Structural specificity effects of trivalent polyamine analogues on the stabilization and conformational plasticity of triplex DNA

Helical polyamines

Polymer microstructures rely on tacticity, yet exploration in polyamines has focused predominantly on atactic polymers. We introduce a method to synthesize a diverse library of ortho and para-cyanobenzenesulfonyl-activated-methyl aziridines using R, S, and racemic alaninol. Living anionic ring-opening polymerization of racemic sulfonyl aziridines yields soluble polymers, while enantiomerically-pure sulfonyl aziridines follow a dispersion polymerization with complete monomer conversion giving access to stereoblock copolymers. Removal of activation groups is achieved using dodecanethiol and tert-butylimino-tri(pyrrolidino)phosphorane to obtain isotactic or atactic linear polypropylene imines (LPPIs). High-purity L-PPIs are obtained in salt and neutral forms with high yields. Stereoblock copolymers of poly-R-block-S-polysulfonamides and respective polypropylene imine stereoblocks are synthesized, revealing helical structures in water influenced by the monomer type and sequence in CD spectroscopy. Molecular dynamics simulations confirm the helical nature of isotactic LPPIs in water. Bulk characterization demonstrates the first crystalline isotactic polyamines via spherulite growth in polarized light, atomic force microscopy and XRD analyses. In cell-transfection studies, the synthesized isotactic LPPIs exhibit lower toxicity and transfection efficiency than commercial hyperbranched polyethylene imine, with longer chains showing increased transfection efficiency. These isotactic polymers open avenues for complex macromolecular architectures with optically active polyamines akin to poly(amino acid)s but lacking hydrolytically cleavable amide links.

Collapse of DNA in packaging and cellular transport

The dawn of molecular biology and recombinant DNA technology arose from our ability to manipulate DNA, including the process of collapse of long extended DNA molecules into nanoparticles of approximately 100 nm diameter. This condensation process is important for the packaging of DNA in the cell and for transporting DNA through the cell membrane for gene therapy. Multivalent cations, such as natural polyamines (spermidine and spermine), were initially recognized for their ability to provoke DNA condensation. Current research is targeted on molecules such as linear and branched polymers, oligopeptides, polypeptides and dendrimers that promote collapse of DNA to nanometric particles for gene therapy and on the energetics of DNA packaging.

Ionic microenvironmental effects on triplex DNA stabilization: cationic counterion effects on poly(dT)·poly(dA)·poly(dT)

The structure and conformation of nucleic acids are influenced by metal ions, polyamines, and the microenvironment. In poly(purine) · poly(pyrimidine) sequences, triplex DNA formation is facilitated by metal ions, polyamines and other ligands. We studied the effects of mono- and di-valent metal ions, and ammonium salts on the stability of triple- and double-stranded structures formed from poly(dA) and poly(dT) by measuring their respective melting temperatures. In the presence of metal ions, the absorbance versus temperature profile showed two transitions: Tm1 for triplex to duplex and single stranded DNA, and Tm2 for duplex DNA melting to single stranded DNA. Monovalent cations (Li(+), Na(+), K(+), Rb(+), Cs(+) and [Formula: see text] ) promoted triplex DNA at concentrations ≥150 mM. Tm1 varied from 49.8 °C in the presence of 150 mM Li(+) to 30.6 °C in the presence of 150 mM K(+). [Formula: see text] was very effective in stabilizing triplex DNA and its efficacy decreased with increasing substitution of the hydrogen atoms with methyl, ethyl, propyl and butyl groups. As in the case of monovalent cations, a concentration-dependent increase in Tm1 was observed with divalent ions and triplex DNA stabilization decreased in the order: Mg(2+) > Ca(2+) > Sr(2+) > Ba(2+). All positively charged cations increased the melting temperature of duplex DNA. Values of Δn (number of ions released) on triplex DNA melting were 0.46 ± 0.06 and 0.18 ± 0.02, respectively, for mono- and di-valent cations, as calculated from 1/Tm1 versus ln[M(+,2+)] plots. The corresponding values for duplex DNA were 0.25 ± 0.02 and 0.12 ± 0.02, respectively, for mono- and di-valent cations. Circular dichroism spectroscopic studies showed distinct conformational changes in triplex DNA stabilized by alkali metal and ammonium ions. Our results might be useful in developing triplex forming oligonucleotide based gene silencing techniques.

Protamine-mediated DNA coating remarkably improves bombardment transformation efficiency in plant cells

We have developed a method by which remarkably higher efficiencies of transient and stable transformation were achieved in bombardment transformation of plants. Over fivefold increase in transient gus gene expression was achieved when rice or maize suspension cells were bombarded with gold particles coated with plasmid DNA in the presence of protamine instead of the conventional spermidine. A 3.3-fold improvement in stable transformation efficiency was also observed using rice suspension cells with the new coating approach. The coated protamine-plasmid DNA complex resisted degradation by a DNase or by rice cell extract much longer than the spermidine-plasmid DNA complex. The results from this study suggest that protamine protects plasmid DNA longer than spermidine when being delivered inside the cells, probably by forming a nano-scale complex, and thus helps improve the efficiency of particle bombardment-mediated plant transformation.

The triple helix: 50 years later, the outcome

Triplex-forming oligonucleotides constitute an interesting DNA sequence-specific tool that can be used to target cleaving or cross-linking agents, transcription factors or nucleases to a chosen site on the DNA. They are not only used as biotechnological tools but also to induce modifications on DNA with the aim to control gene expression, such as by site-directed mutagenesis or DNA recombination. Here, we report the state of art of the triplex-based anti-gene strategy 50 years after the discovery of such a structure, and we show the importance of the actual applications and the main challenges that we still have ahead of us.

An overview of condensing and noncondensing polymeric systems for gene delivery

INTRODUCTIONSelf-assembling synthetic vectors for DNA delivery are designed to fulfill several biological functions. They must be able to deliver their genetic payload specifically to the target tissue/cells in a site-specific manner, while protecting the genetic material from degradation by metabolic or immune pathways. Furthermore, they must exhibit minimal toxicity and be proven safe enough for therapeutic use. Ultimately, they must have the capability to express a therapeutic gene for a finite period of time in an appropriate, regulated fashion. The DNA encapsulated in these vectors may be in a condensed or noncondensed form, depending on the nature of the polymer and the technique used for formulating the vector system. The whole process presents many barriers at both tissue and cellular levels. Overcoming these hurdles is the principal objective for efficient polymer-based DNA therapeutics.

Investigation of complexes formed by interaction of cationic gemini surfactants with deoxyribonucleic acid

Cationic gemini surfactants, N,N-bis(dimethylalkyl)-alpha,omega-alkanediammonium dibromide [C(m)H(2m+1)(CH(3))(2)N(+)(CH(2))(s)N(+)(CH(3))(2)C(m)H(2m+1) x 2 Br(-), or m-s-m], have proven to be effective synthetic vectors for gene delivery (transfection). Complexes (lipoplexes) of gemini compounds, where m = 12, s = 3, 12 and m = 18 : 1(oleyl), s = 2, 3, 6, with DNA have been investigated using isothermal titration calorimetry (ITC), dynamic light scattering (DLS), zeta potential, atomic force microscopy (AFM) and circular dichroism (CD) techniques. The results show that lipoplex properties depend on the structural properties of the gemini surfactants, the presence of the helper lipid dioleoylphosphatidylethanolamine (DOPE), and the titration sequence. ITC data show that the interaction between DNA and gemini surfactants is endothermic and the observed enthalpy vs. charge ratio profile depends upon the titration sequence. Isoelectric points (IP) of lipoplex formation were estimated from the zeta potential measurements and show good agreement with the reaction endpoints (RP) obtained from ITC. DLS data indicate that DNA is condensed in the lipoplex. AFM images suggest that the lipoplex morphology changes from isolated globular-like aggregated particles to larger-size aggregates with great diversity in morphology. This change is further accentuated by the presence of DOPE in the lipoplexes. The results are interpreted in terms of some current models of lipoplex formation.

Highly stable DNA triplexes formed with cationic phosphoramidate pyrimidine alpha-oligonucleotides

The ability of cationic phosphoramidate pyrimidine alpha-oligonucleotides (ONs) to form triplexes with DNA duplexes was investigated by UV melting experiments, circular dichroism spectroscopy and gel mobility shift experiments. Replacement of the phosphodiester linkages in alpha-ONs with positively charged phosphoramidate linkages results in more efficient triplex formation, the triplex stability increasing with the number of positive charges. At a neutral pH and in the absence of magnesium ions, it was found that a fully cationic phosphoramidate alpha-TFO (triplex-forming oligonucleotide) forms a highly stable triplex that melts at a higher temperature than the duplex target. No hysteresis between the annealing and melting curves was noticed; this indicates fast association. Moreover, the recognition of a DNA duplex with a cationic alpha-TFO through Hoogsteen base pairing is highly sequence-specific. To the best of our knowledge, this is the first report of stable triplexes in the pyrimidine motif formed by cationic alpha-oligonucleotides and duplex targets.

Biogenic amines and polyamines: similar biochemistry for different physiological missions and biomedical applications

Biogenic amines are organic polycations derived from aromatic or cationic amino acids. All of them have one or more positive charges and a hydrophobic skeleton. Nature has evolved these molecules to play different physiological roles in mammals, but maintains similar patterns for their metabolic and intracellular handling. As deduced from this review, many questions still remain to be solved around their biochemistry and molecular biology, blocking our aims to control the relevant pathologies in which they are involved (cancer and immunological, neurological, and gastrointestinal diseases). Advances in this knowledge are dispersed among groups working on different biomedical areas. In these pages, we put together the most relevant information to remark how fruitful it can be to learn from Nature and to take advantage of the biochemical similarities (key protein structures and their regulation data on metabolic interplays and binding properties) to generate new hypothesis and develop different biomedical strategies based on biochemistry and molecular biology of these compounds.

Raman study of the interaction between polyamines and a GC oligonucleotide

The interaction between the oligonucleotide d[G(CG)(7)]. d[C(GC)(7)] and the three biogenic polyamines putrescine, spermidine, and spermine under physiological conditions has been studied by Raman spectroscopy. The results indicate the formation of highly ordered aggregated structures in solution, largely stabilized by electrostatic attractions, which have been described as cholesteric phases. Aggregation seems to be preceded by a partial B --> Z conformational transition for spermidine and spermine, which would allow for a deeper oligonucleotide-polyamine interaction. Interaction with the nucleic bases has also been evidenced for aggregates. At low polyamine concentrations the preferential binding sites are similar to those proposed for their interactions with ct-DNA. With increasing the polyamine concentration, the oligonucleotide-polyamine interactions involve both minor and major grooves, which is consistent with the formation of cholesteric phases.

Effect of N8-acetylspermidine deacetylase inhibition on the growth of L1210 cells

A selective inhibitor of N8-acetylspermidine deacetylase has been employed to study the role of N8-acetylspermidine deacetylation in the regulation of L1210 cell growth. This inhibitor, 7-[N-(3-aminopropyl) amino] heptan-2-one (APAH), was found to stimulate the growth of L1210 cells at concentrations between 10 microM and 0.5 mM. Maximum stimulation was seen at 100 microM, resulting in significantly increased rates of cell division and maximum cell density. N8-Acetylspermidine levels in L1210 cells were shown to increase significantly after the APAH treatment as would be expected for deacetylase inhibition. The effects of deacetylase inhibition were mimicked by addition of N8-acetylspermidine to the culture medium at concentrations greater than 1 mM as indicated by a subsequent increase in rate of cell growth and maximum cell density. The magnitudes of the increases in growth observed were not large, but this might be expected in cells that are already in a rapid growth phase. Other exogenously added polyamines including N1-acetylspermidine, spermidine, putrescine, and spermine did not stimulate cell growth. These data suggest that stimulation of cell growth occurs as a consequence of N8-acetylspermidine accumulation and N8-acetylspermidine deacetylase inhibition.

Selectivity of spermine homologs on triplex DNA stabilization

We synthesized seven homologs of spermine (H2N(CH2)3NH(CH2)nNH(CH2)3NH2, where n = 2-9; n = 4 for spermine) and studied their effects on melting temperature (Tm), conformation, and precipitation of poly(dA).2poly(dT). The triplex DNA melting temperature, Tm1 was 34.4 degrees C in the presence of 150 mM KCl. Addition of spermine homologs increased Tm1 in a concentration-dependent and structure-dependent manner, with 3-6-3 (n = 6) exerting optimal stabilization. The dTm1/dlog[polyamine] values were 9-24 for these compounds. The duplex melting temperature, Tm2 was insensitive to homolog concentration and structure, suggesting their ability to stabilize triplex DNA without altering the stability of the underlying duplex. Circular dichroism spectral studies revealed psi-DNA formation in a concentration-dependent and structure-dependent manner. Phase diagrams were constructed showing the critical ionic/polyamine concentrations stabilizing different structures. These compounds also exerted structural specificity effects on precipitating triplex DNA. These data provide new insights into the ionic/structural determinants affecting triplex DNA stability and indicate that 3-6-3 is an excellent ligand to stabilize poly(dA).2poly(dT) triplex DNA under physiologic ionic conditions for antigene therapeutics.

Polycations. 5. Inducement of psi-DNA circular dichroism signals for duplex deoxyribonucleotide homopolymers by polycationic strings

Atypical circular dichroism intensity enhancements previously associated with Psi-DNA condensates are reported for poly(dG-dC):poly(dG-dC) and poly(dA-dT):poly(dA-dT) upon addition to them of a polycationic string salt. Polycationic strings are organic species incorporating several cationic sites in a linear array through the molecule. The effect observed herein with a small molecule model system holds promise for elucidation of the structural details associated with Psi-DNA condensate formation.

Differential effects of cyclopolyamines on the stability and conformation of triplex DNA

Linear polyamines are excellent promoters of triplex DNA formation. The effects of structural rigidization of polyamines on triplex DNA stability are not known at present. We wished to develop a series of polyamine analogs as secondary ligands for triplex DNA stabilization for antigene applications. To accomplish this goal, we synthesized cyclopolyamines by interconnecting the two amino or imino groups of linear polyamines with a --(CH2)n-bridge (n=3,4,5). Melting temperature (Tm) data showed that [4,3]-spermine and [4,4]-spermine stabilized poly(dA) x 2poly(dT) triplex at >25 microM concentrations (Tm = 71 degrees C at 100 microM). The dTm/dlog [polyamine] values for these compounds were 26 and 40, respectively. [4,3]-Spermine and [4,4]-spermine also stabilized triplex DNA formed by a purine-motif triplex-forming oligonucleotide, TG3TG4TG4TG3T with its target duplex, as determined by Tm, circular dichroism (CD) spectroscopy, and electrophoretic mobility shift assay (EMSA). In contrast, [4,4]-putrescine and [4,5]-putrescine as well as [4,5]-spermine had no triplex DNA stabilizing effect. CD spectra also showed triplex DNA aggregation and psi-DNA formation at >100 microM [4,3]-spermine. These data demonstrate that structural rigidization of linear polyamines has a profound effect on their ability to stabilize triplex DNA and provoke conformational transitions.

Ionic effects on the elasticity of single DNA molecules

We used a force-measuring laser tweezers apparatus to determine the elastic properties of lambda-bacteriophage DNA as a function of ionic strength and in the presence of multivalent cations. The electrostatic contribution to the persistence length P varied as the inverse of the ionic strength in monovalent salt, as predicted by the standard worm-like polyelectrolyte model. However, ionic strength is not always the dominant variable in determining the elastic properties of DNA. Monovalent and multivalent ions have quite different effects even when present at the same ionic strength. Multivalent ions lead to P values as low as 250-300 A, well below the high-salt "fully neutralized" value of 450-500 A characteristic of DNA in monovalent salt. The ions Mg2+ and Co(NH3)63+, in which the charge is centrally concentrated, yield lower P values than the polyamines putrescine2+ and spermidine3+, in which the charge is linearly distributed. The elastic stretch modulus, S, and P display opposite trends with ionic strength, in contradiction to predictions of macroscopic elasticity theory. DNA is well described as a worm-like chain at concentrations of trivalent cations capable of inducing condensation, if condensation is prevented by keeping the molecule stretched. A retractile force appears in the presence of multivalent cations at molecular extensions that allow intramolecular contacts, suggesting condensation in stretched DNA occurs by a "thermal ratchet" mechanism.