Antigene, ribozyme and aptamer nucleic acid drugs: progress and prospects

Rapid Detection of Helicobacter pylori by the Naked Eye Using DNA Aptamers

Helicobacter pylori was first isolated from gastritis patients by Barry J. Marshall and J. Robin Warren in 1982, and more than 90% of duodenal ulcers and about 80% of gastric ulcers are caused by H. pylori infection. Most detection methods require sophisticated instruments and professional operators, making detection slow and expensive. Therefore, it is critical to develop a simple, fast, highly specific, and practical strategy for the detection of H. pylori. In this study, we used H. pylori as a target to select unique aptamers that can be used for the detection of H. pylori. In our study, we used random ssDNA as an initial library to screen nucleic acid aptamers for H. pylori. We used binding rate and the fluorescence intensity to identify candidate aptamers. One DNA aptamer, named HPA-2, was discovered through six rounds of positive selection and three rounds of negative selection, and it had the highest affinity constant of all aptamers tested (K _d = 19.3 ± 3.2 nM). This aptamer could be used to detect H. pylori and showed no specificity for other bacteria. Moreover, we developed a new sensor to detect H. pylori with the naked eye for 5 min using illumination from a hand-held flashlight. Our study provides a framework for the development of other aptamer-based methods for the rapid detection of pathogenic bacteria.

Recent advances in the development of gene delivery systems

Background

Gene delivery systems are essentially necessary for the gene therapy of human genetic diseases. Gene therapy is the unique way that is able to use the adjustable gene to cure any disease. The gene therapy is one of promising therapies for a number of diseases such as inherited disorders, viral infection and cancers. The useful results of gene delivery systems depend open the adjustable targeting gene delivery systems. Some of successful gene delivery systems have recently reported for the practical application of gene therapy.

Main body

The recent developments of viral gene delivery systems and non-viral gene delivery systems for gene therapy have briefly reviewed. The viral gene delivery systems have discussed for the viral vectors based on DNA, RNA and oncolytic viral vectors. The non-viral gene delivery systems have also treated for the physicochemical approaches such as physical methods and chemical methods. Several kinds of successful gene delivery systems have briefly discussed on the bases of the gene delivery systems such as cationic polymers, poly(L-lysine), polysaccharides, and poly(ethylenimine)s.

Conclusion

The goal of the research for gene delivery system is to develop the clinically relevant vectors such as viral and non-viral vectors that use to combat elusive diseases such as AIDS, cancer, Alzheimer, etc. Next step research will focus on advancing DNA and RNA molecular technologies to become the standard treatment options in the clinical area of biomedical application.

Portion mismatch in duplex oligonucleotides as inhibitors of bacterial topoisomerase I

The activities of bacterial topoisomerase I can be modulated by non-perfect match duplex oligonucleotides.

A Tandem Oligonucleotide Approach for SNP-Selective RNA Degradation Using Modified Antisense Oligonucleotides

Antisense oligonucleotides have been studied for many years as a tool for gene silencing. One of the most difficult cases of selective RNA silencing involves the alleles of single nucleotide polymorphisms, in which the allele sequence is differentiated by a single nucleotide. A new approach to improve the performance of allele selectivity for antisense oligonucleotides is proposed. It is based on the simultaneous application of two oligonucleotides. One is complementary to the mutated form of the targeted RNA and is able to activate RNase H to cleave the RNA. The other oligonucleotide, which is complementary to the wild type allele of the targeted RNA, is able to inhibit RNase H cleavage. Five types of SNPs, C/G, G/C, G/A, A/G, and C/U, were analyzed within the sequence context of genes associated with neurodegenerative disorders such as Alzheimer’s disease, Parkinson’s disease, ALS (Amyotrophic Lateral Sclerosis), and Machado-Joseph disease. For most analyzed cases, the application of the tandem approach increased allele-selective RNA degradation 1.5–15 fold relative to the use of a single antisense oligonucleotide. The presented study proves that differentiation between single substitution is highly dependent on the nature of the SNP and surrounding nucleotides. These variables are crucial for determining the proper length of the inhibitor antisense oligonucleotide. In the tandem approach, the comparison of thermodynamic stability of the favorable duplexes WT RNA-inhibitor and Mut RNA-gapmer with the other possible duplexes allows for the evaluation of chances for the allele-selective degradation of RNA. A larger difference in thermodynamic stability between favorable duplexes and those that could possibly form, usually results in the better allele selectivity of RNA degradation.

Diseases originate and terminate by genes: unraveling nonviral gene delivery

The world is driving in to the era of transformation of chemical therapeutic molecules to biological genetic material therapeutics, and that is where the biological drugs especially "genes" come into existence. These genes worked as "magical bullets" to specifically silence faulty genes responsible for progression of diseases. Viral gene delivery research is far ahead of nonviral gene delivery technique. However, with more advancement in polymer science, new ways are opening for better and efficient nonviral gene delivery. But efficient delivery method is always considered as a bottleneck for gene delivery as success of which will decide the fate of gene in cells. During the past decade, it became evident that extracellular as well as intracellular barriers compromise the transfection efficiency of nonviral vectors. The challenge for gene therapy research is to pinpoint the rate-limiting steps in this complex process and implement strategies to overcome the biological physiochemical and metabolic barriers encountered during targeting. The synergy between studies that investigate the mechanism of breaking in and breaking out of nonviral gene delivery carrier through various extracellular and intracellular barriers with desired characteristics will enable the rational design of vehicles and revolutionize the treatment of various diseases.

Cell-specific RNA aptamer against human CCR5 specifically targets HIV-1 susceptible cells and inhibits HIV-1 infectivity

The C-C chemokine receptor type 5 (CCR5) is a receptor expressed by T cells and macrophages that serves as a coreceptor for macrophage-tropic HIV-1. Loss of CCR5 is associated with resistance to HIV-1. Here, we combine the live-cell-based SELEX with high-throughput sequencing technology to generate CCR5 RNA aptamers capable of specifically targeting HIV-1 susceptible cells (as small interfering RNA [siRNA] delivery agent) and inhibiting HIV-1 infectivity (as antiviral agent) via block of the CCR5 required for HIV-1 to enter cells. One of the best candidates, G-3, efficiently bound and was internalized into human CCR5-expressing cells. The G-3 specifically neutralized R5 virus infection in primary peripheral blood mononuclear cells, and in vivo generated human CD4(+) T cells with a nanomolar inhibitory concentration 50%. G-3 was also capable of transferring functional siRNAs to CCR5-expressing cells. Collectively, the cell-specific, internalizing, CCR5-targeted aptamers and aptamer-siRNA conjugates offer promise for overcoming some of the current challenges of drug resistance in HIV-1 by providing cell-type- or tissue-specific delivery of various therapeutic moieties.

Layered polymeric capsules inhibiting the activity of RNases for intracellular delivery of messenger RNA

Delivery of luciferase messenger RNA to HEK293T cells is successfully performed by polymer multilayer microcapsules co-encapsulating RNase inhibitors.

Versatile synthesis of amino acid functionalized nucleosides via a domino carboxamidation reaction

Functionalized oligonucleotides have recently gained increased attention for incorporation in modified nucleic acid structures both for the design of aptamers with enhanced binding properties as well as the construction of catalytic DNA and RNA. As a shortcut alternative to the incorporation of multiple modified residues, each bearing one extra functional group, we present here a straightforward method for direct linking of functionalized amino acids to the nucleoside base, thus equipping the nucleoside with two extra functionalities at once. As a proof of principle, we have introduced three amino acids with functional groups frequently used as key-intermediates in DNA- and RNAzymes via an efficient and straightforward domino carboxamidation reaction.

Interplay of LNA and 2'-O-methyl RNA in the structure and thermodynamics of RNA hybrid systems: a molecular dynamics study using the revised AMBER force field and comparison with experimental results

When used in nucleic acid duplexes, locked nucleic acid (LNA) and 2'-O-methyl RNA residues enhance the duplex stabilities, and this makes it possible to create much better RNA aptamers to target specific molecules in cells. Thus, LNA and 2'-O-methyl RNA residues are finding increasingly widespread use in RNA-based therapeutics. Herein, we utilize molecular dynamics (MD) simulations and UV melting experiments to investigate the structural and thermodynamic properties of 13 nucleic acid duplexes, including full DNA, RNA, LNA, and 2'-O-methyl RNA duplexes as well as hybrid systems such as LNA:RNA, 2'-O-methyl RNA:RNA, LNA/2'-O-methyl RNA:RNA, and RNA/2'-O-methyl RNA:RNA duplexes. The MD simulations are based on a version of the Amber force field revised specifically for RNA and LNA residues. Our results indicate that LNA and 2'-O-methyl RNA residues have two different hybridization mechanisms when included in hybrid duplexes with RNA wherein the former underwinds while the latter overwinds the duplexes. These computational predictions are supported by X-ray structures of LNA and 2'-O-methyl RNA duplexes that were recently presented by different groups, and there is also good agreement with the measured thermal stabilities of the duplexes. We find out that the "underwinding" phenomenon seen in LNA and LNA:RNA hybrid duplexes happens due to expansion of the major groove widths (Mgw) of the duplexes that is associated with decrease in the slide and twist values in base-pair steps. In contrast, 2'-O-methyl RNA residues in RNA duplexes slightly overwind the duplexes while the backbone is forced to stay in C3'-endo. Moreover, base-pair stacking in the LNA and LNA:RNA hybrid systems is gradually reduced with the inclusion of LNA residues in the duplexes while no such effect is seen in the 2'-O-methyl RNA systems. Our results show how competition between base stacking and structural rigidity in these RNA hybrid systems influences structures and stabilities. Even though both LNA and 2'-O-methyl RNA residues have C3'-endo sugar puckering, structurally LNA residues have a frozen sugar backbone which provides entropic enhancement of stabilities while the 2'-O-methyl RNA residues are more flexible and maintain base stacking that is almost untouched compared to RNA. Thus, enhancement of the structural stabilities of RNA duplexes by 2'-O-methyl RNA modifications is smaller than for the corresponding LNA modifications. Indeed, our experimental measurements show that on average each 2'-O-methyl RNA and LNA substitution in a RNA duplex enhances duplex stability by 0.2 and 1.4 kcal/mol, respectively. Our computational binding free energy predictions are qualitatively in line with these results. The only exception is for the full 2'-O-methyl RNA duplex, which is overstabilized, implying that further force field revisions are needed. Collectively, the results presented in this paper explain the atomistic details of the structural and thermodynamic roles of LNA and 2'-O-methyl RNA residues in RNA hybrid duplexes, shedding light on the mechanism behind targeting endogenous micro RNA (miRNA) in order to regulate mRNA activity and inhibit gene expression in the cell.

Mannosylated chitosan nanoparticles for delivery of antisense oligonucleotides for macrophage targeting

The therapeutic potential of antisense oligonucleotides (ASODN) is primarily dependent upon its safe and efficient delivery to specific cells overcoming degradation and maximizing cellular uptake in vivo. The present study focuses on designing mannosylated low molecular weight (LMW) chitosan nanoconstructs for safe ODNs delivery by macrophage targeting. Mannose groups were coupled with LMW chitosan and characterized spectroscopically. Mannosylated chitosan ODN nanoparticles (MCHODN NPs) were formulated by self-assembled method using various N/P ratio (moles of amine groups of MCH to phosphate moieties of ODNs) and characterized for gel retardation assay, physicochemical characteristics, cytotoxicity and transfection efficiency, and antisense assay. Complete complexation of MCH/ODN was achieved at charge ratio of 1:1 and above. On increasing the N/P ratio of MCH/ODN, particle size of the NPs decreased whereas zeta potential (ZV) increased. MCHODN NPs displayed much higher transfection efficiency into Raw 264.7 cells (bears mannose receptors) than Hela cells and no significant toxicity was observed at all MCH concentrations. Antisense assay revealed that reduction in lipopolysaccharide (LPS) induced serum TNF-α is due to antisense activity of TJU-2755 ODN (sequence complementary to 3′-UTR of TNF-α). These results suggest that MCHODN NPs are acceptable choice to improve transfection efficiency in vitro and in vivo.

Silencing sexually transmitted infections: topical siRNA-based interventions for the prevention of HIV and HSV

The global impact of sexually transmitted infections (STIs) is significant. The sexual transmission of viruses such as herpes simplex virus type-2 (HSV-2) and the human immunodeficiency virus type-1 (HIV-1), has been especially difficult to control. To date, no effective vaccines have been developed to prevent the transmission of these STIs. Although antiretroviral drugs have been remarkably successful in treating the symptoms associated with these viral infections, the feasibility of their widespread use for prevention purposes may be more limited. Microbicides might provide an attractive alternative option to reduce their spread. In particular, topically applied small inhibitory RNAs (siRNAs) have been shown to not only block transmission of viral STIs to mucosal tissues both in vitro and in vivo, but also confer durable knockdown of target gene expression, thereby circumventing the need to apply a microbicide around the time of sexual encounter, when compliance is mostly difficult. Despite numerous clinical trials currently testing the efficacy of siRNA-based therapeutics, they have yet to be approved for use in the treatment of viral STIs. While several obstacles to their successful implementation in the clinic still exist, promising preclinical studies suggest that siRNAs are a viable modality for the future prevention and treatment of HSV and HIV.

Durable knockdown and protection from HIV transmission in humanized mice treated with gel-formulated CD4 aptamer-siRNA chimeras

The continued spread of HIV underscores the need to interrupt transmission. One attractive strategy, in the absence of an effective vaccine, is a topical microbicide, but the need for application around the time of sexual intercourse leads to poor patient compliance. Intravaginal (IVAG) application of CD4 aptamer-siRNA chimeras (CD4-AsiCs) targeting the HIV coreceptor CCR5, gag, and vif protected humanized mice from sexual transmission. In non-dividing cells and tissue, RNAi-mediated gene knockdown lasts for several weeks, providing an opportunity for infrequent dosing not temporally linked to sexual intercourse, when compliance is challenging. Here, we investigate the durability of gene knockdown and viral inhibition, protection afforded by CCR5 or HIV gene knockdown on their own, and effectiveness of CD4-AsiCs formulated in a gel in polarized human cervicovaginal explants and in humanized mice. CD4-AsiC-mediated gene knockdown persisted for several weeks. Cell-specific gene knockdown and protection were comparable in a hydroxyethylcellulose gel formulation. CD4-AsiCs against CCR5 or gag/vif performed as well as a cocktail in humanized mice. Transmission was completely blocked by CCR5 CD4-AsiCs applied 2 days before challenge. Significant, but incomplete, protection also occurred when exposure was delayed for 4 or 6 days. CD4-AsiCs targeting gag/vif provided some protection when administered only after exposure. These data suggest that CD4-AsiCs are a promising approach for developing an HIV microbicide.

Cellular uptake of covalent conjugates of oligonucleotide with membrane-modifying peptide, peptaibol

Using the membrane-modifying peptide, trichorovin-XIIa (TV-XIIa), which is an 11-residual peptaibol isolated from the fungus Trichoderma viride, we synthesized covalent conjugates of 20-mer oligonucleotide with TV-XIIa to examine the potential use of TV-XIIa in cellular delivery. The results indicated that the conjugates were progressively taken up by human lung carcinoma A549 cells. Next, the antisense effects of the conjugates on p53 protein expression were examined. The p53 expression was significantly decreased by ca. 20-50% in the presence of the conjugates upon treatment with the transfection solution at the concentration of 5 μM.

Intrinsic curvature in duplex DNA inhibits Human Topoisomerase I

Human Topoisomerase I (hTopo I) have been known as a potential target for cancer therapy. A series of duplex DNA with different intrinsic curvatures have been designed as inhibitors to hTopo I. The activities of hTopo I on relaxing supercoiled plasmid pUC 19 are apparently diminished in the presence of the curved DNA. More potent inhibitions and smaller IC(50) are achieved by duplex DNA with higher curvatures. EMSA indicates that hTopo I can recognize the curved DNA through binding interactions. Our studies demonstrate that the activity of hTopo I can be modulated by the intrinsic curvature of linear DNA and provide a new avenue to design curved DNA as hTopo I inhibitors with high therapeutic efficiency and low toxicity.

Smart siRNA delivery systems based on polymeric nanoassemblies and nanoparticles

RNA interference is a post-transcriptional gene-silencing pathway induced by double-stranded small interfering RNA (siRNA). The potential use of siRNA as a therapeutic agent has attracted great attention as a novel approach to the treatment of several intractable diseases. Despite the rapid progress in the therapeutic use of siRNA, systemic application is still controversial due to the limitations of siRNA, such as low enzymatic tolerability, cellular internalization and body distribution after systemic administration. This review describes the recent progress and strategies of siRNA delivery systems based on polyion complexes. Numerous siRNA-containing polyion complex systems bound together through electrostatic interactions between the negatively charged siRNA and positively charged components, including synthetic polymers, biopolymers and nanoparticles, have been developed for the therapeutic application of siRNA. Additionally, stimulus-sensitive smart siRNA carrier systems, including bioreducible polycations and hydrophilic polymer-siRNA conjugates, have been developed to enhance the gene-silencing efficacy of siRNAs.

DNA as therapeutics; an update

Human gene therapy is the introduction of new genetic material into the cells of an individual with the intention of producing a therapeutic benefit for the patient. Deoxyribonucleic acid and ribonucleic acid are used in gene therapy. Over time and with proper oversight, human gene therapy might become an effective weapon in modern medicine's arsenal to help fight diseases such as cancer, acquired immunodeficiency syndrome, diabetes, high blood pressure, coronary heart disease, peripheral vascular disease, neurodegenerative diseases, cystic fibrosis, hemophilia and other genetic disorders. Gene therapy trials in humans are of two types, somatic and germ line gene therapy. There are many ethical, social, and commercial issues raised by the prospects of treating patients whose consent is impossible to obtain. This review summarizes deoxyribonucleic acid-based therapeutics and gene transfer technologies for the diseases that are known to be genetic in origin. Deoxyribonucleic acid-based therapeutics includes plasmids, oligonucleotides for antisense and antigene applications, deoxyribonucleic acid aptamers and deoxyribonucleic acidzymes. This review also includes current status of gene therapy and recent developments in gene therapy research.

Aptamers influence the hemostatic system by activating the intrinsic coagulation pathway in an in vitro Chandler-Loop model

One class of oligonucleotides with a high potential for use in medical applications is short nucleic acids, widely known as aptamers. Although several aptamers are already being used clinically, there are very few studies dealing with the impact aptamers have on the hemostatic system. In this study, we have performed a comprehensive evaluation of the hemostatic system including coagulation, platelets, complement, and inflammatory activation by using different aptamer concentrations and fresh human whole blood in a well-established flow model. We found that single-stranded aptamers did not have a negative influence on platelets, complement, or inflammation but were able to activate factor XII, kallikrein, and prothrombin in a concentration-dependent manner. Consequently, the influence of aptamers on the coagulation system should be taken into consideration before the use of any aptamer-based drugs in patients.

Nick-containing oligonucleotides as human topoisomerase I inhibitors

A series of oligonucleotides with various lengths that contain nick and topoisomerase I-binding sites were designed. The interactions between these oligonucleotides and human topoisomerase I were investigated and the most efficient one among them has displayed IC(50) value of 6.3 nM. Our studies have also demonstrated that the position of the nick as well as the length of the oligonucleotides were crucial factors for the inhibition of this nuclear enzyme.

A Review of Scanning Probe Microscopy Investigations of Liposome-DNA Complexes

Liposome-DNA complexes are one of the most promising systems for the protection and delivery of nucleic acids to combat neoplastic, viral, and genetic diseases. In addition, they are being used as models in the elucidation of many biological phenomena such as viral infection and transduction. In order to understand these phenomena and to realize the mechanism of nucleic acid transfer by liposome-DNA complexes, studies at the molecular level are required. To this end, scanning probe microscopy (SPM) is increasingly being used in the characterization of lipid layers, lipid aggregates, liposomes, and their complexes with nucleic acid molecules. The most attractive attributes of SPM are the potential to image samples with subnanometer spatial resolution under physiological conditions and provide information on their physical and mechanical properties. This review describes the application of scanning tunneling microscopy and atomic force microscopy, the two most commonly applied SPM techniques, in the characterisation of liposome-DNA complexes.

The role of high-resolution imaging in the evaluation of nanosystems for bioactive encapsulation and targeted nanotherapy

Nanotechnology has already started to significantly impact many industries and scientific fields including biotechnology, pharmaceutics, food technology and semiconductors. Nanotechnology-based tools and devices, including high-resolution imaging techniques, enable characterization and manipulation of materials at the nanolevel and further elucidate nanoscale phenomena and equip us with the ability to fabricate novel materials and structures. One of the most promising impacts of nanotechnology is in the area of nanotherapy. Employing nanosystems such as dendrimers, nanoliposomes, niosomes, nanotubes, emulsions and quantum dots, nanotherapy leads toward the concept of personalized medicine and the potential for early diagnoses coupled with efficient targeted therapy. The development of smart targeted nanocarriers that can deliver bioactives at a controlled rate directly to the designated cells and tissues will provide better efficacy and reduced side effects. Nanocarriers improve the solubility of bioactives and allow for the delivery of not only small-molecule drugs but also the delivery of nucleic acids and proteins. This review will focus on nanoscale bioactive delivery and targeting mechanisms and the role of high-resolution imaging techniques in the evaluation and development of nanocarriers.

Architecturally Induced Multiresponsive Vesicles from Well-Defined Polypeptides. Formation of Gene Vehicles

A series of novel, partially labeled amphiphilic triblock copolypeptides, PLL-b-PBLG-d7-b-PLL, has been synthesized, where PLL and PBLG-d7 are poly(L-lysine hydrochloride) and poly(gamma-benzyl-d7-L-glutamate), respectively. The synthetic approach involved the sequential ring-opening polymerization (ROP) of gamma-benzyl-L-glutamate and epsilon-Boc-L-lysine N-carboxy anhydrides by a diamino initiator using high-vacuum techniques, followed by the selective deprotection of the Boc groups. Combined characterization results showed that the copolypeptides exhibit high degrees of molecular and compositional homogeneity. The synthesized copolypeptides had similar molecular weights, while the composition of the middle block ranged between 19 and 74% with respect to the monomeric units. Due to the macromolecular architecture of the copolypeptide and the rigid nature of the middle block, the formation of monolayers was favored, and, surprisingly, vesicles were formed in water at neutral pH over the entire compositional range. The vesicular structures were extensively characterized by static and dynamic light scattering, small-angle neutron scattering, atomic force microscopy, cryo-transmission electron microscopy, scanning electron microscopy, UV and Fourier transform infrared spectroscopy, and circular dichroism. In contrast to other vesicular structures derived from conventional polymers, the formed polypeptidic vesicles possess the unique feature of being stimuli-responsive to pH and temperature. When the copolypeptides were mixed with plasmid DNA (pDNA), large vesicular structures were also formed. The molecular characterization of the vectors was performed with most of the methods mentioned above, and indicated that the pDNA is both partially condensed on the PLL phase and partially encapsulated inside the vesicle. Consequently, the synthesized vectors combine the advantages of the polylysine-DNA systems to condense large amounts of genes, as well as those of the liposome-DNA systems to better protect the encapsulated DNA. These vectors are expected to present better gene transfection efficiency to the cell nucleus.

Dumbbell-shaped circular oligonucleotides as inhibitors of human topoisomerase I

A dumbbell-shaped circular oligonucleotide containing topoisomerase I-binding sites and two mismatched base pairs in its sequence has been designed and synthesized. Our further studies demonstrate that this particularly designed oligonucleotide displays an IC(50) value of 9 nM in its inhibition on the activity of human topoisomerase I, a magnitude smaller than that of camptothecin, an anticancer drug currently in clinical use.

A Functionalized 20-Residue Peptaibol Derivative for Nucleic Acid Delivery

Based on the membrane-modifying peptaibol trichocellin-A-I (1) from Trichoderma viride, we designed a vehicle for the cellular delivery of antisense oligodeoxynucleotides by attaching a (Lys)10 stretch to the C-terminus of 1. The resulting transporter peptide 2, prepared by solid-phase synthesis using Fmoc protocol in combination with amino acid fluorides, was found to be mainly alpha-helical in solution, in contrast to its precursors 1 and 3. The uptake of the complex formed between carrier 2 and a fluorescence-tagged oligonucleotide, i.e., 4, was studied at different charge ratios by confocal laser-scanning microscopy, using two different eukaryotic cell lines: mouse embryonal fibroblast (NIH3T3) and human lung carcinoma (A549) cells. Peptide 2 readily translocated 4 into the cytoplasms of NIH3T3 cells. However, the peptide/oligonucleotide complex was accumulated around the plasma membrane of the A549 cells.

Physicochemical investigation of a lipid with a new core structure for gene transfection: 2-amino-3-hexadecyloxy-2-(hexadecyloxymethyl)propan-1-ol

Cationic liposomes/DNA complexes can be used as nonviral vectors for direct delivery of DNA-based biopharmaceuticals to damaged cells and tissues. In order to obtain more effective and safer liposome-based gene transfection systems, the new cationic lipid 2-amino-3-hexadecyloxy-2-(hexadecyloxymethyl)propan-1-ol (AHHP) was synthesized. In this paper we report on the synthesis of AHHP and investigations of its physical-chemical properties. Langmuir monolayers of AHHP were studied at the air/buffer interface by film balance measurements, grazing incidence X-ray diffraction (GIXD), and infrared reflection absorption spectroscopy (IRRAS). Structure and thermotropic phase behavior of AHHP in aqueous dispersion were examined by small-angle and wide-angle X-ray scattering (SAXS/WAXS) and differential scanning calorimetry (DSC). The results show clear differences in structure and phase behavior of AHHP, both in the monolayer system and in aqueous dispersions, in dependence on the subphase pH due to protonation or deprotonation of the primary amine in the lipid head group. Thermodynamic data derived from pi-A isotherms provide information about the critical temperature (Tc), which is in rough agreement with the temperature of the lipid phase transition from gel to fluid state (Tm) found by X-ray and calorimetry studies of AHHP aqueous dispersions. The packing properties of the molecules in mono- and bilayer systems are very similar. DNA couples to the monolayer of the new lipid at low as well as at high pH but in different amounts. The DNA coupling leads to an alignment of adsorbed DNA strands indicated by the appearance of a Bragg peak. The distance between aligned DNA strands does not change much with increasing monolayer pressure.

RiboaptDB: a comprehensive database of ribozymes and aptamers

BACKGROUND

Catalytic RNA molecules are called ribozymes. The aptamers are DNA or RNA molecules that have been selected from vast populations of random sequences, through a combinatorial approach known as SELEX. The selected oligo-nucleotide sequences (~200 bp in length) have the ability to recognize broad range of specific ligands by forming binding pockets. These novel aptamer sequences can bind to nucleic acids, proteins or small organic and inorganic chemical compounds and have many potential uses in medicine and technology.

RESULTS

The comprehensive sequence information on aptamers and ribozymes that have been generated by in vitro selection methods are included in this RiboaptDB database. Such types of unnatural data generated by in vitro methods are not available in the public 'natural' sequence databases such as GenBank and EMBL. The amount of sequence data generated by in vitro selection experiments has been accumulating exponentially. There are 370 artificial ribozyme sequences and 3842 aptamer sequences in the total 4212 sequences from 423 citations in this RiboaptDB. We included general search feature, and individual feature wise search, user submission form for new data through online and also local BLAST search.

CONCLUSION

This database, besides serving as a storehouse of sequences that may have diagnostic or therapeutic utility in medicine, provides valuable information for computational and theoretical biologists. The RiboaptDB is extremely useful for garnering information about in vitro selection experiments as a whole and for better understanding the distribution of functional nucleic acids in sequence space. The database is updated regularly and is publicly available at http://mfgn.usm.edu/ebl/riboapt/.

Receptor-mediated hepatic uptake of M6P-BSA-conjugated triplex-forming oligonucleotides in rats

Excessive production of extracellular matrix, predominantly type I collagen, results in liver fibrosis. Earlier we synthesized mannose 6-phosphate-bovine serum albumin (M6P-BSA) and conjugated to the type I collagen specific triplex-forming oligonucleotide (TFO) for its enhanced delivery to hepatic stellate cells (HSCs), which is the principal liver fibrogenic cell. In this report, we demonstrate a time-dependent cellular uptake of M6P-BSA-33P-TFO by HSC-T6 cells. Both cellular uptake and nuclear deposition of M6P-BSA-33P-TFO were significantly higher than those of 33P-TFO, leading to enhanced inhibition of type I collagen transcription. Following systemic administration into rats, hepatic accumulation of M6P-BSA-33P-TFO increased from 55% to 68% with the number of M6P per BSA from 14 to 27. Unlike 33P-TFO, there was no significant decrease in the hepatic uptake of (M6P)20-BSA-33P-TFO in fibrotic rats. Prior administration of excess M6P-BSA decreased the hepatic uptake of (M6P)20-BSA-33P-TFO from 66% to 40% in normal rats, and from 60% to 15% in fibrotic rats, suggesting M6P/insulin-like growth factor II (M6P/IGF II) receptor-mediated endocytosis of M6P-BSA-33P-TFO by HSCs. Almost 82% of the total liver uptake in fibrotic rats was contributed by HSCs. In conclusion, by conjugation with M6P-BSA, the TFO could be potentially used for the treatment of liver fibrosis.

The chemical nature of the 2'-substituent in the pentose-sugar dictates the pseudoaromatic character of the nucleobase (pKa) in DNA/RNA

We here show that the pKa (error limit: 0.01 to 0.03 pKa unit) of a nucleobase in a nucleotide can be modulated by the chemical nature of the 2'-substituent at the sugar moiety. This has been evidenced by the measurement of nucleobase pKa in 47 different model nucleoside 3',5'-bis- and 3'-mono-ethylphosphates. The fact that the electronic character of each of the 2'-substituents (Fig. 1) alters the chemical shift of the H2' sugar proton, and also alters the pKa of the nucleobase in the nucleotides has been evidenced by a correlation plot of pKa of N3 of pyrimidine (T/C/U) or pKa of N7 of 9-guaninyl with the corresponding deltaH2' chemical shifts at the neutral pH, which shows linear correlation with high Pearson's correlation coefficients (R = 0.85-0.97). That this modulation of the pKa of the nucleobase by a 2'-substituent is a through-bond as well as through-space effect has been proven by ab initio determined pKa estimation. Interestingly, experimental pKas of nucleobases from NMR titration and the calculated pKas (by ab initio calculations utilizing closed shell HF 6-31G** basis set) are linearly correlated with R = 0.98. It has also been observed that the difference of ground and protonated/de-protonated HOMO orbital energies (DeltaHOMO, a.u.) for the nucleobases (A/G/C/T/U) are well correlated with their pK(a)s in different 2'-substituted 3',5'-bis-ethylphosphate analogs suggesting that only the orbital energy of HOMO can be successfully used to predict the modulation of the chemical reactivity of the nucleobase by the 2'-substituent. It has also been demonstrated that pKa values of nucleobases in 3',5'-bis-ethylphosphates (Table 1) are well correlated with the change in dipole moment for the respective nucleobases after protonation or de-protonation. This work thus unambiguously shows that alteration of the thermodynamic stability (Tm) of the donor-acceptor complexes [ref. 20], as found with various 2'-modified duplexes in the antisense, siRNA or in triplexes by many workers in the field, is a result of alteration of the pseudoaromatic character of the nucleobases engineered by alteration of the chemical nature of the 2'-substitution.

2'-deoxy-2'-fluoro-beta-D-arabinonucleic acid (2'F-ANA) modified oligonucleotides (ON) effect highly efficient, and persistent, gene silencing

To be effective in vivo, antisense oligonucleotides (AS ON) should be nuclease resistant, form stable ON/RNA duplexes and support ribonuclease H mediated heteroduplex cleavage, all with negligible non-specific effects on cell function. We report herein that AS ONs containing a 2′-deoxy-2′-fluoro-β-d-arabinonucleic acid (2′F-ANA) sugar modification not only meet these criteria, but have the added advantage of maintaining high intracellular concentrations for prolonged periods of time which appears to promote longer term gene silencing. To demonstrate this, we targeted the c-MYB protooncogene's mRNA in human leukemia cells with fully phosphorothioated 2′F-ANA–DNA chimeras (PS-2′FANA–DNA) and compared their gene silencing efficiency with AS ON containing unmodified nucleosides (PS-DNA). When delivered by nucleofection, chemically modified ON of both types effected a >90% knockdown of c-MYB mRNA and protein expression, but the PS-2′F-ANA–DNA were able to accomplish this at 20% of the dose of the PS-DNA, and in contrast to the PS-AS DNA, their silencing effect was still present after 4 days after a single administration. Therefore, our data demonstrate that PS-2′F-ANA–DNA chimeras are efficient gene silencing molecules, and suggest that they could have significant therapeutic potential.

DNA-based therapeutics and DNA delivery systems: a comprehensive review

The past several years have witnessed the evolution of gene medicine from an experimental technology into a viable strategy for developing therapeutics for a wide range of human disorders. Numerous prototype DNA-based biopharmaceuticals can now control disease progression by induction and/or inhibition of genes. These potent therapeutics include plasmids containing transgenes, oligonucleotides, aptamers, ribozymes, DNAzymes, and small interfering RNAs. Although only 2 DNA-based pharmaceuticals (an antisense oligonucleotide formulation, Vitravene, (USA, 1998), and an adenoviral gene therapy treatment, Gendicine (China, 2003), have received approval from regulatory agencies; numerous candidates are in advanced stages of human clinical trials. Selection of drugs on the basis of DNA sequence and structure has a reduced potential for toxicity, should result in fewer side effects, and therefore should eventually yield safer drugs than those currently available. These predictions are based on the high selectivity and specificity of such molecules for recognition of their molecular targets. However, poor cellular uptake and rapid in vivo degradation of DNA-based therapeutics necessitate the use of delivery systems to facilitate cellular internalization and preserve their activity. This review discusses the basis of structural design, mode of action, and applications of DNA-based therapeutics. The mechanisms of cellular uptake and intracellular trafficking of DNA-based therapeutics are examined, and the constraints these transport processes impose on the choice of delivery systems are summarized. Finally, the development of some of the most promising currently available DNA delivery platforms is discussed, and the merits and drawbacks of each approach are evaluated.

Condensation of oligonucleotides assembled into nicked and gapped duplexes: potential structures for oligonucleotide delivery

The condensation of nucleic acids into well-defined particles is an integral part of several approaches to artificial cellular delivery. Improvements in the efficiency of nucleic acid delivery in vivo are important for the development of DNA- and RNA-based therapeutics. Presently, most efforts to improve the condensation and delivery of nucleic acids have focused on the synthesis of novel condensing agents. However, short oligonucleotides are not as easy to condense into well-defined particles as gene-length DNA polymers and present particular challenges for discrete particle formation. We describe a novel strategy for improving the condensation and packaging of oligonucleotides that is based on the self-organization of half-sliding complementary oligonucleotides into long duplexes (ca. 2 kb). These non-covalent assemblies possess single-stranded nicks or single-stranded gaps at regular intervals along the duplex backbones. The condensation behavior of nicked- and gapped-DNA duplexes was investigated using several cationic condensing agents. Transmission electron microscopy and light-scattering studies reveal that these DNA duplexes condense much more readily than short duplex oligonucleotides (i.e. 21 bp), and more easily than a 3 kb plasmid DNA. The polymeric condensing agents, poly-l-lysine and polyethylenimine, form condensates with nicked- and gapped-DNA that are significantly smaller than condensates formed by the 3 kb plasmid DNA. These results demonstrate the ability for DNA structure and topology to alter nucleic acid condensation and suggest the potential for the use of this form of DNA in the design of vectors for oligonucleotide and gene delivery. The results presented here also provide new insights into the role of DNA flexibility in condensate formation.

Amperometric method for determining the degree of complexation of polyelectrolytes with cationic surfactants

The complexation of sodium polystyrene sulfonate with monovalent cationic surfactants at a microsized liquid/liquid interface has been studied using electrochemistry. The method is based on measurement of surfactant ion transfer across the interface between two immiscible electrolyte solutions (ITIES). The complexation of various cationic surfactants (alkylpyridinium- and trimethylammonium-) with oligosized polystyrene sulfonate was measured. Binding isotherms were used to determine the degree of binding as a function of the surfactant chain length and type of head group. It was found that the hydrophobicity of the surfactant was the predominant factor. The effect of the polyelectrolyte chain length on the binding mechanism was studied using cetylpyridinium chloride as a complexing agent. It was found that binding affinity, as well as cooperativity of the binding process, decreases with decreasing polyelectrolyte chain length. Thermodynamics of surfactant binding was measured using titration microcalorimetry. The thermodynamic data obtained show that the enthalpy of surfactant binding is not dependent on polymer chain length, but an increase in chain length makes the binding process entropically more favorable.

In vitro thymidine kinase/ganciclovir-based suicide gene therapy using replication defective herpes simplex virus-1 against leukemic B-cell malignancies (MCL, HCL, B-CLL)

A replication defective herpes simplex virus-1 was evaluated as a therapeutic vector. Mantle cell lymphoma (MCL), hairy cell leukemia (HCL), and B-cell chronic lymphocytic leukemia (B-CLL) were chosen because leukemic cells were collectable from peripheral bloods in these diseases. Cells from six MCL, one HCL, and nine B-CLL were infected in vitro with T0Z.1 at 3 multiplicity of infection (MOI). Herpes simplex virus thymidine kinase (HSV-TK)/ganciclovir (GCV)-mediated suicide gene therapy showed 14.7% of mean tumor killing against leukemic B-cell malignancies. The mean tumor-killing effects were 8.7 and 17.1% in MCL and B-CLL, respectively. The effect against HCL was 29%. The study indicates that herpes simplex virus (HSV)-based gene therapy might be an effective strategy.

Innovations in oligonucleotide drug delivery

Oligonucleotides (ONs) are a new class of therapeutic compounds under investigation for the treatment of a variety of disease states, such as cancer and HIV, and for FDA approval of an anti-CMV retinitis antisense molecule (Vitravene trade mark, Isis Pharmaceuticals). However, these molecules are limited not only by poor cellular uptake, but also by a general lack of understanding regarding the mechanism(s) of ON cellular uptake. As a result, various delivery vehicles have been developed that circumvent the proposed mechanism of uptake, endocytosis, while improving target specific delivery and/or drug stability. This review describes various traditional and novel delivery mechanisms that have been employed to improve ON cellular delivery, cost effectiveness, and therapeutic efficacy.

Synthesis and hybridization studies of a 5-aminopentanoic acid nucleobase (APN) dimer

We have prepared a 5-aminopentanoic acid nucleobase (APN) dimer and investigated its hybridization capabilities to complementary DNA using both UV melting and NMR techniques.

Conformation and ion-binding of oligonucleotides

The effective charge and the conformation of oligonucleotides may influence their pharmaceutical properties. Therefore, a method based on the convective diffusion process was used to measure both the diffusion coefficient and the effective charge number of four oligonucleotides with different chain lengths. Determinations were carried out at physiological ionic strength and at two temperatures, 20 and 40 degrees C. The results indicate that the longer oligonucleotides, i.e. number of nucleotides in the molecule from 15 to 30, are strongly ion-paired (75-80%) and the shorter oligonucleotide (seven nucleotides) is only ca. 50% ion-paired. The extent of ion-binding was not dependent on temperature. The conformation of the oligonucleotides appeared to be fairly compact in 0.15 M NaCl solution. The compact conformation and strong ion-pairing may influence the pharmacokinetics of oligonucleotides, possibly facilitating distribution into tissues.

Structure-Function Analysis of RNAs Generated by In Vivo and In Vitro Selection

Today, the concept of Darwinian evolution plays a significant role in studying structure-function relationships concerning known molecules and in helping to design previously unknown molecules with desired functionalities. Results from

Trends and developments in liposome drug delivery systems

Since the discovery of liposomes or lipid vesicles derived from self-forming enclosed lipid bilayers upon hydration, liposome drug delivery systems have played a significant role in formulation of potent drugs to improve therapeutics. Currently, most of these liposome formulations are designed to reduce toxicity and to some extent increase accumulation at the target site(s) in a number of clinical applications. The current pharmaceutical preparations of liposome-based therapeutics stem from our understanding of lipid-drug interactions and liposome disposition mechanisms including the inhibition of rapid clearance of liposomes by controlling size, charge, and surface hydration. The insight gained from clinical use of liposome drug delivery systems can now be integrated to design liposomes targeted to tissues and cells with or without expression of target recognition molecules on liposome membranes. Enhanced safety and heightened efficacy have been achieved for a wide range of drug classes, including antitumor agents, antivirals, antifungals, antimicrobials, vaccines, and gene therapeutics. Additional refinements of biomembrane sensors and liposome delivery systems that are effective in the presence of other membrane-bound proteins in vivo may permit selective delivery of therapeutic compounds to selected intracellular target areas.

Bile acid-oligodeoxynucleotide conjugates: synthesis and liver excretion in rats

The synthesis of bile acid oligodeoxynucleotide conjugates via the 3-OH group of the bile acids is described. When used in vivo in rats, covalent conjugation of an oligodeoxynucleotide via a linker to cholic acid resulted in an increased biliary excretion of bile acid-oligodeoxynucleotide conjugates compared to unconjugated oligodeoxynucleotides.

Downregulation of c-Ki-ras promoter activity by triplex-forming oligonucleotides endogenously generated in human 293 cells

Exogenous triplex-forming oligodeoxynucleotides (TFO) have the capacity to modulate in vivo the expression of individual genes. As the administration of TFO to cells is not without problems, we analyzed the possibility of generating them directly in the cell, using specific expression vectors. We constructed three vectors, mU6-GA, mU6-CA, and mU6-CT, that direct the synthesis in human 293 cells of 76-mer CU, GU, and AG motif TFO (rTFO) potentially capable of binding to a critical poly (R x Y) sequence contained in the promoter of the Ki-ras proto-oncogene. The ability of the CU, GU, and AG motif rTFO to interact with the double helix of the c-Ki-ras target was investigated in vitro by footprinting and band-shift experiments, using both synthetic and endogenously synthesized oligoribonucleotides. The human 293 cells were transfected with DNA mixtures containing a plasmid, which bears the reporter chloramphenicol acetyltransferase (CAT) gene downstream from the c-Ki-ras promoter (pKRS-413), as well as an rTFO-generating vector (mU6-GA, mU6-CA, or mU6-CT). As control, the cells were transfected with DNA mixtures containing vector mU6-C1 or mU6-C2. These generated transcripts unable to form triple helices with the poly (R x Y) sequence of the c-Ki-ras promoter. Intracellular synthesis of the 76-mer CU, GU, and AG rTFO by mU6-GA, mU6-CA, and mU6-CT was checked by Northern blot hybridization. Through beta-gal and CAT ELISA immunoassays, we found that the 293 cells transfected with either mU6-GA, mU6-CA, or mU6-CT showed a significant inhibition of CAT expression compared with cells transfected with control plasmids mU6-C1 or mU6-C2. The results of five separate transient transfection experiments showed that endogenous GU and AG rTFO, generated by mU6-CA and mU6-CT, produce, respectively, 40% (+/- 4% SE) and 47% (+/- 8% SE) CAT inhibition, whereas CU rTFO, generated by mU6-GA, produces 38% (+/- 7% SE) CAT inhibition. In conclusion, this study suggests that it is possible to downregulate the expression of an individual gene through the use of recombinant vectors encoding the information for the intracellular synthesis of short triplex-forming RNA strands.