Designer zinc finger proteins: tools for creating artificial DNA-binding functional proteins

Human mesenchymal stem cells exhibit altered mitochondrial dynamics and poor survival in high glucose microenvironment

BACKGROUND

Mesenchymal stem cells (MSCs) are a type of stem cells that possess relevant regenerative abilities and can be used to treat many chronic diseases. Diabetes mellitus (DM) is a frequently diagnosed chronic disease characterized by hyperglycemia which initiates many multisystem complications in the long-run. DM patients can benefit from MSCs transplantation to curb down the pathological consequences associated with hyperglycemia persistence and restore the function of damaged tissues. MSCs therapeutic outcomes are found to last for short period of time and ultimately these regenerative cells are eradicated and died in DM disease model.

AIM

To investigate the impact of high glucose or hyperglycemia on the cellular and molecular characteristics of MSCs.

METHODS

Human adipose tissue-derived MSCs (hAD-MSCs) were seeded in low (5.6 mmol/L of glucose) and high glucose (25 mmol/L of glucose) for 7 d. Cytotoxicity, viability, mitochondrial dynamics, and apoptosis were deplored using specific kits. Western blotting was performed to measure the protein expression of phosphatidylinositol 3-kinase (PI3K), TSC1, and mammalian target of rapamycin (mTOR) in these cells.

RESULTS

hAD-MSCs cultured in high glucose for 7 d demonstrated marked decrease in their viability, as shown by a significant increase in lactate dehydrogenase (P < 0.01) and a significant decrease in Trypan blue (P < 0.05) in these cells compared to low glucose control. Mitochondrial membrane potential, indicated by tetramethylrhodamine ethyl ester (TMRE) fluorescence intensity, and nicotinamide adenine dinucleotide (NAD+)/NADH ratio were significantly dropped (P < 0.05 for TMRE and P < 0.01 for NAD+/NADH) in high glucose exposed hAD-MSCs, indicating disturbed mitochondrial function. PI3K protein expression significantly decreased in high glucose culture MSCs (P < 0.05 compared to low glucose) and it was coupled with significant upregulation in TSC1 (P < 0.05) and downregulation in mTOR protein expression (P < 0.05). Mitochondrial complexes I, IV, and V were downregulated profoundly in high glucose (P < 0.05 compared to low glucose). Apoptosis was induced as a result of mitochondrial impairment and explained the poor survival of MSCs in high glucose.

CONCLUSION

High glucose impaired the mitochondrial dynamics and regulatory proteins in hAD-MSCs ensuing their poor survival and high apoptosis rate in hyperglycemic microenvironment.

Sequence-Specific Recognition of Double-Stranded DNA by Peptide Nucleic Acid Forming Double-Duplex Invasion Complex

Peptide nucleic acid (PNA) is an analog of natural nucleic acids, where the sugar-phosphate backbone of DNA is replaced by an electrostatically neutral N-(2-aminoethyl)glycine backbone. This unique peptide-based backbone enables PNAs to form a very stable duplex with the complementary nucleic acids via Watson–Crick base pairing since there is no electrostatic repulsion between PNA and DNA·RNA. With this high nucleic acid affinity, PNAs have been used in a wide range of fields, from biological applications such as gene targeting, to engineering applications such as probe and sensor developments. In addition to single-stranded DNA, PNA can also recognize double-stranded DNA (dsDNA) through the formation of a double-duplex invasion complex. This double-duplex invasion is hard to achieve with other artificial nucleic acids and is expected to be a promising method to recognize dsDNA in cellula or in vivo since the invasion does not require the prior denaturation of dsDNA. In this paper, we provide basic knowledge of PNA and mainly focus on the research of PNA invasion.

Strategies for Multienzyme Assemblies

Proteins are not designed to be standalone entities and must coordinate their collective action for optimum performance. Nature has developed through evolution the ability to co-localize the functional partners of a cascade enzymatic reaction in order to ensure efficient exchange of intermediates. Inspired by these natural designs, synthetic scaffolds have been created to enhance the overall biological pathway performance. In this chapter, we describe several DNA- and protein-based scaffold approaches to assemble artificial enzyme cascades for a wide range of applications. We highlight the key benefits and drawbacks of these approaches to provide insights on how to choose the appropriate scaffold for different cascade systems.

Importance of two-dimensional cation clusters induced by protein folding in intrinsic intracellular membrane permeability

Two-dimensional cation clusters formed on the surface of proteins play an important role in their intracellular translocation.

Investigation of the Characteristics of NLS-PNA: Influence of NLS Location on Invasion Efficiency

Peptide nucleic acid can recognise sequences in double-stranded DNA (dsDNA) through the formation of a double-duplex invasion complex. This double-duplex invasion is a promising method for the recognition of dsDNA in cellula because peptide nucleic acid (PNA) invasion does not require the prior denaturation of dsDNA. To increase its applicability, we developed PNAs modified with a nuclear localisation signal (NLS) peptide. In this study, the characteristics of NLS-modified PNAs were investigated for the future design of novel peptide-modified PNAs.

Reduce and Control: A Combinatorial Strategy for Achieving Sustained HIV Remissions in the Absence of Antiretroviral Therapy

Human immunodeficiency virus (HIV-1) indefinitely persists, despite effective antiretroviral therapy (ART), within a small pool of latently infected cells. These cells often display markers of immunologic memory and harbor both replication-competent and -incompetent proviruses at approximately a 1:100 ratio. Although complete HIV eradication is a highly desirable goal, this likely represents a bridge too far for our current and foreseeable technologies. A more tractable goal involves engineering a sustained viral remission in the absence of ART––a “functional cure.” In this setting, HIV remains detectable during remission, but the size of the reservoir is small and the residual virus is effectively controlled by an engineered immune response or other intervention. Biological precedence for such an approach is found in the post-treatment controllers (PTCs), a rare group of HIV-infected individuals who, following ART withdrawal, do not experience viral rebound. PTCs are characterized by a small reservoir, greatly reduced inflammation, and the presence of a poorly understood immune response that limits viral rebound. Our goal is to devise a safe and effective means for replicating durable post-treatment control on a global scale. This requires devising methods to reduce the size of the reservoir and to control replication of this residual virus. In the following sections, we will review many of the approaches and tools that likely will be important for implementing such a “reduce and control” strategy and for achieving a PTC-like sustained HIV remission in the absence of ART.

An antipyrine based fluorescence "turn-on" dual sensor for Zn2+ and Al3+ and its selective fluorescence "turn-off" sensing towards 2,4,6-trinitrophenol (TNP) in the aggregated state

A 2,6-diformyl-p-cresol (DFC)-4-amino antipyrine (AP) based dual signaling fluorescent Schiff base ligand (DFCAP) is found to exhibit colorimetric and fluorescence turn on selective sensing towards metal ions, Zn2+ and Al3+. It also exhibits a significant aggregation induced emission (AIE) phenomenon by controlling the water-THF solvent ratio which provides robust green emissive fluorogenic aggregates with well-defined morphologies. Turn-on fluorescence enhancements as high as 195 fold and 168 fold in methanol for Al3+ and Zn2+ at 480 nm and 508 nm, respectively, were noticed. The binding constants and stoichiometry determined from the fluorescence titration data are K = 7.63 × 104 M-1 and 3.42 × 104 M-1 and 1 : 1 complexation for both Al3+ and Zn2+ respectively, supported by Job's method. DFCAP shows high sensitivity towards the detection of Zn2+ and Al3+ ions with very low detection limit values of ca. ∼21 nM and 30 nM respectively. Besides by applying its attractive AIE feature, the green emissive hydrosol functions as a good chemosensor with high sensitivity for a selected explosive TNP through ground state complexation with a LOD value of ca. ∼1.74 μM and especially a high Stern-Volmer quenching constant of ca. ∼4.14 × 105 M-1. For instant 'naked eye' response for the trace detection of TNP in the solution state, we fabricated a simple paper strip that could detect TNP on-site in a fast, inexpensive and simple way.

Nickel(ii)-promoted specific hydrolysis of zinc finger proteins

The (S/T)XH sequence in Cys₂His₂zinc fingers can be hydrolytically cleaved by Ni(ii) ions. This reaction can be applied for purification, inhibition or activation of designed zinc finger fusion proteins.

Next stop for the CRISPR revolution: RNA-guided epigenetic regulators

Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins offer a breakthrough platform for cheap, programmable, and effective sequence-specific DNA targeting. The CRISPR-Cas system is naturally equipped for targeted DNA cutting through its native nuclease activity. As such, groups researching a broad spectrum of biological organisms have quickly adopted the technology with groundbreaking applications to genomic sequence editing in over 20 different species. However, the biological code of life is not only encoded in genetics but also in epigenetics as well. While genetic sequence editing is a powerful ability, we must also be able to edit and regulate transcriptional and epigenetic code. Taking inspiration from work on earlier sequence-specific targeting technologies such as zinc fingers (ZFs) and transcription activator-like effectors (TALEs), researchers quickly expanded the CRISPR-Cas toolbox to include transcriptional activation, repression, and epigenetic modification. In this review, we highlight advances that extend the CRISPR-Cas toolkit for transcriptional and epigenetic regulation, as well as best practice guidelines for these tools, and a perspective on future applications.

Intrinsic cell permeability of the GAGA zinc finger protein into HeLa cells

We examined the intrinsic cell permeability of a GAGA zinc finger obtained from the Drosophila melanogaster transcription factor and analyzed its mechanism of cellular uptake using confocal microscopy and flow cytometry. HeLa cells were treated with the Cy5-labeld GAGA peptides (containing a fluorescent chromophore) to detect fluorescence signals from the fluorescent labeling peptides by confocal microscopy. The results clearly indicated that GAGA peptides possess intrinsic cell permeability for HeLa cells. Based on the results of the flow cytometry analysis and the theoretical net positive charge of the GAGA peptides, the efficiency of cellular uptake of the GAGA peptides was predicted to depend on the net positive charge of the GAGA peptide as well as the cationic component ratio of Arg residues to Lys residues.

Efficient cleavage of DNA oligonucleotides by a non-FokI-type zinc finger nuclease containing one His₄-type finger domain derived from the first finger domain of Sp1

In this study, we sought to improve the hydrolytic activity of a His4-type single finger domain (f2), which was previously derived from the second finger domain (f2') of the Sp1 zinc finger protein (Sp1wt), which has 3 tandem finger domains (f1', f2', and f3'). To this end, 2 His4-type single finger domains were generated by mutating 2 Cys residues participating in Zn(II) coordination with the His residues in the first (f1') and third finger (f3') domains of Sp1wt. Circular dichroism spectroscopy results showed that the first and second His4-type zinc finger domains (f1 and f2) adopted folded ββα structures in the presence of Zn(II), but that the third His4-type zinc finger domain (f3) did not. Non-FokI-type zinc finger nucleases containing 3 or 4 finger domains were also prepared by combining a His4-type zinc finger domain with the Sp1wt scaffold. We studied their DNA-binding abilities and hydrolytic activities against DNA oligonucleotides by performing gel-mobility-shift assays. The results showed that f1 had higher hydrolytic activity for a DNA oligonucleotide with a GC box (5'-GGG GCG GGG-3'), compared with that of f2, although both His4-type single finger domains had similar DNA-binding affinities. The difference in the hydrolytic activity between f1 and f2 was ascribed not only to the zinc coordinate structure, but also to its folding structure and the stability of finger domain.

Engineered transcriptional systems for cyanobacterial biotechnology

Cyanobacteria can function as solar-driven biofactories thanks to their ability to perform photosynthesis and the ease with which they are genetically modified. In this review, we discuss transcriptional parts and promoters available for engineering cyanobacteria. First, we go through special cyanobacterial characteristics that may impact engineering, including the unusual cyanobacterial RNA polymerase, sigma factors and promoter types, mRNA stability, circadian rhythm, and gene dosage effects. Then, we continue with discussing component characteristics that are desirable for synthetic biology approaches, including decoupling, modularity, and orthogonality. We then summarize and discuss the latest promoters for use in cyanobacteria regarding characteristics such as regulation, strength, and dynamic range and suggest potential uses. Finally, we provide an outlook and suggest future developments that would advance the field and accelerate the use of cyanobacteria for renewable biotechnology.

A role for hydrogen bonding in DNA recognition by the non-classical CCHHC type zinc finger, NZF-1

The non-classical zinc finger protein, Neural Zinc Finger Factor-1, contains six Cys2His2Cys domains. All three cysteines and the second histidine directly bind Zn(II). Using a combination of mutagenesis, metal coordination and DNA binding studies, we report that the first histidine is involved in a functionally important hydrogen bonding interaction.

Specific enrichment of prokaryotic DNA using a recombinant DNA-binding protein

Targeted enrichment of DNA is often necessary for its detection and characterization in complex samples. We describe the development and application of the novel molecular tool for the specific enrichment of prokaryotic DNA. A fused protein comprising the DNA-binding subunit of the bacterial topoisomerase II, gyrase, was expressed, purified, and immobilized on magnetic particles. We demonstrated the specific affinity of the immobilized protein towards bacterial DNA and investigated its efficiency in the samples with high background of eukaryotic DNA. The reported approach allowed for the selective isolation and further detection of as few as 5 pg Staphylococcus aureus DNA from the sample with 4 × 10(6)-fold surplus of human DNA. This method is a promising approach for the preparation of such type of samples, for example in molecular diagnostics of sepsis.

Designing hydrolytic zinc metalloenzymes

Zinc is an essential element required for the function of more than 300 enzymes spanning all classes. Despite years of dedicated study, questions regarding the connections between primary and secondary metal ligands and protein structure and function remain unanswered, despite numerous mechanistic, structural, biochemical, and synthetic model studies. Protein design is a powerful strategy for reproducing native metal sites that may be applied to answering some of these questions and subsequently generating novel zinc enzymes. From examination of the earliest design studies introducing simple Zn(II)-binding sites into de novo and natural protein scaffolds to current studies involving the preparation of efficient hydrolytic zinc sites, it is increasingly likely that protein design will achieve reaction rates previously thought possible only for native enzymes. This Current Topic will review the design and redesign of Zn(II)-binding sites in de novo-designed proteins and native protein scaffolds toward the preparation of catalytic hydrolytic sites. After discussing the preparation of Zn(II)-binding sites in various scaffolds, we will describe relevant examples for reengineering existing zinc sites to generate new or altered catalytic activities. Then, we will describe our work on the preparation of a de novo-designed hydrolytic zinc site in detail and present comparisons to related designed zinc sites. Collectively, these studies demonstrate the significant progress being made toward building zinc metalloenzymes from the bottom up.

SP transcription factor paralogs and DNA-binding sites coevolve and adaptively converge in mammals and birds

Functional modification of regulatory proteins can affect hundreds of genes throughout the genome, and is therefore thought to be almost universally deleterious. This belief, however, has recently been challenged. A potential example comes from transcription factor SP1, for which statistical evidence indicates that motif preferences were altered in eutherian mammals. Here, we set out to discover possible structural and theoretical explanations, evaluate the role of selection in SP1 evolution, and discover effects on coregulatory proteins. We show that SP1 motif preferences were convergently altered in birds as well as mammals, inducing coevolutionary changes in over 800 regulatory regions. Structural and phylogenic evidence implicates a single causative amino acid replacement at the same SP1 position along both lineages. Furthermore, paralogs SP3 and SP4, which coregulate SP1 target genes through competitive binding to the same sites, have accumulated convergent replacements at the homologous position multiple times during eutherian and bird evolution, presumably to preserve competitive binding. To determine plausibility, we developed and implemented a simple model of transcription factor and binding site coevolution. This model predicts that, in contrast to prevailing beliefs, even small selective benefits per locus can drive concurrent fixation of transcription factor and binding site mutants under a broad range of conditions. Novel binding sites tend to arise de novo, rather than by mutation from ancestral sites, a prediction substantiated by SP1-binding site alignments. Thus, multiple lines of evidence indicate that selection has driven convergent evolution of transcription factors along with their binding sites and coregulatory proteins.

Novel domain combinations in proteins encoded by chimeric transcripts

Motivation: Chimeric RNA transcripts are generated by different mechanisms including pre-mRNA trans-splicing, chromosomal translocations and/or gene fusions. It was shown recently that at least some of chimeric transcripts can be translated into functional chimeric proteins.

Results: To gain a better understanding of the design principles underlying chimeric proteins, we have analyzed 7,424 chimeric RNAs from humans. We focused on the specific domains present in these proteins, comparing their permutations with those of known human proteins. Our method uses genomic alignments of the chimeras, identification of the gene–gene junction sites and prediction of the protein domains. We found that chimeras contain complete protein domains significantly more often than in random data sets. Specifically, we show that eight different types of domains are over-represented among all chimeras as well as in those chimeras confirmed by RNA-seq experiments. Moreover, we discovered that some chimeras potentially encode proteins with novel and unique domain combinations. Given the observed prevalence of entire protein domains in chimeras, we predict that certain putative chimeras that lack activation domains may actively compete with their parental proteins, thereby exerting dominant negative effects. More generally, the production of chimeric transcripts enables a combinatorial increase in the number of protein products available, which may disturb the function of parental genes and influence their protein–protein interaction network.

Availability: our scripts are available upon request.

Contact:avalencia@cnio.es

Supplementary information:Supplementary data are available at Bioinformatics online.

Development of safer gene delivery systems to minimize the risk of insertional mutagenesis-related malignancies: a critical issue for the field of gene therapy

Integrating gene delivery systems allow for a more stable transgene expression in mammalian cells than the episomal ones. However, the integration of the shuttle vector within the cellular chromosomal DNA is associated with the risk of insertional mutagenesis, which, in turn, may cause malignant cell transformation. The use of a retroviral-derived vector system was responsible for the development of leukemia in five children, who participated in various clinical trials for the treatment of severe combined immunodeficiency (SCID-X1) in France and in the United Kingdom. Unfortunately, the hematological malignancy claimed the life of one patient in 2004, who was enrolled in the French clinical trial. In addition, adeno-associated-viral-(AAV-) mediated gene transfer induced tumors in animal models, whereas the Sleeping Beauty (SB) DNA transposon system was associated with insertional mutagenesis events in cell culture systems. On these grounds, it is necessary to develop safer gene delivery systems for the genetic manipulation of mammalian cells. This paper discusses the latest achievements that have been reported in the field of vector design.

Control of enzyme reaction by a designed metal-ion-dependent α-helical coiled-coil protein

Regulation of protein function by external stimuli is a fascinating target for de novo design. We have constructed a peptide that assembles into a homotrimer in the presence of metal ions, such as Ni(2+), Cu(2+), and Zn(2+). We fused the peptide construct to the DNA-binding domain (DBD) of the heat shock factor from Saccharomyces cerevisiae, which binds tandem repeats of the heat shock element (HSE). However, the fusion protein bound to the natural three tandem HSEs even in the absence of metal ions, although mainly as the dimerized protein. Using "skipped" HSEs containing six additional nucleotides inserted between two adjacent HSEs, to prevent interactions between the DBDs, we found the fusion protein bound to the new DNA target in a metal-ion-dependent manner, as monitored by a HindIII protection assay. The fusion protein containing two metal binding sites in the metal-ion-controlled domain inhibited RNA transcription by T7 RNA polymerase in the presence of metal ions, in a template containing skipped HSEs downstream of the T7 promoter. The designed protein therefore regulates the functions of the enzyme in a metal-ion-dependent manner.

Towards artificial metallonucleases for gene therapy: recent advances and new perspectives

The process of DNA targeting or repair of mutated genes within the cell, induced by specifically positioned double-strand cleavage of DNA near the mutated sequence, can be applied for gene therapy of monogenic diseases. For this purpose, highly specific artificial metallonucleases are developed. They are expected to be important future tools of modern genetics. The present state of art and strategies of research are summarized, including protein engineering and artificial ‘chemical’ nucleases. From the results, we learn about the basic role of the metal ions and the various ligands, and about the DNA binding and cleavage mechanism. The results collected provide useful guidance for engineering highly controlled enzymes for use in gene therapy.

Interaction identification of Zif268 and TATA(ZF) proteins with GC-/AT-rich DNA sequence: A theoretical study

Molecular dynamics (MD) simulations for Zif268 (a zinc-finger-protein binding specifically to the GC-rich DNA)-d(A(1) G(2) C(3) G(4) T(5) G(6) G(7) G(8) C(9) A(10) C(11) )(2) and TATA(ZF) (a zinc-finger-protein recognizing the AT-rich DNA)-d(A(1) C(2) G(3) C(4) T(5) A(6) T(7) A(8) A(9) A(10) A(11) G(12) G(13) )(2) complexes have been performed for investigating the DNA binding affinities and specific recognitions of zinc fingers to GC-rich and AT-rich DNA sequences. The binding free energies for the two systems have been further analyzed by using the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method. The calculations of the binding free energies reveal that the affinity energy of Zif268-DNA complex is larger than that of TATA(ZF) -DNA one. The affinity between the zinc-finger-protein and DNA is mainly driven by more favorable van-der-Waals and nonpolar/solvation interactions in both complexes. However, the affinity energy difference of the two binding systems is mainly caused by the difference of van-der-Waals interactions and entropy components. The decomposition analysis of MM-PBSA free energies on each residue of the proteins predicts that the interactions between the residues with the positive charges and DNA favor the binding process; while the interactions between the residues with the negative charges and DNA behave in the opposite way. The interhydrogen-bonds at the protein-DNA interface and the induced intrafinger hydrogen bonds between the residues of protein for the Zif268-DNA complex have been identified at some key contact sites. However, only the interhydrogen-bonds between the residues of protein and DNA for TATA(ZF) -DNA complex have been found. The interactions of hydrogen-bonds, electrostatistics and van-der-Waals type at some new contact sites have been identified. Moreover, the recognition characteristics of the two studied zinc-finger-proteins have also been discussed.

Theoretical design of a specific DNA-Zinc-finger protein interaction with semi-empirical quantum chemical methods

The interactions of a zinc-finger (ZF) protein with DNA containing the specific recognition site of the ZF and with a non-specific DNA were studied with the semi-empirical quantum chemical method of PM6/Mozyme. The ZF protein (1MEY)-DNA complex structures were generated by docking calculations. The complex structures were reoptimized with the PM6/Mozyme method with implicit solvation in water. The structures were also calculated in the gas phase. The interaction enthalpies between the protein and DNA within the complexes obtained in the PM6/Mozyme with solvation optimized structures were calculated with the single-point PM6-DH2/Mozyme method (PM6 with dispersion, H-bond correction and Mozyme) with solvation. The results supported the specific and non-specific interactions in the complexes obtained from the docking experiments. The binding enthalpies of the specific and non-specific DNA binding to the protein differed significantly. The interactions between the nucleic acid strands in duplexes were also evaluated; these interactions between the base pairs were different because of the different "G…C:A…T" ratios in the DNA molecules studied. The stacking interactions between the nucleic bases were also characterized in the DNA duplexes.

Update on fetal hemoglobin gene regulation in hemoglobinopathies

PURPOSE OF REVIEW

The developmental switch from fetal to adult hemoglobin has long fascinated biologists and attracted hematologists given its importance for patients with hemoglobin disorders. New discoveries have reinvigorated the field of globin gene regulation. These results hold promise for improved treatment of the major hemoglobinopathies.

RECENT FINDINGS

Both genome-wide association studies and traditional linkage studies have identified several genetic loci involved in silencing fetal hemoglobin. BCL11A is a potent silencer of fetal hemoglobin in both mouse and humans. It controls the beta-globin gene cluster in concert with other factors. KLF1, a vital erythroid transcription factor, activates BCL11A and assists in coordinating the switch from fetal to adult hemoglobin. A regulatory network of cell-intrinsic and cell-extrinsic factors maintains the epigenetic homeostasis of the beta-globin cluster and accounts for the precise lineage-specific and developmental stage-specific regulation of the globin genes.

SUMMARY

With an improved understanding of pathways involved in the switch from fetal to adult hemoglobin, new targets have emerged for the treatment of the common hemoglobin disorders, sickle cell anemia and beta-thalassemia.

Synthetic circuits, devices and modules

The aim of synthetic biology is to design artificial biological systems for novel applications. From an engineering perspective, construction of biological systems of defined functionality in a hierarchical way is fundamental to this emerging field. Here, we highlight some current advances on design of several basic building blocks in synthetic biology including the artificial gene control elements, synthetic circuits and their assemblies into devices and modules. Such engineered basic building blocks largely expand the synthetic toolbox and contribute to our understanding of the underlying design principles of living cells.

Rationalizing the development of live attenuated virus vaccines

The design of vaccines against viral disease has evolved considerably over the past 50 years. Live attenuated viruses (LAVs)-those created by passaging a virus in cultured cells-have proven to be an effective means for preventing many viral diseases, including smallpox, polio, measles, mumps and yellow fever. Even so, empirical attenuation is unreliable in some cases and LAVs pose several safety issues. Although inactivated viruses and subunit vaccines alleviate many of these concerns, they have in general been less efficacious than their LAV counterparts. Advances in molecular virology--creating deleterious gene mutations, altering replication fidelity, deoptimizing codons and exerting control by microRNAs or zinc finger nucleases--are providing new ways of controlling viral replication and virulence and renewing interest in LAV vaccines. Whereas these rationally attenuated viruses may lead to a new generation of safer, more widely applicable LAV vaccines, each approach requires further testing before progression to human testing.

Rationalizing the development of live attenuated virus vaccines

The design of vaccines against viral disease has evolved considerably over the past 50 years. Live attenuated viruses (LAVs)-those created by passaging a virus in cultured cells-have proven to be an effective means for preventing many viral diseases, including smallpox, polio, measles, mumps and yellow fever. Even so, empirical attenuation is unreliable in some cases and LAVs pose several safety issues. Although inactivated viruses and subunit vaccines alleviate many of these concerns, they have in general been less efficacious than their LAV counterparts. Advances in molecular virology--creating deleterious gene mutations, altering replication fidelity, deoptimizing codons and exerting control by microRNAs or zinc finger nucleases--are providing new ways of controlling viral replication and virulence and renewing interest in LAV vaccines. Whereas these rationally attenuated viruses may lead to a new generation of safer, more widely applicable LAV vaccines, each approach requires further testing before progression to human testing.