Designing immunostimulatory double stranded messenger RNA with maintained translational activity through hybridization with poly A sequences for effective vaccination.

Messenger (m)RNA vaccines require a safe and potent immunostimulatory adjuvant. In this study, we introduced immunostimulatory properties directly into mRNA molecules by hybridizing them with complementary RNA to create highly immunogenic double stranded (ds)RNAs. These dsRNA formulations, comprised entirely of RNA, are expected to be safe and highly efficient due to antigen expression and immunostimulation occurring simultaneously in the same antigen presenting cells. In this strategy, design of dsRNA is important. Indeed, hybridization using full-length antisense (as)RNA drastically reduced translational efficiency. In contrast, by limiting the hybridized portion to the mRNA poly A region, efficient translation and intense immunostimulation was simultaneously obtained. The immune response to the poly U-hybridized mRNAs (mRNA:pU) was mediated through Toll-like receptor (TLR)-3 and retinoic acid-inducible gene (RIG)-I. We also demonstrated that mRNA:pU activation of mouse and human dendritic cells was significantly more effective than activation using single stranded mRNA. In vivo mouse immunization experiments using ovalbumin showed that mRNA:pU significantly enhanced the intensity of specific cellular and humoral immune responses, compared to single stranded mRNA. Our novel mRNA:pU formulation can be delivered using a variety of mRNA carriers depending on the purpose and delivery route, providing a versatile platform for improving mRNA vaccine efficiency.

Structural basis for the molecular recognition of polyadenosine RNA by Nab2 Zn fingers.

The yeast poly(A) RNA binding protein, Nab2, facilitates poly(A) tail length regulation together with targeting transcripts to nuclear pores and their export to the cytoplasm. Nab2 binds polyadenosine RNA primarily through a tandem repeat of CCCH Zn fingers. We report here the 2.15 Å resolution crystal structure of Zn fingers 3-5 of Chaetomium thermophilum Nab2 bound to polyadenosine RNA and establish the structural basis for the molecular recognition of adenosine ribonucleotides. Zn fingers 3 and 5 each bind two adenines, whereas finger 4 binds only one. In each case, the purine ring binds in a surface groove, where it stacks against an aromatic side chain, with specificity being provided by a novel pattern of H-bonds, most commonly between purine N6 and a Zn-coordinated cysteine supplemented by H-bonds between purine N7 and backbone amides. Residues critical for adenine binding are conserved between species and provide a code that allows prediction of finger-binding stoichiometry based on their sequence. Moreover, these results indicate that, in addition to poly(A) tails, Nab2 can also recognize sequence motifs elsewhere in transcripts in which adenosines are placed at key positions, consistent with its function in mRNP organization and compaction as well as poly(A) tail length regulation.

Isoquinoline alkaloids and their binding with polyadenylic acid: potential basis of therapeutic action.

After fifty years of DNA targeting through intercalators and groove binders and related studies now the current focus is in RNA targeting. Polyadenylic acid [poly(A)] tail of mRNA has been recently established as a potential drug target due to its significant role in the initiation of translation, maturation and stability of mRNA as well as in the production of alternate proteins in eukaryotic cells. Isoquinoline group of alkaloids have their importance in contemporary biomedical research and drug discovery programme due to extensive pharmacological and biological activity. Very recently some small molecule alkaloids of the isoquinoline group have been found to bind poly(A) with remarkably high affinity leading to self structure formation. The alkaloids have a high binding affinity towards single stranded poly(A) whereas their binding with double stranded poly(A) is weak. Among the alkaloids discussed here, berberine and coralyne are found to be capable to induce self-structure in poly(A). All the binding phenomena are characterized by electrostatic interaction between RNA and the alkaloids and the mode of binding revealed as full or partial intercalation. This review focuses on the structural and biological significance of poly(A) and the recent developments in the use of plant alkaloids and their synthetic analogs to control the structure and function of this RNA for the development of new alkaloid based molecules specifically targeted to poly(A) structures.

RNA specific molecules: cytotoxic plant alkaloid palmatine binds strongly to poly(A).

The cytotoxic plant alkaloid palmatine was found to bind strongly by partial intercalation to single stranded poly(A) structure with binding affinity (Ka) of (8.36+/-0.26) x 10(5) M(-1). The binding of palmatine was characterized to be exothermic and enthalpy driven with one palmatine for every two adenine residues. On the other hand, the binding to the double stranded poly(A) has been found to be significantly weak. This study identifies poly(A) as a potential bio-target for the alkaloid palmatine and its use as a lead compound in antitumor drug screening.

Functional coupling of cleavage and polyadenylation with transcription of mRNA.

Cleavage and polyadenylation define the 3' ends of almost all eukaryotic mRNAs and are thought to occur during transcription. We describe a human in vitro system utilizing an immobilized template, in which transcripts in RNA polymerase II elongation complexes are efficiently cleaved and polyadenylated. Because the cleavage rate of free RNA is much slower, we conclude that cleavage is functionally coupled to transcription. Inhibition of positive transcription elongation factor b (P-TEFb) had only a modest negative effect on cleavage, as long as transcripts were long enough to contain the polyadenylation signal. In contrast, removal of the carboxyl-terminal domain of the large subunit of RNA polymerase II had a dramatic negative effect on cleavage. Unexpectedly, the 5' portion of transcript after cleavage remained associated with the template in a functional, polyadenylation-competent complex. Efficient cleavage required 5' capping by the human capping enzyme, but the reduction of cleavage seen of transcripts in COOH-terminal domain-less polymerase elongation complexes, was not because of lack of capping.

Evi-1 expression in Xenopus.

The Evi-1 gene was first identified as a site for viral integration in murine myeloid leukemia. Evi-1 is a zinc finger transcription factor that has been implicated in the development of myeloid neoplasia. In humans, disruption of the Evi-1 locus, by chromosomal rearrangements, is associated with myeloid leukemia and myelodyplastic syndromes. Here, we report the cloning and developmental pattern of expression of Xenopus Evi-1. xEvi-1 is expressed during oogenesis and during embryonic development. In situ hydridization reveals that xEvi-1 has a dynamic expression profile during early embryonic development. Expression of Evi-1 is detected by in situ hybridization in the pronephric tissue, the brain and in neural crest derivatives of the head and neck.

Silica morphogenesis by alternative processing of silaffins in the diatom Thalassiosira pseudonana.

For almost 200 years scientists have been fascinated by the ornate cell walls of the diatoms. These structures are made of amorphous silica, exhibiting species-specific, mostly porous patterns in the nano- to micrometer range. Recently, from the diatom Cylindrotheca fusiformis unusual phosphoproteins (termed silaffins) and long chain polyamines have been identified and implicated in biosilica formation. However, analysis of the role of silaffins in morphogenesis of species-specific silica structures has so far been hampered by the difficulty of obtaining structural data from these extremely complex proteins. In the present study, the five major silaffins from the diatom Thalassiosira pseudonana (tpSil1H, -1L, -2H, -2L, and -3) have been isolated, functionally analyzed, and structurally characterized, mak- ing use of the recently available genome data from this organism. Surprisingly, the silaffins of T. pseudonana and C. fusiformis share no sequence homology but are similar regarding amino acid composition and post-translational modifications. Silaffins tpSil1H and -2H are higher molecular mass isoforms of tpSil1L and -2L, respectively, generated in vivo by alternative processing of the same precursor polypeptides. Interestingly, only tpSil1H and -2H but not tpSil1L and -2L induce the formation of porous silica patterns in vitro, suggesting that the alternative processing event is an important step in morphogenesis of T. pseudonana biosilica.

Structure of poly (I).poly (A).poly (I).

The molecular structure of poly (I).poly (A).poly (I) has been determined and refined using the continuous intensity data on layer lines in the x-ray diffraction pattern obtained from an oriented fiber of this polymorphic RNA complex. The polymer forms a 12-fold right-handed triple-helix of pitch 39.7A and each base-triplet is stabilized by quasi Crick-Watson-Hoogsteen hydrogen bonds. The ribose rings in all the three strands have C3'-endo conformations. The final R-value for this best structure is 0.24 and the x-ray fit is significantly superior to all the alternative structures where the different chains might have different furanose conformations. This all-purine triple-helix, counter-intuitively, has a diameter roughly 3A shorter than that of DNA and RNA triple-helices containing a homopurine and two complementary homopyrimidine strands. Its compact, grooveless cylindrical shape is consistent with the lack of lateral organization.

Nucleotide chain length and the morphology of complexes with cationic amphiphiles: (31)P-NMR observations.

31P-NMR and UV spectroscopies were used to study the interactions between cationic amphiphile-containing lipid bilayers and either a phosphorothioate oligonucleotide (OligoS) (n=21) or polyadenylic acid (PolyA) (n approximately 18,000). Multilamellar vesicles (MLVs) were composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) or 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) in binary mixture with either of the cationic lipids, N-[1-(2, 3-dioleoyloxy)propyl]-N',N',N'-trimethylammonium chloride (DOTAP) or cetyltrimethylammonium bromide (CTAB). A UV-difference assay showed that OligoS binding ceased above a 1:1 anion/cation ratio, while PolyA binding continued until a 2:1 ratio was reached, indicating a 'flat' conformation for bound OligoS, but not necessarily for PolyA. Cross-polarization (31)P-NMR of the nucleotide chains bound to 100% DOTAP MLVs produced spectra virtually identical to those of dry powders of OligoS or PolyA, indicating effective immobilization of the surface-bound nucleotide chains. Hahn echo (31)P-NMR showed that MLVs composed of binary mixtures of POPC with DOTAP or CTAB retained a lamellar bilayer architecture upon adding nucleotide chains. At less than stoichiometric anion/cation ratios little or no signal attributable to free nucleotide chains was visible. A narrow signal at the chemical shift expected for phosphorothiodiesters or phosphodiesters became visible at greater levels of added OligoS or PolyA, respectively, indicating the presence of mobile nucleotide chains. Salt addition caused complete desorption of the nucleotide chains. When POPC was replaced with DOPE, binding of OligoS or PolyA produced non-bilayer lipid phases in the presence of DOTAP, but not in the presence of CTAB.

Translocon-associated protein alpha transcripts are induced by granulocyte-macrophage colony-stimulating factor and exhibit complex alternative polyadenylation.

The cloning of full length cDNA for the translocon-associated protein alpha subunit, previously called signal sequence receptor alpha, is reported as a result of differential display experiments in search of genes induced by granulocyte-macrophage colony-stimulating factor. Its messenger RNA was more abundant in growing cells than in either factor-deprived cells or quiescent cells and comprised four species, each having microheterogeneity, as a result of complex alternative polyadenylation apparently dependent on arrays of non-canonical polyadenylation signals. Radiation hybrid mapping of the gene showed that the gene is on the short arm of chromosome 6.

CA/TG sequence at the 5' end of oligo(A)-tracts strongly modulates DNA curvature.

An analysis of the base pair doublet geometries in available crystal structures indicates that the often reported intrinsic curvature of DNA containing oligo-(d(A).d(T)) tracts may also depend on the nature of the flanking sequences. The presence of CA/TG doublet in particular at the 5' end of these tracts is expected to enhance their intrinsic bending property. To test this proposition, three oligonucleotides, d(GAAAAAC-CCCCC), d(CCCCCCAAAAAG), d(GAAAAATTTTTC), and their complementary sequences were synthesized to study the effect of various flanking sequences, at the 5' and 3' ends of the A-tracts, on the curvature of DNA in solution. An analysis of the polyacrylamide gel electrophoretic mobilities of these sequences under different conditions of salts and temperatures (below their melting points) clearly showed that the oligomer with CA/TG sequence in the center was always more retarded than the oligomer with AC/GT sequence, as well as the oligomer with AT/AT sequence. Hydroxyl radical probing of the sequences with AC/GT and CA/TG doublet junctions gives a similar cutting pattern in the A-tracts, which is quite different from that in the C-tracts, indicating that the oligo(A)-tracts have similar structures in the two oligomers. KMnO4 probing shows that the oligomer with a CA/TG doublet junction forms a kink that is responsible for its inherent curvature and unusual electrophoretic mobility. UV melting shows a reduced thermal stability of the duplex with CA/TG doublet junction, and circular dichroism (CD) studies indicate that a premelting transition occurs in the oligomer with CA/TG doublet step before global melting but not in the oligomer with AC/GT doublet step, which may correspond to thermally induced unbending of the oligomer. These observations indicate that the CA/TG doublet junction at the 5' end of the oligo(A)-tract has a crucial role in modulating the overall curvature in DNA.

Expression of the rat arginine vasopressin gene in transgenic mice.

A line of mice has been developed which are transgenic for an 8.2-kilobase (kb) genomic clone of the rat vasopressin (VP) gene. Using a polymerase chain reaction technique, the rat VP (rVP) transgene was shown to have tissue-specific mRNA expression in the hypothalamus, temporal lobe, parietal cerebral cortex, cerebellum, and posterior pituitary, similar to the tissue distribution of endogenous mouse and rat VP expression. Expression of transgenic rVP mRNA was also found in the lung and pancreas of the transgenic mice, sites of known ectopic expression of VP. Using two methods, Northern blot analysis with species-specific cRNA probes and a quantitative polymerase chain reaction technique, the quantity of rVP transgene mRNA was shown to regulate appropriately in response to an osmotic stimulus. After 72 h of water deprivation, the quantity of transgenic rVP mRNA increased 6.8 +/- 3.0-fold. This was not significantly different than the fold increase in mouse VP mRNA quantity seen in nontransgenic mice (4.8 +/- 1.5) but was significantly different (P < 0.05) than the 1.2 +/- 0.03-fold increase in rat VP mRNA seen in normal rats after water deprivation. In the rat hypothalamus, VP mRNA poly(A) tail length increases with osmotic stimulation, while in the mouse it does not. The poly(A) tail of transgenic rVP mRNA expressed in mouse hypothalamus did not increase in length after osmotic stimulation.(ABSTRACT TRUNCATED AT 250 WORDS)

Is poly(A) tail length altered by aging or dietary restriction?

We examined age- and diet-related alterations in RNA poly(A) tail length using high-resolution gel electrophoresis followed by Northern hybridization. The results demonstrate conclusively that there is no age-related decrease in the size of the Poly(A) tail of RNA isolated from the male Fischer 344 rat. In contrast, our results suggest that there is actually a slight age-related increase in the length of the poly(A) tail isolated from the liver and hypothalamus of these rats. Dietary restriction did not affect either poly(A) tail length or its age-related increase. These data demonstrate conclusively that oligo(dT) probes can be used to standardize RNA hybridization experiments between animals of different ages and dietary groups. In addition, these data provide further evidence that the ratio between RNA polymerase I and RNA polymerase II activity does not change with age.

Spectroscopic study of the interaction between poly-(9-vinyladenine) and single or multistrand RNA.

The interaction between poly(9-vinyladenine) (PVAd) and poly[r(U)] was investigated by means of uv, CD, 1H-, and 31P-nmr spectroscopies. The interaction was dependent on the molecular weight of PVAd determined by uv and CD spectroscopies. Based on imino proton nmr, it was clearly found that PVAd formed the complex with poly[r(U)] by complementary hydrogen bonding. The interaction of PVAd with double- and triple-stranded helices of RNA was also investigated by uv melting behavior and 31P-nmr spectroscopy. The results suggested that PVAd could not interact with the double-stranded poly[r(A)].poly[r(U)] but did with the triple-stranded RNA.