Differences in DNA Condensation and Release by Lysine and Arginine Homopeptides Govern Their DNA Delivery Efficiencies

Peptide dendrimer/lipid hybrid systems are efficient DNA transfection reagents: structure--activity relationships highlight the role of charge distribution across dendrimer generations

Efficient DNA delivery into cells is the prerequisite of the genetic manipulation of organisms in molecular and cellular biology as well as, ultimately, in nonviral gene therapy. Current reagents, however, are relatively inefficient, and structure-activity relationships to guide their improvement are hard to come by. We now explore peptide dendrimers as a new type of transfection reagent and provide a quantitative framework for their evaluation. A collection of dendrimers with cationic and hydrophobic amino acid motifs (such as KK, KA, KH, KL, and LL) distributed across three dendrimer generations was synthesized by a solid-phase protocol that provides ready access to dendrimers in milligram quantities. In conjunction with a lipid component (DOTMA/DOPE), the best reagent, G1,2,3-KL ((LysLeu)8(LysLysLeu)4(LysLysLeu)2LysGlySerCys-NH2), improves transfection by 6-10-fold over commercial reagents under their respective optimal conditions. Emerging structure-activity relationships show that dendrimers with cationic and hydrophobic residues distributed in each generation are transfecting most efficiently. The trigenerational dendritic structure has an advantage over a linear analogue worth up to an order of magnitude. The success of placing the decisive cationic charge patterns in inner shells rather than previously on the surface of macromolecules suggests that this class of dendrimers significantly differs from existing transfection reagents. In the future, this platform may be tuned further and coupled to cell-targeting moieties to enhance transfection and cell specificity.

Modification of a designed amphipathic cell-penetrating peptide and its effect on solubility, secondary structure, and uptake efficiency

The development of safe and efficient nonviral gene delivery carriers has received a great deal of attention in the past decade. A class of amphipathic peptides has shown to be able to cross cell membranes and deliver cargo to the intracellular environment. Here, we introduce an 18-mer amphipathic peptide, C6M1, as a modified version of peptide C6 for short interfering RNA (siRNA) delivery. The importance of tryptophan residues and the effect of peptide sequence modification on its solubility, secondary structure, cytotoxicity, and uptake efficiency were investigated. The solubility of C6M1 in aqueous solutions was greatly enhanced compared to that of C6, confirmed by surface tension and anilinonaphthalene-8-sulfonic acid fluorescence measurements. C6M1 had a random/helical structure in water with the ability to attain a helical conformation in the presence of anionic components or membrane-mimicking environments. The modification significantly reduced the cytotoxicity of the peptide, making it a safer carrier for siRNA delivery. C6M1 was also found ∼90% more efficient than C6 in delivering Cy3-labeled siRNA in Chinese hamster ovary cells.

Polyarginine molecular weight determines transfection efficiency of calcium condensed complexes

Cell penetrating peptides (CPPs) have been extensively studied in polyelectrolyte complexes as a means to enhance the transfection efficiency of plasmid DNA (pDNA). Increasing the molecular weight of CPPs often enhances gene expression but poses a risk of increased cytotoxicity and immunogenicity compared to low molecular weight CCPs. Conversely, low molecular weight CPPs typically have low transfection efficiency due to large complex size. Complexes made using low molecular weight CPPs were found to be condensed to a small size by adding calcium. In this study, complexes of low molecular weight polyarginine and pDNA were condensed with calcium. These complexes showed high transfection efficiency and low cytotoxicity in A549 carcinomic human alveolar basal epithelial cells. The relationships between transfection efficiency and polyarginine size (5, 7, 9, or 11 amino acids), polyarginine/pDNA charge ratios, and calcium concentrations were studied. Polyarginine 7 was significantly more effective than other polyarginines under most formulation conditions, suggesting a link between cell penetration ability and transfection efficiency.

Thermodynamics of ideal proteinogenic homopolymer chains as a function of the energy spectrum E, helical propensity ω and enthalpic energy barrier

A reformulation and generalization of the Zwanzig model (ZW model) for ideal homopolymer chains poly-X, where X represents any of the twenty naturally occurring proteinogenic amino acid residues is presented. This reformulation and generalization provides a direct connection between coarse-grained parameters originally proposed in the ZW model with variables from the Lifson-Roig (LR) theory, such as the helical propensity per residue ω, and new variables introduced here, such as the energy gap Δ between unfolded and folded structures, as well as the ratio f of the energy scales involved. This enables us to discover the relevance of the energy spectrum E to the onset of configurational phase transitions. From the configurational partition function Q, thermodynamic properties such as the configurational entropy S, specific heat v and average energy <E> are calculated in terms of the number of residues K, temperature T, helical propensity ω and energy barrier ΔH for different poly-X chains in vacuo. Results obtained here provide substantial evidence that configurational phase transitions for ideal poly-X chains correspond to first-order phase transitions. An anomalous behavior of the thermodynamic functions <E>, Cv, S with respect to the number K of residues is also highlighted. On-going methods of solution are outlined.

Transfection of mammalian cells using block copolypeptide vesicles

An arginine-leucine block copolypeptide (R60 L20 ) is synthesized, which is capable of forming vesicles with controllable sizes, able to transport hydrophilic cargo across the cell membrane, and exhibit relatively low cytotoxicity. The R60 L20 vesicles also possess the ability to deliver DNA into mammalian cells for transfection. Although the transfection efficiency is lower than that of the commercially available transfection agent Lipofectamine 2000, the R60 L20 vesicles are able to achieve transfection with significantly lower cytotoxicity and immunogenicity. This behavior is potentially due to its stronger interaction with DNA which subsequently provides better protection against anionic heparin.

Comparison of nanocomplexes with branched and linear peptides for siRNA delivery

Efficient delivery of small interfering RNA (siRNA) remains the greatest technological barrier to the clinical implementation of RNA interference strategies. We are investigating the relationship between the biophysical properties of siRNA nanocomplexes and their transfection efficiency as an approach to the generation of improved formulations. Peptide-based formulations are of great interest, and so in this study we have compared nanocomplex formulations for siRNA delivery containing linear and branched oligolysine or oligoarginine peptides. Peptides were combined with cationic liposomes in siRNA formulations and compared for transfection efficiency, siRNA packaging efficiency, biophysical properties, and particle stability. Nanocomplexes containing linear peptides were more condensed and stable than branched peptide formulations; however, their silencing activity was lower, suggesting that their greater stability might limit siRNA release within the cell. Thus, differences in transfection appeared to be associated with differences in packaging and stability, indicating the importance of optimizing this feature in siRNA nanocomplexes.

Bioreducible polymers as a determining factor for polyplex decomplexation rate and transfection

Polyplex formation (complexation) and gene release from the polyplexes (decomplexation) are major events in polymeric gene delivery; however, the effect of the decomplexation rate on transfection has been rarely investigated. This study employed mixed polymers of poly((L)-lysine) (PLL: MW ~7.4 kDa) and reducible PLL (RPLL) (MW ~6.7 kDa) to design decomplexation rate-controllable PLL(100-x)RPLL(x)/pDNA complexes (PRL(x) polyplexes). The transfection efficiency of a model gene (luciferase) in MCF7 and HEK293 cell lines increased with increasing x (RPLL content) in the PRL(x) polyplexes until peaking at x = 2.5 and 10, respectively, after which point transfection efficiency declined rapidly. In MCF7 cells, PRL(2.5) polyplex produced 3 or 223 times higher gene expression than PLL or RPLL polyplexes, respectively. Similarly, the transfection efficiency of PRL(10) polyplex-transfected HEK293 cells was 3.8 or 67 times higher than that of PLL or RPLL polyplexes, respectively. The transfection results were not apparently related to the particle size, surface charge, complexation/compactness, cellular uptake, or cytotoxicity of the tested polyplexes. However, the decomplexation rate varied by RPLL content in the polyplexes, which in turn influenced the gene transfection. The nuclear localization of pDNA delivered by PRL(x) polyplexes showed a similar trend to their transfection efficiencies. This study suggests that an optimum decomplexation rate may result in high nuclear localization of pDNA and transfection. Understanding in decomplexation and intracellular localization of pDNA may help develop more effective polyplexes.

Efficient intracellular delivery of nucleic acid pharmaceuticals using cell-penetrating peptides

Over the last 20 years, researchers have designed or discovered peptides that can permeate membranes and deliver exogenous molecules inside a cell. These peptides, known as cell-penetrating peptides (CPPs), typically consist of 6-30 residues, including HIV TAT peptide, penetratin, oligoarginine, transportan, and TP10. Through chemical conjugation or noncovalent complex formation, these structures successfully deliver bioactive and membrane-impermeable molecules into cells. CPPs have also gained attention as an attractive vehicle for the delivery of nucleic acid pharmaceuticals (NAPs), including genes/plasmids, short oligonucleotides, and small interference RNAs and their analogues, due to their high internalization efficacy, low cytotoxicity, and flexible structural design. In this Account, we survey the potential of CPPs for the design and optimization of NAP delivery systems. First, we describe the impact of the N-terminal stearylation of CPPs. Endocytic pathways make a major contribution to the cellular uptake of NAPs. Stearylation at the N-terminus of CPPs with stearyl-octaarginine (R8), stearyl-(RxR)(4), and stearyl-TP10 prompts the formation of a self-assembled core-shell nanoparticle with NAPs, a compact structure that promotes cellular uptake. Researchers have designed modifications such as the addition of trifluoromethylquinoline moieties to lysine residues to destabilize endosomes, as exemplified by PepFect 6, and these changes further improve biological responsiveness. Alternatively, stearylation also allows implantation of CPPs onto the surface of liposomes. This feature facilitates "programmed packaging" to establish multifunctional envelope-type nanodevices (MEND). The R8-MEND showed high transfection efficiency comparable to that of adenovirus in non-dividing cells. Understanding the cellular uptake mechanisms of CPPs will further improve CPP-mediated NAP delivery. The cellular uptake of CPPs and their NAP complex involves various types of endocytosis. Macropinocytosis, a mechanism which is also activated in response to stimuli such as growth factors or viruses, is a primary pathway for arginine-rich CPPs because high cationic charge density promotes this endocytic pathway. The use of larger endosomes (known as macropinosomes) rather than clathrin- or caveolae-mediated endocytosis has been reported in macropinocytosis which would also facilitate the endocytosis of NAP nanoparticles into cells.

Synthesis and in vitro inhibition properties of oligonucleotide conjugates carrying amphipathic proline-rich peptide derivatives of the sweet arrow peptide (SAP)

In this study, a series of derivatives of the amphipathic proline-rich sweet arrow peptide (SAP) were covalently linked to antisense oligonucleotides designed to inhibit Renilla luciferase gene. Oligonucleotide-peptide conjugates carrying lysine (Lys) and ornithine (Orn) residues were prepared using the stepwise approach by assembling first the peptide sequence followed by the assembly of the DNA molecule. The resulting Lys, Orn-conjugates were transformed to the corresponding arginine and homoarginine oligonucleotide-peptide conjugates by reaction with O-methylisourea. The introduction of the SAP at 3'-termini of a phosphorothioate oligonucleotide did not affect the ability to inhibit gene expression when transfected with lipofectamine. However, these conjugates were not able to enter cells without transfecting agent. Further studies using SAP as a transfection agent showed promising results for the conjugates carrying the Orn-SAP. All conjugates showed high duplex stabilities.

Structural rearrangements and chemical modifications in known cell penetrating peptide strongly enhance DNA delivery efficiency

Amphipathic peptides with unusual cellular translocation properties have been used as carriers of different biomolecules. However, the parameters which control the delivery efficiency of a particular cargo by a peptide and the selectivity of cargo delivery are not very well understood. In this work, we have used the known cell penetrating peptide pVEC (derived from VE-cadherin) and systematically changed its amphipathicity (from primary to secondary) as well as the total charge and studied whether these changes influence the plasmid DNA condensation ability, cellular uptake of the peptide-DNA complexes and in turn the efficiency of DNA delivery of the peptide. Our results show that although the efficiency of DNA delivery of pVEC is poor, modification of the same peptide to create a combination of nine arginines along with secondary amphipathicity improves its plasmid DNA delivery efficiency, particularly in presence of an endosomotropic agent like chloroquine. In addition, presence of histidines along with 9 arginines and secondary amphipathicity shows efficient DNA delivery with low toxicity even in absence of chloroquine in multiple cell lines. We attribute these enhancements in transfection efficiency to the differences in the mechanism of complex formation by the different variants of the parent peptide which in turn are related to the chemical nature of the peptide itself. These results exhibit the importance of understanding the physicochemical parameters of the carrier and complex in modulating gene delivery efficiency. Such studies can be helpful in improving peptide design for delivery of different cargo molecules.