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Nucleic-acid therapeutics: basic principles and recent applications

Key Points

  • Although conceptually elegant, the prospect of using nucleic-acid molecules for treating human diseases remains tantalizing, but uncertain. The main cause of this uncertainty is the apparent randomness with which these materials modulate the expression of their intended targets.

  • Strategies for modulating gene expression can be directed towards perturbing the process of transcription, or post-transcriptional events, including mRNA processing and translation. Conveniently, these approaches can be categorized as 'anti-gene' or 'anti-mRNA.'

  • Gene targeting can be accomplished by homologous recombination, triple-helix-forming oligodeoxynucleotides (TFOs) and decoy molecules.

  • Targeting mRNA can be accomplished by various strategies as well, including the use of antisense DNA, antisense RNA and RNA-decoy molecules.

  • A new approach that has received a great deal of attention in the past year is called post-transcriptional gene silencing, or RNA interference (RNAi).

  • Molecule delivery to targeted cells specific compartments within cells, and identification of hybridization-accessible sequence within the genomic DNA or RNA remain core stumbling blocks that hold up progress in the field.

  • Nucleic acids that are used for experimental purposes and those designed for the clinic are now routinely modified to enhance their stability, as well as the strength of their hybridization with RNA.

  • Many successful uses of this strategy in the laboratory have been reported. Despite the fact that the mechanism whereby these molecules modulate gene expression is not always certain, clinical development of nucleic-acid compounds has proceeded to the point at which a number of these drugs have entered Phase I/II, and in a few cases, Phase III trials.

  • RNA-encoding proteins that are involved in key signal-transduction pathways and transcription factors are the primary targets. Some encouraging reports of the clinical usefulness of these molecules, either alone, or predominantly in combination with other treatment modalities, have been reported.

Abstract

The sequencing of the human genome and the elucidation of many molecular pathways that are important in disease have provided unprecedented opportunities for the development of new therapeutics. The types of molecule in development are increasingly varied, and include antisense oligonucleotides and ribozymes. Antisense technology and catalytic nucleic-acid enzymes are important tools for blocking the expression of abnormal genes. One FDA-approved antisense drug is already in the clinic for the treatment of cytomegalovirus retinitis, and other nucleic-acid therapies are undergoing clinical trials. This article reviews different strategies for modulating gene expression, and discusses the successes and problems that are associated with this type of therapy.

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Figure 1: Triple-helix formation at the nucleotide level.
Figure 2: Strategies for inhibiting translation.
Figure 3: Hypothetical RNAi mechanism.
Figure 4: Effect of c-MYB-targeted ODNs on c-MYB mRNA expression in marrow cells.

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Acknowledgements

This work is supported by a grant from the National Institutes of Health. A.M.G. is a Distinguished Clinical Scientist of the Doris Duke Charitable Foundation. The editorial assistance of E. R. Bien and M. Goodrum is gratefully acknowledged.

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Correspondence to Alan M. Gewirtz.

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DATABASES

Cancer.gov

breast cancer

chronic myelogenous leukaemia

colon cancer

non-Hodgkin's lymphoma

NSCLC

ovarian cancer

LocusLink

ABL

adenosine A1 receptor

BCL2

BCR

CD34

DICER

α-globin

β-globin

haemoglobin

HER2

ICAM-1

IGF1R

c-MYB

c-MYC

2′,5′-oligodenylate synthetase

PKA

PKC

PKCα

PKR

c-RAF

ribonucleotide reductase

RNase H

RNase L

VEGFR1

Medscape DrugInfo

cidofovir

foscarnet

ganciclovir

Gleevec

rituximab

Vitravene

OMIM

Crohn's disease

psoriasis

FURTHER INFORMATION

Encyclopedia of Life Sciences

antisense nucleic acids in biotechnology

American Society of Hematology

FDA

Glossary

EXOGENOUS NUCLEIC ACIDS

In this context, synthetic oligonucleotides of varying chemistry (typically 16–25 nucleotides), which are introduced into cells by various means, or simply (although inefficiently) by concentration-driven endocytosis.

ANTISENSE

Reverse complement of any DNA or RNA sequence.

TRIPLE-HELIX-FORMING OLIGODEOXYNUCLEOTIDE

(TFO). A synthetic, single-stranded oligodeoxynucleotide, which, through Hoogsten-bond formation, hybridizes to purine/pyrymidine-rich sequences in double-stranded DNA. Formation of stable triple helices can prevent the unwinding that is necessary for transcription of the targeted region or block the binding of transcription-factor complexes.

MAJOR GROOVE AND MINOR GROOVE

Channels formed by the twisting of two complementary DNA strands around each other to form a double helix. The major groove is 22 Å wide and the minor groove is 12 Å wide.

HOOGSTEEN BOND

Triple-helix-forming oligonucleotides hybridize with purine bases that comprise polypurine/polypyrimidine tracks in the DNA. The hydrogen bonds that are formed under these conditions are referred to as Hoogsteen bonds after the individual who first described them. They can form in parallel or antiparallel (reverse-Hoogsteen) orientations.

NUCLEOSOME

A packing unit for DNA within the cell nucleus, which gives the chromatin a 'beads-on-a-string' structure. The 'beads' consist of complexes of nuclear proteins (histones) and DNA, and the 'string' consists of DNA only. A histone octamer forms a core around which the double-stranded DNA helix is wound twice.

LEXITROPSIN

A molecule that extragenetically reads the base sequence of double-stranded DNA.

RIBOZYME

RNA molecule that contains one of a variety of catalytic motifs that cleave RNA to which it hybridizes.

DNAzyme

A DNA molecule that contains a catalytic motif that cleaves RNA to which it hybridizes.

MORPHOLINO OLIGODEOXYNUCLEOTIDE

(PMO). The base is attached to a morpholino instead of a ribofuranosyl ring, and the backbone is composed of a phosphorodiamidate linkage.

RESTENOSIS

A reduction in lumenal size after an inter-arterial coronary intervention.

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Opalinska, J., Gewirtz, A. Nucleic-acid therapeutics: basic principles and recent applications. Nat Rev Drug Discov 1, 503–514 (2002). https://doi.org/10.1038/nrd837

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