Single-stranded Poly Research Articles

Study of complexation of single-stranded poly(rA) and poly(rU) with methylene blue

To reveal the effect of DNA- or RNA-specific low-molecular compounds on cellular processes on the molecular level, we have carried out the studies with the application of spectroscopic methods. It is necessary for the understanding of structural-functional properties of nucleic acids in cell. In this work the interaction of DNA-specific thiazine dye methylene blue (MB) with synthetic polynucleotides poly(rA) and poly(rU) was studied. The interaction of MB with synthetic polyribonucleotides poly(rA) and poly(rU) was examined in the solution with high ionic strength in a wide phosphate-to-dye (P/D) range, using the absorption and fluorescence spectroscopies, as well as the fluorescence 2D spectra and 3D spectra analyses were given. Values of the fluorescence quenching constants for the complexes of MB with poly(rA) and poly(rU) were calculated (KSV is the Stern-Volmer quenching constant). Two different modes of MB binding to single-stranded (ss-) poly(rA) and poly(rU) and to their hybrid double-stranded (ds-) structure – poly(rA)-poly(rU) were identified. This ligand binds to ss-poly(rA) and poly(rA)-poly(rU) by semi-intercalation and electrostatic modes, but to ss-poly(rU) the prevailing mode is the electrostatic interaction. Communicated by Ramaswamy H. Sarma

Long and Covalently Conjugated Branched DNA Structures for in Situ Gelation in Vivo

Long and Covalently Conjugated Branched DNA Structures for in Situ Gelation in Vivo

Fabrication of an artificial ionic gate inspired by mercury-resistant bacteria for simple and sensitive detection of mercury ion

Bioremediation of mercury pollution by mercury-resistant bacteria requires the key steps of mercury ions (Hg2+) capture and transportation. Inspired by the functions of mercury transporters in mercury-resistant bacteria, we have fabricated an artificial ionic gate, which may further behave as an Hg2+ biosensor. The gate is constructed by using the asymmetrically modified porous anodic alumina (PAA) film capable of forming Hg2+-activated complexes to control ionic current, while the gate works due to the changes between graphene oxide (GO) and different DNA structures. Specifically, single strand poly(T)n DNA on PAA film may transform into duplex structure through T-Hg2+-T coordination chemistry when Hg2+ exists. Compared with the ring by ring delivery via S-Hg intermediates in bacteria, this artificial gate may show better flexibility for Hg2+ transport, because the poly(T)n-Hg2+ complex can be wrapped in a chain structure with controllable DNA length. Furthermore, with the advantages of simple structure, convenient operation and good practicality, the constructed artificial Hg2+-activated ionic gate has been developed as a biosensor for sensitive detection of Hg2+, with the limit of detection (LOD) down to 0.07 fM. The fabricated ionic gate may be used for building an instrument that can absorb and detect Hg2+ from wastewater in the future.

Adsorption of Polyadenylic acid on graphene oxide: experiments and computer modeling

In this work, we study the adsorption of poly(rA) on graphene oxide (GO) using AFM and UV absorption spectroscopies. A transformation of the homopolynucleotide structure on the GO surface is observed. It is found that an energetically favorable conformation of poly(rA) on GO is achieved after a considerable amount of time (days). It is revealed that GO can induce formation of self-structures of single-stranded poly(rA) including a duplex at pH 7. The phenomenon is analyzed by polymer melting measurements and observed by AFM. Details of the noncovalent interaction of poly(rA) with graphene are also investigated using molecular dynamics simulations. The adsorption of (rA)10 oligonucleotide on graphene is compared with the graphene adsorption of (rC)10. DFT calculations are used to determine equilibrium structures and the corresponding interaction energies of the adenine-GO complexes with different numbers of the oxygen-containing groups. The IR intensities and vibrational frequencies of free and adsorbed adenines on the GO surface are calculated. The obtained spectral transformations are caused by the interaction of adenine with GO.

Metathesis Cyclopolymerization Triggered Self-Assembly of Azobenzene-Containing Nanostructure.

Azobenzene (AB) units were successfully introduced into poly(1,6-heptadiyne)s in order to ensure smooth synthesis of double- and single-stranded poly(1,6-heptadiyne)s (P1 and P2) and simultaneously realize the self-assembly by Grubbs-III catalyst-mediated metathesis cyclopolymerization (CP) of AB-functionalized bis(1,6-heptadiyne) and 1,6-heptadiyne monomers (M1 and M2). Monomers and polymers were characterized by 1H NMR, mass spectroscopy, and GPC techniques. The double-stranded poly(1,6-heptadiyne)s exhibited a large scale of ordered ladder nanostructure. This result was attributed to the π−π attractions between end groups along the longitudinal axis of the polymers and van der Waals interactions between the neighboring polymeric backbones. While the Azo chromophore connected in the side chain of P2 induced conformation of micelles nanostructure during the CP process without any post-treatment. Furthermore, the photoisomerization of Azo units had an obviously different regulatory effect on the conjugated degree of the polymer backbone, especially for the single-stranded P2, which was attributed to the structural differences and the interaction between AB chromophores in the polymers.

Auxiliary domains of the HrpB bacterial DExH-box helicase shape its RNA preferences

ABSTRACTRNA helicases are fundamental players in RNA metabolism: they remodel RNA secondary structures and arrange ribonucleoprotein complexes. While DExH-box RNA helicases function in ribosome biogenesis and splicing in eukaryotes, information is scarce about bacterial homologs. HrpB is the only bacterial DExH-box protein whose structure is solved. Besides the catalytic core, HrpB possesses three accessory domains, conserved in all DExH-box helicases, plus a unique C-terminal extension (CTE). The function of these auxiliary domains remains unknown. Here, we characterize genetically and biochemically Pseudomonas aeruginosa HrpB homolog. We reveal that the auxiliary domains shape HrpB RNA preferences, affecting RNA species recognition and catalytic activity. We show that, among several types of RNAs, the single-stranded poly(A) and the highly structured MS2 RNA strongly stimulate HrpB ATPase activity. In addition, deleting the CTE affects only stimulation by structured RNAs like MS2 and rRNAs, while deletion of accessory domains results in gain of poly(U)-dependent activity. Finally, using hydrogen-deuterium exchange, we dissect the molecular details of HrpB interaction with poly(A) and MS2 RNAs. The catalytic core interacts with both RNAs, triggering a conformational change that reorients HrpB. Regions within the accessory domains and CTE are, instead, specifically responsive to MS2. Altogether, we demonstrate that in bacteria, like in eukaryotes, DExH-box helicase auxiliary domains are indispensable for RNA handling.

Spectroscopic study on binding of TMPyP4+ porphyrin to single-stranded poly(rA)

Binding of tetracationic porphyrin (TMPyP4+) to poly(rA) has been studied in neutral buffered solution of low ionic strength in a wide range of molar phosphate-to-dye ratios (P/D) using absorption spectroscopy, polarized fluorescence and fluorimetric titration. Two competitive binding modes were identified: partial intercalation of porphyrin chromophores between adenine bases prevailing at P/D > 20 and its outside binding to poly(rA) backbone dominating at P/D < 6. Both of them were accompanied by enhancement of the porphyrin emission. Absence of the emission quenching near stoichiometric P/D ratios allowed us to assume that external binding occurs without the self-stacking of the chromophores.

Nuclear body formation by Arabidopsis CPL1-RCF3 complex requires single-stranded RNA-binding domains

Arabidopsis thaliana CARBOXYL-TERMINAL DOMAIN (CTD) PHOSPHATASE-LIKE 1 (CPL1) and REGULATOR OF CBF GENE EXPRESSION 3 (RCF3) form a complex that function in RNA quality control under various abiotic and biotic stresses. Amino acid sequences show double-stranded RNA-binding motif 1(DRM1) and multiple K-homology (KH) domains in CPL1 and RCF3, respectively. Here we showed that both CPL1 and RCF3 specifically binds to single-stranded poly(C) RNA at DRM1 and multiple KH domains. We also showed that in planta, more than 3 KH domains are sufficient for RCF3 to form a complex with CPL1 in nuclear bodies. However, larger RCF3 fragments were necessary to form speckle structures, suggesting that polyvalent molecular interactions around RCF3 are essential for forming the nuclear structures necessary to process various precursor transcripts.

Functional Block Copolymers Carrying One Double-Stranded Ladderphane and One Single-Stranded Block in a Facile Metathesis Cyclopolymerization Procedure.

In order to improve the poor film-forming ability of polymeric ladderphane, di-block copolymers containing perylene diimide (PDI)-linked double-stranded poly(1,6–heptadiyne) ladderphane and branched alkyl side chains modified single-stranded poly(1,6–heptadiyne) were synthesized by metathesis cyclopolymerization (MCP) using Grubbs third-generation catalyst (Ru–III) in tetrahydrofuran solvent. The first block containing the ladderphane structure leads to higher thermal-stability, wider UV–vis absorption, lower LUMO level and ladderphane-induced rigidity and poor film-forming ability. The second block containing long alkyl chains is crucial for the guarantee of excellent film-forming ability. By comparing the effect of ladderphane structure on the resulted copolymers, single-stranded poly(1,6–heptadiyne) derivatives with PDI pedant were also processed. The structures of copolymers were proved by 1H NMR and gel permeation chromatography, electrochemical, photophysical, and thermal-stability performance were achieved by cyclic voltammetry (CV), UV-visible spectroscopy and thermogravimetric analysis (TGA) measurements. According to the experiment results, both copolymers possessed outstanding film-forming ability, which cannot be realized by small PDI molecules and oligomers. And they can serve as a superior candidate as for n-type materials, especially for their relatively wide range of light absorption (λ = 200~800 nm), and lower LUMO level (−4.3 and −4.0 eV).

A New DNA Repair-Related Platform for Pharmaceutical Outlook in Cancer Therapies: Ultrashort Single-Stranded Polynucleotides

Thio- and cyano- modified single-stranded poly(dNTP) sequences of different molecular sizes (20–200 n) and the same lengths routine poly(dNTP) and poly(NTP) species were tested for their impact on catalytic activities of β-like DNA polymerases from chromatin of HL-60, WERI-1A and Y-79 cells as well as for the affinity patterns in DNApolβ-poly(dNTP)/(NTP) pairs, respectively. An essential link between the lengths of ultrashort (50–100 n) single-stranded poly(dNTP) sequences of different structures and their inhibitory effects towards the cancer-specific DNA polymerases β was found. A possible significance of this phenomenon for both DNA repair suppression in tumors and a consequent anti-cancer activity of the DNA repair related short poly(dNTP) fragments is under discussion.

Self-Assembly of DNA-Minocycline Complexes by Metal Ions with Controlled Drug Release.

Here we reported a study of metal ions-assisted assembly of DNA-minocycline (MC) complexes and their potential application for controlling MC release. In the presence of divalent cations of magnesium or calcium ions (M2+), MC, a zwitterionic tetracycline analogue, was found to bind to phosphate groups of nucleic acids via an electrostatic bridge of phosphate (DNA)-M2+-MC. We investigated multiple parameters for affecting the formation of DNA-Mg2+-MC complex, including metal ion concentrations, base composition, DNA length, and single- versus double-stranded DNA. For different nitrogen bases, single-stranded poly(A)20 and poly(T)20 showed a higher MC entrapment efficiency of DNA-Mg2+-MC complex than poly(C)20 and poly(G)20. Single-stranded DNA was also found to form a more stable DNA-Mg2+-MC complex than double-stranded DNA. Between different divalent metal ions, we observed that the formation of DNA-Ca2+-MC complex was more stable and efficient than the formation of DNA-Mg2+-MC complex. Toward drug release, we used agarose gel to encapsulate DNA-Mg2+-MC complexes and monitored MC release. Some DNA-Mg2+-MC complexes could prolong MC release from agarose gel to more than 10 days as compared with the quick release of free MC from agarose gel in less than 1 day. The released MC from DNA-Mg2+-MC complexes retained the anti-inflammatory bioactivity to inhibit nitric oxide production from pro-inflammatory macrophages. The reported study of metal ion-assisted DNA-MC assembly not only increased our understanding of biochemical interactions between tetracycline molecules and nucleic acids but also contributed to the development of a highly tunable drug delivery system to mediate MC release for clinical applications.

Primer-Like Inhibitors for DNA Repair Enzymes of the AML-HL60 and WERI-1A/Y79 Malignant Cells

A conventionally synthesized thio- and cyano-modified single-stranded poly(dNTP) sequences of different molecular sizes (20n - 200n) and the same lengths routine poly(dNTP) and poly(NTP) species were obtained through the good services provided by the Russian Federal Bioorganic Products Group and by the ThermoFischer, Inc., and then tested for their impact on catalytic activities of β-like DNA polymerases from chromatin of HL-60, WERI-1A and Y-79 cells as well as for the affinity patterns in DNApolβ-poly(dNTP)/ (NTP) pairs, respectively. An essential link between the lengths of ultrashort (50n - 100n) single-stranded poly(dNTP) sequences of different structures and their inhibitory effects towards the cancer-specific DNA polymerases β has been found. A possible significance of this phenomenon for both DNA repair suppression in tumors and a consequent anti-cancer activity of the DNA repair related short poly(dNTP) fragments has been for the first time emphasized with a respect to their pharmacophore revealing potential. Thus, this work presents an experimental attempt to upgrade a contemporary attitude towards the DNA derived products applied for anti-cancer agenda, particularly, for acute myeloid leukemia and retinoblastoma cell DNA repair machinery breakdown. In this study, tumor specific DNA polymerases β were found of being the targets for attack promoted with the primer-like single-stranded DNA fragments followed by consequent cytostatic phenomena. A novel concept of the DNA related anti-cancer medicines is under discussion.

Fluorescent sensor array for discrimination of biothiols based on poly(thymine/cytosine)-templated copper nanoparticles

In medicine, the detection and identification of biothiols have received increasing attention due to their crucial roles in life activities. Hence, we present a facile, rapid, and effective method for identification of five kinds of biothiols including glutathione (GSH), l-cysteine (Cys), dithiothreitol (DTT), 2-mercaptoethanol (MCE), and 3-mercaptopropionic acid (MPA). The proposed sensor array is fabricated based on single-stranded poly (thymine/cytosine)-templated fluorescent copper nanoparticles (CuNPs), which are controlled through thymine-Hg2+-thymine (T-Hg2+-T) and cytosine-Ag+-cytosine (CAg+C) coordination. The results show that single-stranded poly T and poly C are used as a highly efficient template, and ascorbic acid acts as a reductant to form CuNPs. Owing to the different thiol binding affinity between Hg2+ (pKd = 3.90) and Ag+ (pKd = 5.50), the sensor array produces a unique pattern of fluorescence variations when it interacts with the five biothiols. Linear discriminant analysis (LDA) is applied to analyze the fluorescence pattern and generated a clustering map for a clear identification of the five biothiols. By employing this “turn-on” sensor array, five thiols were successfully discirminated at the 50 nM level in buffer solution and serum samples.

Dual Roles of Poly(dA:dT) Tracts in Replication Initiation and Fork Collapse

Replication origins, fragile sites, and rDNA have been implicated as sources of chromosomal instability. However, the defining genomic features of replication origins and fragile sites are among the least understood elements of eukaryote genomes. Here, we map sites of replication initiation and breakage in primary cells at high resolution. We find that replication initiates between transcribed genes within nucleosome-depleted structures established by long asymmetrical poly(dA:dT) tracts flanking the initiation site. Paradoxically, long (>20bp) (dA:dT) tracts are also preferential sites of polar replication fork stalling and collapse within early-replicating fragile sites (ERFSs) and late-replicating common fragile sites (CFSs) andat the rDNA replication fork barrier. Poly(dA:dT) sequences are fragile because long single-strand poly(dA) stretches at the replication fork are unprotected by the replication protein A (RPA). We propose that the evolutionary expansion of poly(dA:dT) tracts in eukaryotic genomes promotes replication initiation, but at the cost of chromosome fragility.

Binding affinity and in vitro cytotoxicity of harmaline targeting different motifs of nucleic acids: An ultimate drug designing approach

The work focuses towards interaction of harmaline, with nucleic acids of different motifs by multispectroscopic and calorimetric techniques. Findings of this study suggest that binding constant varied in the order single-stranded (ss) poly(A)>double-stranded calf thymus (CT) DNA>double-stranded poly(G)·poly(C)>clover leaf tRNAPhe . Prominent structural changes of ss poly(A), CT DNA, and poly(G)· poly(C) with concomitant induction of optical activity in the bound achiral alkaloid molecule was observed, while with tRNAPhe , very weak induced circular dichroism perturbation was seen. The interaction was predominantly exothermic, enthalpy driven, and entropy favored with CT DNA and poly(G)·poly(C), while it was entropy driven with poly(A) and tRNAPhe . Intercalated state of harmaline inside poly(A), CT DNA, and poly(G)·poly(C) was shown by viscometry, ferrocyanide quenching, and molecular docking. All these findings unequivocally pointed out preference of harmaline towards ss poly(A) inducing self-structure formation. Furthermore, harmaline administration caused a significant decrease in proliferation of HeLa and HepG2 cells with GI50 of 28μM and 11.2μM, respectively. Nucleic acid fragmentation, cellular ultramorphological changes, decreased mitochondrial membrane potential, upregulation of p53 and caspase 3, generation of reactive oxygen species, and a significant increase in the G2 /M population made HepG2 more prone to apoptosis than are HeLa cells.

Linear and circular dichroism characterization of thionine binding mode with DNA polynucleotides

The binding mode of thionine (3,7-diamino-5-phenothiazinium) with alternating and non-alternating DNA polynucleotides at low binding ratios was conclusively determined using linear and circular dichroism spectroscopies. The binding to [poly(dG-dC)]2 and poly(dG)·poly(dC) was purely intercalative and was insensitive to ionic strength. Intercalative binding to [poly(dA-dT)]2 is observed at low ionic strength, but a shift of some dye to an non-intercalative mode is observed as the background salt concentration increases. With poly(dA)·poly(dT), intercalative binding is unfavourable, although some dye molecules may intercalate at low ionic strength, and groove binding is strongly promoted with increasing concentration of background salt. However, stacking with bases is observed with single-stranded poly(dA) and with triplex poly(dT)⁎poly(dA)·poly(dT) which suggests that the unusual structure of poly(dA)·poly(dT) precludes intercalation. Thionine behaves similarly to the related dye methylene blue, and small differences may be attributed either to the ability of thionine to form H-bonds that stabilize intercalation or to its improved stacking interactions in the basepair pocket on steric grounds.

Chiral Selective Stacking of a Cationic Porphyrin along Z-Form Poly[d(A-T)2

In this study, the binding mode of porphyrin-free single-stranded poly[d(AT)] and trans-BMPyP was observed in the Z-form trans-BMPyP-poly[d(A-T)2] complex induced by extensive stacking depending on the temperature and concentration through circular dichroism (CD). The Z-form trans-BMPyP-poly[d(A-T)2] complex (R = 0.30) retained the Z-form DNA structure at a low temperature (20 °C) by the trans-BMPyP molecules. When the temperature was increased to 60 °C, the DNA was almost unfolded as a single-stranded poly[d(AT)], but the extensive stacking binding mode of trans-BMPyP was maintained and the shape of the porphyrin Soret band was symmetrically changed in comparison with the shape of the Z-form DNA. However, when the temperature was raised to 80 °C, the extensive stacking binding mode of trans-BMPyP was also unfolded almost completely. The binding mode of the trans-BMPyP-single-stranded poly[d(AT)] complex was very similar to the already known binding mode of porphyrins and a double-stranded DNA. The binding mode was dependent on the concentration ratio ([porphyrin]/[DNA]): a monomeric binding mode at a concentration ratio of 0.04, a moderate groove binding mode at a concentration ratio between 0.08 and 0.16, and extensive stacking at a concentration ratio between 0.20 and 0.30. The same result was obtained when the temperature of the Z-form DNA (R = 0.30) was increased to 60 °C. However, those binding modes were not found in cis-BMPyP, which was because, in the extensive stacking of trans-BMPyP along the DNA skeleton, the distance between the two positive methylpyridine ions at the trans site and thymine, one of the DNA bases, is decreased, creating a much more hydrophobic environment. In addition, the poly AT sequences found from the CD spectra for the binding of trans-BMPyP-poly[d(A-T)2] and trans-BMPyP-poly[d(AT)] (R = 0.30) showed that both of them underwent effective extensive stacking and that the chirality of extensive stacking was dependent on the form of DNA.

Nucleic acid binding and other biomedical properties of artificial oligolysines.

In the present study, we report the interaction of an artificial oligolysine (referred to as AOL) realized in our laboratory with targets of biomedical importance. These included polyinosinic acid (poly rI) and its complex with polycytidylic acid (poly I:C), RNAs with well-known interferon-inducing ability, and double-stranded (ds) DNA. The ability of the peptide to bind both single-stranded poly rI and ds poly I:C RNAs emerged from our circular dichroism (CD) and ultraviolet (UV) studies. In addition, we found that AOL forms complexes with dsDNA, as shown by spectroscopic binding assays and UV thermal denaturation experiments. These findings are encouraging for the possible use of AOL in biomedicine for nucleic acid targeting and oligonucleotide condensation, with the latter being a key step preceding their clinical application. Moreover, we tested the ability of AOL to bind to proteins, using serum albumin as a model protein. We demonstrated the oligolysine–protein binding by CD experiments which suggested that AOL, positively charged under physiological conditions, binds to the protein regions rich in anionic residues. Finally, the morphology characterization of the solid oligolysine, performed by scanning electron microscopy, showed different crystal forms including cubic-shaped crystals confirming the high purity of AOL.

Targeting different RNA motifs by beta carboline alkaloid, harmalol: a comparative photophysical, calorimetric, and molecular docking approach

RNA has attracted recent attention for its key role in gene expression and targeting by small molecules for therapeutic intervention. This work focuses towards understanding interaction of harmalol, a DNA intercalator, with RNAs of different motifs viz. single-stranded A-form poly(A), double-stranded A-form of poly(C)·poly(G), and clover leaf tRNAphe by different spectroscopic, calorimetric, and molecular modeling techniques. Results of this study converge to suggest that (i) binding constant varied in the order poly(C)·poly(G) > tRNAphe > poly(A), (ii) non-cooperative binding of harmalol to poly(C)·poly(G) and poly(A) and cooperative binding with tRNAphe, (iii) significant structural changes of poly(C)·poly(G) and tRNAphe with concomitant induction of optical activity in the bound achiral alkaloid molecules, while with poly(A) no induced Circular dichroism (CD) perturbation was observed, (iv) the binding was predominantly exothermic, enthalpy-driven, entropy-favored with poly(C)·poly(G), while it was entropy driven with tRNAphe and poly(A), (v) a hydrophobic contribution and comparatively large role of non polyelectrolytic forces to Gibbs energy changes with poly(C)·poly(G) and tRNAphe and (vi) intercalated state of harmalol inside poly(C)·poly(G) structure as revealed from molecular docking was supported by the viscometric and ferrocyanide quenching data. All these findings unequivocally pointed out that harmalol prefers binding with poly(C)·poly(G), compared to tRNAphe and poly(A); this results serve as data for the development of RNA-based antiviral drugs.

PCBP2 Modulates Neural Apoptosis and Astrocyte Proliferation After Spinal Cord Injury.

PCBP2, a member of the poly(C)-binding protein (PCBP) family, plays a pivotal role in posttranscriptional and translational regulation by interacting with single-stranded poly(C) motifs in target mRNAs. It is reported that several PCBP family members are involved in human malignancies. However, the distribution and function of PCBP2 in the central nervous system (CNS) remain unclear. In this study, we performed an acute spinal cord injury (SCI) model in adult rats and investigated the dynamic changes of PCBP2 expression in the spinal cord. Western blot and immunohistochemistry analysis revealed that PCBP2 presented in normal spinal cord. It gradually increased, reached a peak at 3day, and then declined to basal levels at 14days after SCI. We observed that the expression of PCBP2 was enhanced in the gray and white matter. Immunofluorescence indicated that PCBP2 was located in the neurons and astrocytes. Moreover, colocalization of PCBP2/active caspase-3 was detected in neurons, and colocalization of PCBP2/proliferating cell nuclear antigen was detected in astrocytes after SCI. These results indicated that PCBP2 might play an important role in neuronal apoptosis and astrocyte proliferation. In vitro, PCBP2-specific siRNA-transfected neuron showed significantly decrease of neuronal apoptosis and expression of cell cycle related proteins following glutamate stimulation. Meanwhile, PCBP2 knockdown also reduced primary astrocytes proliferation. All above indicated that PCBP2 might play a crucial role in cell proliferation and apoptosis. Collectively, our data suggested that PCBP2 might play important roles in CNS pathophysiology after SCI.