-ligand interactions between surfaces of communicating cells are necessary prerequisites for cell proliferation, cell differentiation and immune defense. Cell-adhesion events have also been proposed for pathological conditions such as cancer growth, metastasis, and host-cell invasion by parasites such as Trypanosoma cruzi. RNA and DNA aptamers (aptus = Latin, fit) that have been selected from combinatorial nucleic acid libraries are capable of binding to cell-adhesion receptors leading to a halt in cellular processes induced by outside signals as a consequence of blockage of receptor-ligand interactions. We outline here a novel approach using RNA aptamers that bind to T. cruzi receptors and interrupt host-cell invasion in analogy to existing procedures of blocking selectin adhesion and function in vitro and in vivo.

In vitro selected oligonucleotides as receptors in binding assays

This paper describes a new binding assay that uses oligodeoxyribonucleotides (DNAs) obtained by the in vitro selection method instead of antibodies. DNAs that specifically bound to a target molecule were selected, labeled with some probes, and then used to detect the target molecule by staining or competitive binding assay.