Peptide nucleic acids: expanding the scope of nucleic acid recognition

Chemically modified nucleic acids and DNA intercalators as tools for nanoparticle assembly

The self-assembly of inorganic nanoparticles to larger structures is of great research interest as it allows the fabrication of novel materials with collective properties correlated to the nanoparticles' individual characteristics. Recently developed methods for controlling nanoparticle organisation have enabled the fabrication of a range of new materials. Amongst these, the assembly of nanoparticles using DNA has attracted significant attention due to the highly selective recognition between complementary DNA strands, DNA nanostructure versatility, and ease of DNA chemical modification. In this review we discuss the application of various chemical DNA modifications and molecular intercalators as tools for the manipulation of DNA-nanoparticle structures. In detail, we discuss how DNA modifications and small molecule intercalators have been employed in the chemical and photochemical DNA ligation in nanostructures; DNA rotaxanes and catenanes associated with reconfigurable nanoparticle assemblies; and DNA backbone modifications including locked nucleic acids, peptide nucleic acids and borane nucleic acids, which affect the stability of nanostructures in complex environments. We conclude by highlighting the importance of maximising the synergy between the communities of DNA chemistry and nanoparticle self-assembly with the aim to enrich the library of tools available for the manipulation of nanostructures.

Noncovalent Attachment of Chemical Moieties to siRNAs Using Peptide Nucleic Acid as a Complementary Linker

Bioconjugation of siRNAs with chemical moieties is an effective strategy to improve the stability and cellular uptake of siRNAs. However, chemical conjugations of siRNAs are always challenging because of siRNAs' extremely poor stability. Therefore, a new strategy to attach a chemical moiety to siRNA without chemical reaction is highly needed. Peptide nucleic acids (PNAs) are DNA analogues in which the phosphate ribose ring in the backbone is replaced with a polyamide. Compared to DNA, PNA has a higher affinity for complementary DNA and better chemical stability. We, therefore, employed PNAs as a complementary linker to attach chemical moieties to siRNAs by annealing. The objective of this study is to develop an easy but efficient strategy to noncovalently attach chemical moieties to siRNAs without chemical modification of the siRNAs. We identified a PNA complementary sequence for hybridizing with siRNAs. Also, we compared the stability and silencing effects of different siRNA-PNA chimeras, which were annealed at different termini of the siRNA. siRNAs with a PNA annealed to the 3' end of the sense strand exhibited enhanced stability in the serum and maintained a good silencing effect. The siRNA-PNA chimera was then employed in two delivery systems to deliver the PCBP2 siRNA, a potential antifibrotic siRNA, to hepatic stellate cells. In both systems, the chimera demonstrated high cellular uptake and silencing activity. The results suggested that the siRNA-PNA chimera is an easy and efficient approach to attach targeting ligands or chemical moieties to siRNAs without chemical modification of the siRNA. This new technology will greatly reduce the difficulty and cost in conjugating chemical moieties to siRNAs.

Design and characterization of symmetric nucleic acids via molecular dynamics simulations

Asymmetry (5'→3') associated with each strand of the deoxyribonucleic acid (DNA) is inherent in the sugar-phosphate backbone connectivity and is essential for replication and transcription. We note that this asymmetry is due to one single chemical bond (C_3' to C_2' ) in each nucleotide unit, and the absence of this bond results in directionally symmetric nucleic acids. We also discovered that creation of an extra chemical bond (C_5' to C_2' ) can lead to a symmetric backbone. Keeping their potential synthetic and therapeutic interest in mind, we designed a few novel symmetric nucleic acids. We investigated their conformational stability and flexibility via detailed all atom explicit solvent 100-ns long molecular dynamics simulations and compared the resulting structures with that of regular B-DNA. Quite interestingly, some of the symmetric nucleic acids retain the overall double helical structure indicating their potential for integration in physiological DNA without causing major structural perturbations.

Quantum mechanical studies of DNA and LNA

Quantum mechanical (QM) methodology has been employed to study the structure activity relations of DNA and locked nucleic acid (LNA). The QM calculations provide the basis for construction of molecular structure and electrostatic surface potentials from molecular orbitals. The topologies of the electrostatic potentials were compared among model oligonucleotides, and it was observed that small structural modifications induce global changes in the molecular structure and surface potentials. Since ligand structure and electrostatic potential complementarity with a receptor is a determinant for the bonding pattern between molecules, minor chemical modifications may have profound changes in the interaction profiles of oligonucleotides, possibly leading to changes in pharmacological properties. The QM modeling data can be used to understand earlier observations of antisense oligonucleotide properties, that is, the observation that small structural changes in oligonucleotide composition may lead to dramatic shifts in phenotypes. These observations should be taken into account in future oligonucleotide drug discovery, and by focusing more on non RNA target interactions it should be possible to utilize the exhibited property diversity of oligonucleotides to produce improved antisense drugs.

Synthesis and biological properties of caffeic acid-PNA dimers containing guanine

Caffeic acid (CA; 3,4-dihydroxycinnamic acid) is endowed with high antioxidant activity. CA derivatives (such as amides) have gained a lot of attention due to their antioxidative, antitumor and antimicrobial properties as well as stable characteristics. Caffeoyl-peptide derivatives showed different antioxidant activity depending on the type and the sequence of amino acid used. For these reasons, we decided to combine CA with Peptide Nucleic Acid (PNA) to test whether the new PNA-CA amide derivatives would result in an improvement or gain of CA's biological (i.e., antioxidant, cytotoxic, cytoprotective) properties. We performed the synthesis and characterization of seven dimer conjugates with various combinations of nucleic acid bases and focused NMR studies on the model compound ga-CA dimer. We demonstrate that PNA dimers containing guanine conjugated to CA exhibited different biological activities depending on composition and sequence of the nucleobases. The dimer ag-CA protected HepG2, SK-B-NE(2), and C6 cells from a cytotoxic dose of hydrogen peroxide (H₂O₂).

Fluorescence-based detection and quantification of features of cellular senescence

Cellular senescence is a spontaneous organismal defense mechanism against tumor progression which is raised upon the activation of oncoproteins or other cellular environmental stresses that must be circumvented for tumorigenesis to occur. It involves growth-arrest state of normal cells after a number of active divisions. There are multiple experimental routes that can drive cells into a state of senescence. Normal somatic cells and cancer cells enter a state of senescence upon overexpression of oncogenic Ras or Raf protein or by imposing certain kinds of stress such as cellular tumor suppressor function. Both flow cytometry and confocal imaging analysis techniques are very useful in quantitative analysis of cellular senescence phenomenon. They allow quantitative estimates of multiple different phenotypes expressed in multiple cell populations simultaneously. Here we review the various types of fluorescence methodologies including confocal imaging and flow cytometry that are frequently utilized to study a variety of senescence. First, we discuss key cell biological changes occurring during senescence and review the current understanding on the mechanisms of these changes with the goal of improving existing protocols and further developing new ones. Next, we list specific senescence phenotypes associated with each cellular trait along with the principles of their assay methods and the significance of the assay outcomes. We conclude by selecting appropriate references that demonstrate a typical example of each method.

Extension of the PNA world by functionalized PNA monomers eligible candidates for inverse Diels Alder Click Chemistry

Progress in genome research led to new perspectives in diagnostic applications and to new promising therapies. On account of their specificity and sensitivity, nucleic acids (DNA/RNA) increasingly are in the focus of the scientific interest. While nucleic acids were a target of therapeutic interventions up to now, they could serve as excellent tools in the future, being highly sequence-specific in molecular diagnostics. Examples for imaging modalities are the representation of metabolic processes (Molecular Imaging) and customized therapeutic approaches ("Targeted Therapy"). In the individualized medicine nucleic acids could play a key role; this requires new properties of the nucleic acids, such as stability. Due to evolutionary reasons natural nucleic acids are substrates for nucleases and therefore suitable only to a limited extent as a drug. To use DNA as an excellent drug, modifications are required leading e.g. to a peptide nucleic acid (PNA). Here we show that an easy substitution of nucleobases by functional molecules with different reactivity like the Reppe anhydride and pentenoic acid derivatives is feasible. These derivatives allow an independent multi-ligation of functionalized compounds, e.g. pharmacologically active ones together with imaging components, leading to local concentrations sufficient for therapy and diagnostics at the same time. The high chemical stability and ease of synthesis could enhance nucleic chemistry applications and qualify PNA as a favourite for delivery. This system is not restricted to medicament material, but appropriate for the development of new and highly efficient drugs for a sustainable pharmacy.

Nucleobase-containing peptides: an overview of their characteristic features and applications

Reports on nucleobase-containing chiral peptides (both natural and artificial) and achiral pseudopeptides are reviewed. Their synthesis, structural features, DNA and RNA-binding ability, as well as some other interesting applications which make them promising diagnostic/therapeutic agents of great importance in many areas of biology and therapy are taken into critical consideration.

Effect of terminal amino acids on the stability and specificity of PNA-DNA hybridisation

The effect of various charged or hydrophobic amino acids on the hybridisation of fully complementary and mismatch PNA-DNA duplexes was investigated via UV melting curve analysis. The results described here show that the thermal stability and binding specificity of PNA probes can be modified by conjugation to amino acids and these effects should be considered in experimental design when conjugating PNA sequences to solubility enhancing groups or cell transport peptides. Where stabilisation of a duplex is important, without there being a corresponding need for specific binding to fully complementary targets, the conjugation of multiple lysine residues to the C-terminus of PNA may be the best probe design. If, however, the key is to obtain maximum discrimination between fully complementary and mismatch targets, a replacement of glutamic acid for lysine as the routine solubility enhancing group is recommended.

Multicolor PRINS and multicolor PNA

Both PRimed IN Situ (PRINS) and Peptide Nucleic Acid (PNA) technologies have emerged as research techniques, but they have quickly evolved to applications in biological diagnosis assays. The two procedures now constitute efficient alternatives to the conventional fluorescence in situ hybridization (FISH) procedure for in situ chromosome identification and aneuploidy detection. They present several advantages (specificity, speed, discriminating ability) that make them very attractive for a number of cytogenetic purposes. Multicolor PRINS and PNA protocols have been described for the specific identification of human chromosomes. Various applications have already been developed in human genetics and new adaptations are ongoing.

Towards computing with proteins

Can proteins be used as computational devices to address difficult computational problems? In recent years there has been much interest in biological computing, that is, building a general purpose computer from biological molecules. Most of the current efforts are based on DNA because of its ability to self-hybridize. The exquisite selectivity and specificity of complex protein-based networks motivated us to suggest that similar principles can be used to devise biological systems that will be able to directly implement any logical circuit as a parallel asynchronous computation. Such devices, powered by ATP molecules, would be able to perform, for medical applications, digital computation with natural interface to biological input conditions. We discuss how to design protein molecules that would serve as the basic computational element by functioning as a NAND logical gate, utilizing DNA tags for recognition, and phosphorylation and exonuclease reactions for information processing. A solution of these elements could carry out effective computation. Finally, the model and its robustness to errors were tested in a computer simulation.

New approaches to fluorescence in situ hybridization

Fluorescence in situ hybridization (FISH) is a nonisotopic labeling and detection method that provides a direct way to determine the relative location or copy number of specific DNA sequences in nuclei or chromosomes. With recent advancements, this technique has found increased application in a number of research areas, including cytogenetics, prenatal diagnosis, cancer research and diagnosis, nuclear organization, gene loss and/or amplification, and gene mapping. The availability of different types of probe and the increasing number of FISH techniques has made it a widespread and diversely applied technology. Multicolor karyotyping by multicolor FISH and spectral karyotyping interphase FISH and comparative genomic hybridization allow genetic analysis of previously intractable targets. We present a brief overview of FISH technology and describe in detail methods of probe labeling and detection for different types of tissue sample, including microdissected nuclei from formalin-fixed paraffin-embedded tissue sections.

The potential for gene-targeted radiation therapy of cancers

Targeted cancer therapy is the mantra now chanted by oncologists of all types. Everyone hopes that the rapid expansion in the knowledge of cancer cell genetics, signaling, regulatory factors and other changes that underlie malignant transformation and metastasis will lead to innovative approaches for the treatment of cancers. To date, successful targeted therapies have been derived from pharmaceutical chemistry - designing chemical compounds intended to disrupt a crucial pathway for malignant cells to survive, grow and metastasize. Radiotherapy also has a goal of more-selective targeting of therapeutic radiation effects to only tumor cells. In this review, we describe our efforts to create a form of gene-targeted radiation therapy by using the unique radiation effects of radionuclides that decay by the Auger process attached to oligonucleotide carrier-molecules that are capable of forming triplex DNA structures with target sequences in the genome of the human cancer cell.

Conformationally constrained PNA analogues: structural evolution toward DNA/RNA binding selectivity

Since its discovery 12 years ago, aminoethylglycyl peptide nucleic acid (aeg-PNA) has emerged as one of the successful DNA mimics for potential therapeutic and diagnostic applications. An important requisite for in vivo applications that has received inadequate attention is engineering PNA analogues for able discrimination between DNA and RNA as binding targets. Our approach toward this aim is based on structural preorganization of the backbone to hybridization-competent conformations to impart binding selectivity. This strategy has allowed us to design locked PNAs to achieve specific hybridization with DNA or RNA with aims to increase the binding strength without losing the binding specificity. This Account presents results of our rationale in design of different conformationally constrained PNA analogues, their synthesis, and evaluation of hybridization specificities.

Down-regulation of amyloid precursor protein by peptide nucleic acid in vivo

Alzheimer's disease (AD) is a neurodegenerative disease associated with increased expression of amyloid precursor protein (APP) and the deposition of its proteolytic cleavage products, the amyloid-beta peptides, Abeta(1-40) and Abeta(1-42). Peptide nucleic acids (PNAs) have been shown to block the expression of proteins at transcriptional and translational levels. In this study we used a sense and an antisense PNA specifically targeted to APP to inhibit the transcription and translation of APP by complementary binding to DNA or mRNA, respectively. Using Western blotting, APP showed a drastic decrease (50% and 90% reduction, in two separate experiments, as compared with saline control) with the injection of sense APP. mRNA levels were higher at the same time point after injection of APP sense PNA, most probably because of a compensatory mechanism in response to the drop of APP that might have occurred at an earlier time point (0-1 h) and was reflected in a drop at the protein level at 1 h. The injection of antisense PNA showed about 70% decrease in APP as measured by Western blotting. Unmodified PNA can be used in vivo to reduce the levels of APP, which plays a critical role in the development of AD.

Two sides of the coin: affinity and specificity of nucleic acid interactions

During the past decade, synthetic nucleobase oligomers have found wide use in biochemical sciences, biotechnology and molecular medicine, both as research and/or diagnostic tools and as therapeutics. Numerous applications of common and modified oligonucleotides and oligonucleotide mimics rely on their ability to sequence-specifically recognize nucleic acid targets (DNA or RNA) by forming duplexes or triplexes. In general, these applications would benefit significantly from enhanced binding affinities of nucleobase oligomers in the formation of various secondary structures. However, for high-affinity probes, the selectivity of sequence recognition must also be improved to avoid undesirable associations with mismatched DNA and RNA sites. Here, we review recent progress in understanding the molecular mechanisms of nucleic acid interactions and the development of new high-affinity plus high-specificity oligonucleotides and their mimics, with particular emphasis on peptide nucleic acids.

Impedance-based detection of DNA sequences using a silicon transducer with PNA as the probe layer

Electrochemical impedance measurements were used for the detection of single-strand DNA sequences using a peptide nucleic acid (PNA) probe layer immobilized onto Si/SiO2 chips. An epoxysilane layer is first immobilized onto the Si/SiO2 surface. The immobilization procedure consists of an epoxide/amine coupling reaction between the amino group of the PNA linker and the epoxide group of the silane. A 20-nucleotide sequence of PNA was used. Impedance measurements allow for the detection of the changes in charge distribution at the oxide/solution interface following modifications to the oxide surface. Due to these modifications, there are significant shifts in the semiconductor's flat-band potential after immobilization and hybridization. The results obtained using this direct and rapid approach are supported by fluorescence measurements according to classical methods for the detection of nucleic acid sequences.

Peptide nucleic acids targeted to the amyloid precursor protein

The depositing in brain of amyloid beta peptide (Abeta), which is formed by the cleavage of amyloid precursor protein (APP), is likely an etiologic factor in Alzheimer's disease (AD). Of the different forms of Abeta, Abeta(1-42) causes fibril formation and increases aggregation at elevated levels, which can lead to neuronal death. It is hypothesized that if the levels of Abeta, particularly Abeta(1-42), were reduced, then the onset of AD would be slowed or possibly prevented. Therefore, we are using peptide nucleic acids (PNAs) targeted to APP, as well as other key proteins, to try to decrease plasma and brain levels of Abeta(1-40) and Abeta(1-42). This research project was designed to utilize the expertise of our laboratory in the use of PNAs, a third-generation antisense or antigene molecule, to knock down proteins in brain. Antisense compounds specifically knock down the expression of a particular protein by inhibiting translation at the level of mRNA. On the other hand, antigene compounds knock down expression at the level of transcription. For experiments involving antisense strategies, there are several advantages to using PNAs as opposed to the traditional oligonucleotide molecules. We report here the ongoing studies with mice and rats with PNAs targeting APP, as well as BACE.

FISHing with locked nucleic acids (LNA): evaluation of different LNA/DNA mixmers

Locked Nucleic Acids (LNA) constitute a novel class of DNA analogues that have an exceptionally high affinity towards complementary DNA and RNA. Using human classical satellite-2 repeat sequence clusters as targets, we demonstrate that LNA/DNA mixmers oligonucleotides are excellent probes for FISH combining high binding affinity with short hybridization time and even with the ability to hybridize without prior thermal denaturation of the template.

Detection of gamma-globin mRNA in fetal nucleated red blood cells by PNA fluorescence in situ hybridization

OBJECTIVES

Fetal nucleated red blood cells (NRBC) that enter the peripheral blood of the mother are suitable for non-invasive prenatal diagnosis. The application of peptide nucleic acid (PNA) probes for tyramide amplified flow fluorescence in situ hybridization (FISH) detection of gamma-globin mRNA in fixed fetal NRBC is investigated.

METHODS

Hemin-induced K562 cells or nucleated blood cells (NBC) from male cord blood were mixed with NBC from non-pregnant women and analysed using both slide and flow FISH protocols. Post-chorionic villus sampling (CVS) blood samples from pregnant females carrying male fetuses were flow-sorted (2 x 10(6) NBC/sample). Y chromosome-specific PNA FISH was used to confirm that the identified gamma-globin mRNA stained cells were of fetal origin.

RESULTS

Flow FISH isolated gamma-globin mRNA positive NBCs showing characteristic cytoplasmic staining were all Y positive. The amplification system generated a population of false positive cells that were, however, easy to distinguish from the NRBCs in the microscope.

CONCLUSION

The gamma-globin mRNA specific PNA probes can be used for detection and isolation of fetal NRBCs from maternal blood. The method has additional potential for the study of gamma-globin mRNA levels or the frequency of adult NRBC (F cells) in patients with hemoglobinopathies.

Synthesis of amino- and guanidino-G-clamp PNA monomers

Syntheses of the protected amino- and guanidino-G-clamp PNA monomers, 9a and 9b, respectively, have been accomplished in eight steps from 5-bromouracil. Enhanced stacking interactions and additional hydrogen bonds with guanine should increase the affinity of PNAs incorporating these cytosine analogues for their complementary strands. [reaction: see text]

Using peptide nucleic acids as gene-expression modifiers to reduce beta-amyloid levels

The deposition of amyloid beta peptide (A beta) is an early and critical aspect of Alzheimer's disease. A beta is formed by the cleavage of amyloid precursor protein (APP). Studies of familial forms of Alzheimer's disease indicate that elevated secretion of A beta, particularly A beta(1-42), is likely to be an etiologic agent in the disease. A beta(1-42) is known to cause fibril formation and at elevated levels increases aggregation, which can lead to neuronal death. It has, therefore, been hypothesized that if the levels of A betaB, particularly A beta(1-42), could be reduced that onset of Alzheimer's disease could be slowed or possibly prevented. We, therefore, propose using PNAs targeted to APP to decrease plasma and brain levels of A beta(1-40) and A beta(1-42). This research project is designed to expand upon the discovery in our laboratory that systemic administration of antisense or antigene treatments utilizing peptide nucleic acids (PNAs) can be used to target and shut down proteins. Antisense strategies are methods of specifically targeting a particular protein by inhibiting translation by complementary binding to mRNA, while antigene methods inhibit transcription by complementary binding to DNA. For experiments involving antisense strategies, there are several advantages to using PNAs as opposed to the traditional oligonucleotide approaches. We initially preformed our studies in rats and identified a PNA sequence that was able to significantly reduce the levels of A beta(1-41) in rat brain compared to vehicle control rats. We have switched to mice so that we can prepare to perform our experiments in a transgenic animal model of Alzheimer's disease. We have, however, run into several technical difficulties with using mice compared to rats. In spite of this, we have identified one PNA sequence that specifically lowers mouse brain A beta(1-40) A beta(1-42) by 37% and 47%, respectively.

Peptide nucleic acids specifically cause antigene effects in vivo by systemic injection

Peptide nucleic acids (PNAs) are uncharged DNA analogs that hybridize to complementary sequences with high affinity and stability. We previously showed that PNAs, after intraperitoneal injection into rats, are effective antisense compounds in vivo. The present study was designed to test whether PNAs also have antigene effects in vivo. The renin-angiotensin system is critical in the control of blood pressure. We designed and synthesized sense (antigene) PNAs to angiotensinogen, which is the precursor protein that leads to angiotensin I and II. Spontaneously hypertensive rats received intraperitoneal injections of either 20 mg/kg sense-angiotensinogen-PNA, mismatch-angiotensinogen PNA, or saline. Only the sense-angiotensinogen PNA treatment resulted in a significant decrease in plasma angiotensin I, systolic blood pressure, and liver and brain angiotensinogen mRNA levels. Thus, these results demonstrate on the molecular, protein, and physiological levels that antigene PNAs are effective in vivo upon systemic administration.

Peptide nucleic acids targeted to the mouse proNPFF(A) reveal an endogenous opioid tonus

Pharmacological studies have implicated the anti-opioid neuropeptide FF (NPFF) in the modulation of pain transmission. Since its physiological role has not yet been fully elucidated, the present study examined whether antisense peptide nucleic acid (PNA) complementary to the NPFF precursor (proNPFF(A)) modified pain sensitivity. Mice received three intraperitoneal (i.p.) injections (10mg/kg) of antisense PNA (As-proNPFF(A)) over a period of 24h. As-proNPFF(A) treatment significantly increased the basal tail withdrawal latency in the tail-flick test. This analgesia persisted during 2 days and was completely reversed by naloxone. Thus, antisense PNAs, by decreasing anti-opioid effects, revealed a basal endogenous opioid activity. Our results evidence a physiological interplay between NPFF and opioid systems and further support the use of PNA as effective antisense agents, for studying gene function in vivo.

Pharmacokinetics and tissue distribution of a peptide nucleic acid after intravenous administration

Peptide nucleic acids (PNAs) are DNA analogs that hybridize to complementary nucleic sequences with high affinity and stability. In our previous work, we showed that a PNA complementary to a 12-base pair (bp) sequence of the coding region of the rat neurotensin receptor (rNTR1) mRNA is effective in significantly blocking a rat's central responses to neurotensin (NT), even when the PNA is injected intraperitoneally (i.p.). Using a novel gel shift detection assay to detect PNA, we have now used this same PNA sequence to derive its pharmacokinetic variables and its tissue distribution in the rat. The PNA has a distribution half-life of 3 +/- 3 minutes and an elimination half-life of 17 +/- 3 minutes. The total plasma clearance and volume of distribution of this PNA were 3.4 +/- 0.9 ml/min x kg and 60 +/- 30 ml/kg. Two hours after dosing, the PNA was found at detectable but low levels in all organs examined-in order of decreasing concentration: kidney, liver, heart, brain, and spleen. Approximately 90% of the PNA dose was recovered as unchanged parent compound in the urine 24 hours after administration.

Phosphates, DNA, and the search for nonterrean life: a second generation model for genetic molecules

Phosphate groups are found and used widely in biological chemistry. We have asked whether phosphate groups are likely to be important to the functioning of genetic molecules, including DNA and RNA. From observations made on synthetic analogs of DNA and RNA where the phosphates are replaced by nonanionic linking groups, we infer a set of rules that highlight the importance of the phosphodiester backbone for the proper functioning of DNA as a genetic molecule. The polyanionic backbone appears to give DNA the capability of replication following simple rules, and evolving. The polyanionic nature of the backbone appears to be critical to prevent the single strands from folding, permitting them to act as templates, guiding the interaction between two strands to form a duplex in a way that permits simple rules to guide the molecular recognition event, and buffering the sensitivity of its physicochemical properties to changes in sequence. We argue that the feature of a polyelectrolyte (polyanion or polycation) may be required for a "self-sustaining chemical system capable of Darwinian evolution." The polyelectrolyte structure therefore may be a universal signature of life, regardless of its genesis, and unique to living forms as well.

Hybridization of PNA to structured DNA targets: quadruplex invasion and the overhang effect

Peptide nucleic acid (PNA) probes have been synthesized and targeted to quadruplex DNA. UV-vis and CD spectroscopy reveal that the quadruplex structure of the thrombin binding aptamer (TBA) is disrupted at 37 degrees C by a short PNA probe. The corresponding DNA probe fails to bind to the stable secondary structure at this temperature. Thermal denaturation experiments indicate surprisingly high thermal and thermodynamic stabilities for the PNA-TBA hybrid. Our results point to the nonbonded nucleobase overhangs on the DNA as being responsible for this stability. This "overhang effect" is found for two different PNA-DNA sequences and a variety of different overhang lengths and sequences. The stabilization offered by the overhangs assists the PNA in overcoming the stable secondary structure of the DNA target, an effect which may be significant in the targeting of biological nucleic acids, which will always be much longer than the PNA probe. The ability of PNA to invade a structured DNA target expands its potential utility as an antigene agent or hybridization probe.

Targeting large molecules to mitochondria

Mitochondrial function is central to a range of cell processes and mitochondrial dysfunction contributes to a number of human diseases. Consequently there is growing interest in delivering large molecules such as nucleic acids, proteins, enzyme mimetics, drugs and probes to mitochondria within cells. The reasons for doing this are to understand how mitochondria function in the cell and to develop therapies for diseases involving mitochondrial damage. Here we review the methods that have been used to target large molecules to mitochondria and discuss some approaches under development.

Approaches and limitations to gene therapy for mitochondrial diseases

Mitochondrial dysfunction may be caused by mutations in either the nuclear and/or the mitochondrial genome. Since 1988, mitochondrial DNA mutations have been linked to retinopathies, myopathies, neurodegenerative diseases, and possibly normal aging. Adequate drug therapies for these disorders have yet to be discovered. Therefore, gene therapy must be considered as a possible alternative. In this review, we will discuss the possibilities and the problems associated with gene therapy for mitochondrial disorders.

Targeting peptide nucleic acid (PNA) oligomers to mitochondria within cells by conjugation to lipophilic cations: implications for mitochondrial DNA replication, expression and disease

The selective manipulation of mitochondrial DNA (mtDNA) replication and expression within mammalian cells has proven difficult. One promising approach is to use peptide nucleic acid (PNA) oligomers, nucleic acid analogues that bind selectively to complementary DNA or RNA sequences inhibiting replication and translation. However, the potential of PNAs is restricted by the difficulties of delivering them to mitochondria within cells. To overcome this problem we conjugated a PNA 11mer to a lipophilic phosphonium cation. Such cations are taken up by mitochondria through the lipid bilayer driven by the membrane potential across the inner membrane. As anticipated, phosphonium-PNA (ph-PNA) conjugates of 3.4-4 kDa were imported into both isolated mitochondria and mitochondria within human cells in culture. This was confirmed by using an ion-selective electrode to measure uptake of the ph-PNA conjugates; by cell fractionation in conjunction with immunoblotting; by confocal microscopy; by immunogold-electron microscopy; and by crosslinking ph-PNA conjugates to mitochondrial matrix proteins. In all cases dissipating the mitochondrial membrane potential with an uncoupler prevented ph-PNA uptake. The ph-PNA conjugate selectively inhibited the in vitro replication of DNA containing the A8344G point mutation that causes the human mtDNA disease 'myoclonic epilepsy and ragged red fibres' (MERRF) but not the wild-type sequence that differs at a single nucleotide position. Therefore these modified PNA oligomers retain their selective binding to DNA and the lipophilic cation delivers them to mitochondria within cells. When MERRF cells were incubated with the ph-PNA conjugate the ratio of MERRF to wild-type mtDNA was unaffected, even though the ph-PNA content of the mitochondria was sufficient to inhibit MERRF mtDNA replication in a cell-free system. This unexpected finding suggests that nucleic acid derivatives cannot bind their complementary sequences during mtDNA replication. In summary, we have developed a new strategy for targeting PNA oligomers to mitochondria and used it to determine the effects of PNA on mutated mtDNA replication in cells. This work presents new approaches for the manipulation of mtDNA replication and expression, and will assist in the development of therapies for mtDNA diseases.

Intrathecal administration of PNA targeting galanin receptor reduces galanin-mediated inhibitory effect in the rat spinal cord

Peptide nucleic acids (PNA) are nucleic acid analogues containing neutral amide backbone, forming stable and tight complexes with complementary DNA/RNA. However, it is unclear whether unmodified PNA can efficiently penetrate neuronal tissue in order to act as antisense reagent. Here we show that intrathecal (i.t.) injection of an unmodified antisense PNA complementary to the rat galanin receptor type 1 (GalR1) mRNA is able to block the inhibitory effect of i.t. administered galanin on spinal nociceptive transmission. Autoradiographic ligand binding studies using [125I]galanin show that the unmodified PNA is able to reduce the density of galanin binding sites in the dorsal horn. Thus, unmodified PNA applied i.t. appears to function as an effective antisense reagent in rat spinal cord in vivo.

An artificial primosome: design, function, and applications

Double-stranded (ds) DNA is capable of the sequence-specific accommodation of an additional oligodeoxyribonucleotide strand by the peptide nucleic acid(PNA)-assisted formation of a so-called PD-loop. We demonstrate here that the PD-loop may function as an artificial primosome within linear, nonsupercoiled DNA duplexes. DNA polymerase with its strand displacement activity uses this construct to initiate the primer extension reaction at a designated dsDNA site. The primer is extended by several hundred nucleotides. The efficiency of dsDNA priming by the artificial primosome assembly is comparable to the single-stranded DNA priming used in various assays. The ability of the PD-loop structure to perform like an artificial primosome on linear dsDNA may find applications in biochemistry, molecular biology, and molecular biotechnology, as well as for DNA diagnostics. In particular, multiple labels can be incorporated into a chosen dsDNA site resulting in ultrasensitive direct quantification of specific sequences. Furthermore, nondenaturing dsDNA sequencing proceeds from the PD-loop. This approach opens the way to direct isothermal reading of the DNA sequence against a background of unrelated DNA, thereby eliminating the need for purification of the target DNA.

Sequence-specific targeting of duplex DNA by peptide nucleic acids via triplex strand invasion

Because of a set of exceptional chemical, physical, and biological properties, polyamide or peptide nucleic acids (PNAs) hold a distinctive position among various synthetic ligands designed for DNA-targeting purposes. Cationic pyrimidine PNAs (cpyPNAs) represent a special group of PNAs, which effectively form strand invasion triplexes with double-stranded DNA (dsDNA) also known as P-loops. Extraordinary stability of the invasion triplexes and high sequence specificity of their formation combined with local opening of the DNA double helix within the P-loops make these complexes very attractive for sequence-specific manipulation with dsDNA. Important for applications is the fact that the discrimination between correct and mismatched binding sites in dsDNA by cpyPNAs is a nonequilibrium, kinetically controlled process. Therefore, a careful choice of experimental conditions that are optimal for the kinetic discrimination of correct versus mismatched cpyPNA binding is crucial for sequence-specific recognition of dsDNA by cpyPNAs. The experimental and theoretical data presented make it possible to select those solution parameters and cpyPNA constructions that are most favorable for sequence specificity without compromising the affinity of dsDNA targeting.

Peptide nucleic acid-assisted topological labeling of duplex dna

Peptide nucleic acids (PNAs) are a family of synthetic polyamide mimics of nucleic acids that offer a variety of applications. Pyrimidine bis-PNAs can be used for rational design of novel interlocked DNA nanostructures, earring labels, representing locked pseudorotaxanes or locked catenanes. These structures are created through DNA ligase-mediated catenation of duplex DNA with a circularized oligonucleotide tag at a designated DNA site. The assembly is performed via formation of the PD-loop consisting of a pair of bis-PNA openers and the probe oligonucleotide. The openers locally expose one of the two strands of duplex DNA for hybridizing the probe, whose termini are complementary to the displaced DNA strand. After hybridization, they are in juxtaposition and can subsequently be linked by DNA ligase. As a result, a true topological link forms at a precise position on the DNA double helix yielding locked, earring-like label. DNA topological labeling can be done both in solution and, for longer templates, within the agarose gel plug. Accordingly, highly localized DNA detection with rolling circle amplification of hybridization signal and effective micromanipulations with DNA duplexes become possible through precise spatial positioning of various ligands on the DNA scaffold.