Therapeutic RNA and DNA enzymes

Inorganic nanovectors for nucleic acid delivery

Nucleic acids show immense potential to treat cancer, acquired immune deficiency syndrome, neurological diseases and other incurable human diseases. Upon systemic administration, they encounter a series of barriers and hence barely reach the site of action, the cell. Intracellular delivery of nucleic acids is facilitated by nanovectors, both viral and non-viral. A major advantage of non-viral vectors over viral vectors is safety. Nanovectors evaluated specifically for nucleic acid delivery include polyplexes, lipoplexes and other cationic carrier-based vectors. However, more recently there is an increased interest in inorganic nanovectors for nucleic acid delivery. Nevertheless, there is no comprehensive review on the subject. The present review would cover in detail specific properties and types of inorganic nanovectors, their preparation techniques and various biomedical applications as therapeutics, diagnostics and theranostics. Future prospects are also suggested.

Ribozymes and siRnas: from structure to preclinical applications

The discovery that nucleic acids mediated the inhibition of gene expression in a sequence-specific manner has provided the scientific community with a potentially important tool to analyse gene function and validate drug targets. Selective inhibition of gene expression by ribozymes and small interfering RNAs (siRNAs) is being explored for potential therapeutics against viral infections, inflammatory disorders, haematological diseases and cancer. In order to be used as pharmaceutical drugs, chemical modifications are necessary to increase their stability in vivo. However, such modifications should not affect either the ribozyme cleavage activity or the incorporation of the siRNAs into the RNA interference (RNAi) targeting complex and subsequent mRNA cleavage. To attain stability, ribozymes and siRNAs must also overcome several other problems, including accessibility to target messenger RNAs (mRNAs), efficient delivery to target cells and unwanted non-specific effects.

Zn2+-dependent deoxyribozymes that form natural and unnatural RNA linkages

We report Zn(2+)-dependent deoxyribozymes that ligate RNA. The DNA enzymes were identified by in vitro selection and ligate RNA with k(obs) up to 0.5 min(-)(1) at 1 mM Zn(2+) and 23 degrees C, pH 7.9, which is substantially faster than our previously reported Mg(2+)-dependent deoxyribozymes. Each new Zn(2+)-dependent deoxyribozyme mediates the reaction of a specific nucleophile on one RNA substrate with a 2',3'-cyclic phosphate on a second RNA substrate. Some of the Zn(2+)-dependent deoxyribozymes create native 3'-5' RNA linkages (with k(obs) up to 0.02 min(-)(1)), whereas all of our previous Mg(2+)-dependent deoxyribozymes that use a 2',3'-cyclic phosphate create non-native 2'-5' RNA linkages. On this basis, Zn(2+)-dependent deoxyribozymes have promise for synthesis of native 3'-5'-linked RNA using 2',3'-cyclic phosphate RNA substrates, although these particular Zn(2+)-dependent deoxyribozymes are likely not useful for this practical application. Some of the new Zn(2+)-dependent deoxyribozymes instead create non-native 2'-5' linkages, just like their Mg(2+) counterparts. Unexpectedly, other Zn(2+)-dependent deoxyribozymes synthesize one of three unnatural linkages that are formed upon the reaction of an RNA nucleophile other than a 5'-hydroxyl group. Two of these unnatural linkages are the 3'-2' and 2'-2' linear junctions created when the 2'-hydroxyl of the 5'-terminal guanosine of one RNA substrate attacks the 2',3'-cyclic phosphate of the second RNA substrate. The third unnatural linkage is a branched RNA that results from attack of a specific internal 2'-hydroxyl of one RNA substrate at the 2',3'-cyclic phosphate. When compared with the consistent creation of 2'-5' linkages by Mg(2+)-dependent ligation, formation of this variety of RNA ligation products by Zn(2+)-dependent deoxyribozymes highlights the versatility of transition metals such as Zn(2+) for mediating nucleic acid catalysis.

Applications of nucleic acid technology in the CNS

This review examines applications of nucleic acid technology in the form of catalytic nucleic acids (ribozymes and DNAzymes) and RNA interference (RNAi) in the CNS. The basic mechanism of catalytic nucleic acids and RNAi is reviewed, and potentials and problems highlighted. Recent advances in chemical modifications and delivery techniques are summarized. Applications in the CNS, including their use in primary neuronal cells, organotypic slice culture and the brain in vivo are further discussed.

Evolution of aptamers with a new specificity and new secondary structures from an ATP aptamer

Small changes in target specificity can sometimes be achieved, without changing aptamer structure, through mutation of a few bases. Larger changes in target geometry or chemistry may require more radical changes in an aptamer. In the latter case, it is unknown whether structural and functional solutions can still be found in the region of sequence space close to the original aptamer. To investigate these questions, we designed an in vitro selection experiment aimed at evolving specificity of an ATP aptamer. The ATP aptamer makes contacts with both the nucleobase and the sugar. We used an affinity matrix in which GTP was immobilized through the sugar, thus requiring extensive changes in or loss of sugar contact, as well as changes in recognition of the nucleobase. After just five rounds of selection, the pool was dominated by new aptamers falling into three major classes, each with secondary structures distinct from that of the ATP aptamer. The average sequence identity between the original aptamer and new aptamers is 76%. Most of the mutations appear to play roles either in disrupting the original secondary structure or in forming the new secondary structure or the new recognition loops. Our results show that there are novel structures that recognize a significantly different ligand in the region of sequence space close to the ATP aptamer. These examples of the emergence of novel functions and structures from an RNA molecule with a defined specificity and fold provide a new perspective on the evolutionary flexibility and adaptability of RNA.

Electroporation-mediated delivery of catalytic oligodeoxynucleotides for manipulation of vascular gene expression

The development of inexpensive and effective approaches to transiently decrease gene expression in vivo would be useful for the study of physiological processes in living animals. DNAzymes are a novel class of DNA oligonucleotides that can catalytically cleave target mRNAs and thereby reduce protein production. However, current methods for their delivery in vivo are limited and inefficient. In this study, we show that electroporation can be used to deliver DNAzymes to the intact mesenteric vasculature of rats. With the use of PKC-epsilon as a target, a set of wild-type and mutant control DNAzymes was designed and shown to reduce both PKC-epsilon mRNA and protein levels in cultured smooth muscle cells in a specific manner. The wild-type DNAzyme reduced PKC-epsilon protein levels by 70% at 24 h in two different cell lines without decreasing the levels of the five other PKC isoforms tested. When delivered to the intact vasculature using electroporation, the DNAzyme reduced PKC-epsilon protein levels by >60% without affecting these other PKC isoforms. Electroporation was required for oligonucleotide transfer and was able to deliver the DNAzymes to multiple cell layers in the vessel wall. Protein levels were reduced maximally by 24 h postelectroporation and returned to normal by 48 h. These results suggest that electroporation can be used to deliver DNAzymes and other DNA oligonucleotides to the vasculature in vivo and can decrease gene expression for a window of time that can be used for experimental studies.

A continuous kinetic assay for RNA-cleaving deoxyribozymes, exploiting ethidium bromide as an extrinsic fluorescent probe

We describe a rapid and inexpensive method to monitor the kinetics of small RNA-cleaving deoxyribozymes, based on the exogenous fluorophore ethidium bromide. Ethidium binds preferentially to double-stranded nucleic acids, and its fluorescence emission increases dramatically upon intercalation. Thus, ethidium can be used in single-turnover experiments to measure both annealing of the deoxyribozyme to its substrate and release of the products. Under conditions in which dissociation of the product is fast compared with cleavage, the apparent rate of product release reflects the cleavage step. The method was developed for characterizing the so-called 8-17 catalytic DNA, but its general applicability in the deoxyribozyme field was verified using the 10-23 RNA-cleaving construct. Catalysis by both deoxyribozymes was not inhibited in the presence of substoichiometric amounts of ethidium, and the rates obtained through the ethidium assay were virtually identical to the rates determined using radiolabeled substrates. In contrast, the assay cannot be applied to the large, structured ribozymes, and its use to study the kinetics of the small hammerhead ribozyme was hampered by the presence on the catalyst of at least one high-affinity ethidium binding site.

Targeting Raf-1 gene expression by a DNA enzyme inhibits juvenile myelomonocytic leukemia cell growth

Juvenile myelomonocytic leukemia (JMML) is an aggressive childhood disorder with few therapeutic options. Granulocyte-macrophage colony-stimulating factor (GM-CSF) and tumor necrosis factor-alpha (TNF-alpha) promote JMML cell growth. A hyperactive function of the ras oncogene is a hallmark of JMML. We therefore targeted the protein kinase Raf-1 downstream of Ras using a DNA enzyme that degrades mRNA-Raf-1. Western blots of JMML cell lysates revealed phosphorylated Raf-1 protein, indicating constitutive activation. Addition of GM-CSF, but not TNF-alpha, increased phosphorylation of both Raf-1 and the mitogen-activated protein kinases (MAPKs) JNK-1 and ERK-1. Depletion of Raf-1 protein markedly impaired activation of MAPKs, induced substantial inhibition of JMML cell colony formation, and virtually abolished GM-CSF hypersensitivity in JMML cells. Exogenous TNF-alpha, but not GM-CSF, restored colony formation of JMML cells pretreated with the enzyme. We could not detect any effect of the enzyme on the proliferation of normal bone marrow cells, indicating its specificity and potential safety. When immunodeficient mice engrafted with JMML cells were treated continuously with the enzyme via a peritoneal osmotic mini-pump for 4 weeks, a profound reduction in the JMML cell numbers in the recipient murine bone marrows was found. We conclude that GM-CSF is a chief regulator of JMML growth and exerts its proleukemic effects primarily via the Ras/Raf-1 signaling cascade. TNF-alpha plays a permissive role, being dependent upon GM-CSF to induce JMML cell proliferation. The DNA enzyme efficiently catabolized mRNA-Raf-1 with subsequent inhibition of JMML cell growth, suggesting its potential as a mechanism-based therapy in this fatal leukemia.

Targeted therapy for malignant melanoma

There has been much development in the field of targeted therapy for melanoma stemming from efforts to decrease treatment-related toxicities and enhance specific cytotoxicity. This review focuses on three modalities of targeted melanoma therapy based on the biology of the targeting mechanism. The first of these modalities is immunotherapy, which functions to generate a specific antimelanoma immunity. A second modality utilizes metabolic pathways of melanin synthesis to target melanoma cells specifically. A third modality ensues from recent advances in molecular biology and the identification of genes responsible for the malignant transformation of normal melanocytes to melanomas. This work has furthered our understanding of the basis of malignancy, as well as the development of novel strategies aimed at targeting aberrant growth in melanoma.