Genomes and Genes
Summary: A group of cytosine ribonucleotides in which the phosphate residues of each cytosine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.
- Ohshima H, Hirano N, Takahashi H. A hexanucleotide sequence (dC1-dC6 tract) restricts the dC-specific cleavage of single-stranded DNA by endonuclease IV of bacteriophage T4. Nucleic Acids Res. 2007;35:6681-9 pubmed..A model for the dCs tract-dependent cleavage is proposed. ..
- Sletmoen M, Stokke B. Structural properties of poly C-scleroglucan complexes. Biopolymers. 2005;79:115-27 pubmed..An ultraviolet (UV) detector allowed specific detection of the polynucleotide. The poly-cytidylic acid (poly C) shifted to coelution with the linear fraction of the scleroglucan following the renaturation of poly C-..
- Ha P, Tong B, Westra W, Sanchez Cespedes M, Parrella P, Zahurak M, et al. Mitochondrial C-tract alteration in premalignant lesions of the head and neck: a marker for progression and clonal proliferation. Clin Cancer Res. 2002;8:2260-5 pubmed..These alterations are valuable as additional markers of histopathological progression. ..
- Perez M, Cruz F, Presa P. Distribution properties of polymononucleotide repeats in molluscan genomes. J Hered. 2005;96:40-51 pubmed..This research allows a better understanding of the distribution patterns of single repeats in eukaryotes. ..
- Chaly T, Montrel M. Hydrogen-ion binding of polycytidylic acid immobilized between Langmuir layers of dimethyldioctadecylammonium (DODA) in thin multilayer films. Biosens Bioelectron. 2000;15:93-8 pubmed..This hysteresis points to a marked transference of both types of molecules during the film titration. This behavior also depends upon the types of molecules from which the films were made. ..
- Cannistraro V, Kennell D. The reaction mechanism of ribonuclease II and its interaction with nucleic acid secondary structures. Biochim Biophys Acta. 1999;1433:170-87 pubmed..Duplex strand binding by RNase II made complex DNA or RNA structures accessible to degradation by other nucleases and further verified the PDE I footprinting method. ..
- Denman R, Sung Y. Species-specific and isoform-specific RNA binding of human and mouse fragile X mental retardation proteins. Biochem Biophys Res Commun. 2002;292:1063-9 pubmed..Finally, these data demonstrate that each FMRP variant binds RNAs uniquely, resulting in a set of proteins with differing affinities. ..
- Wang H, Ng T. A ribonuclease from Chinese ginseng (Panax ginseng) flowers. Protein Expr Purif. 2004;33:195-9 pubmed..The characteristics of this ribonuclease were different from those of ribonuclease previously purified from ginseng roots. ..
- Duke G, Palmenberg A. Cloning and synthesis of infectious cardiovirus RNAs containing short, discrete poly(C) tracts. J Virol. 1989;63:1822-6 pubmed
- Evdokimov I, Salianov V, Skuridin S, Dembo A. [Some X-ray diffraction parameters of liquid-crystalline dispersions of nucleic acid-chitosan complexes ]. Mol Biol (Mosk). 2002;36:706-14 pubmed..in the polymeric chain of chitosan molecule combining with NA molecule is the factor that affects the spatial structure of resulting dispersions. ..
- Choi H, Kim C, Hwang C, Song K, Law P, Wei L, et al. Novel function of the poly(C)-binding protein alpha CP3 as a transcriptional repressor of the mu opioid receptor gene. FASEB J. 2007;21:3963-73 pubmed..Our data suggest that alphaCP3 can function as a repressor of MOR transcription dependent on the MOR poly(C) sequence. We demonstrate for the first time a role of alphaCP3 as a transcriptional repressor in MOR gene regulation. ..
- Saheki A, Fukui Y, Hoshi Y, Fukui H, Seki J, Tamai I. Influence of preparation method on polynucleotide conformation and pharmacological activity of lipoplex. Int J Pharm. 2011;406:117-21 pubmed publisher..Our results indicate that polynucleotide conformation in lipoplex is markedly influenced by the preparation method, and the polynucleotide conformation in lipoplex has a substantial effect on pharmacological activity. ..
- Cannistraro V, Kennell D. The processive reaction mechanism of ribonuclease II. J Mol Biol. 1994;243:930-43 pubmed..abstract truncated at 400 words) ..
- Beier D, Frank R. Molecular characterization of two-component systems of Helicobacter pylori. J Bacteriol. 2000;182:2068-76 pubmed
- Sakurai K, Mizu M, Shinkai S. Polysaccharide--polynucleotide complexes. 2. Complementary polynucleotide mimic behavior of the natural polysaccharide schizophyllan in the macromolecular complex with single-stranded RNA and DNA. Biomacromolecules. 2001;2:641-50 pubmed..Furthermore, stoichiometric study suggested that the complex structure is a triple helix consisting of two s-SPG and one poly(C) or poly(A) chains. ..
- Kirches E, Krause G, Warich Kirches M, Weis S, Schneider T, Meyer Puttlitz B, et al. High frequency of mitochondrial DNA mutations in glioblastoma multiforme identified by direct sequence comparison to blood samples. Int J Cancer. 2001;93:534-8 pubmed..Our data suggest that the same mechanisms that generate inherited mtDNA polymorphisms are strongly enhanced in gliomas and produce somatic mutations. ..
- Ulrich K, Wölfle S, Mayer A, Heeg K, Braunbeck T, Erdinger L, et al. Extractable organic matter of standard reference material 1649a influences immunological response induced by pathogen-associated molecular patterns. Environ Sci Pollut Res Int. 2010;17:1257-67 pubmed publisher..Further investigation of these observations is required to understand the molecular mechanisms underlying adverse health effects of APM reported in epidemiological studies. ..
- Gidden J, Ferzoco A, Baker E, Bowers M. Duplex formation and the onset of helicity in poly d(CG)n oligonucleotides in a solvent-free environment. J Am Chem Soc. 2004;126:15132-40 pubmed..The presence of helical structures in the ion mobility experiments indicates that the duplexes retain "solution structures" in the gas phase on the millisecond time scale. ..
- Chowdhury S, Islam M, Kumar G. Binding of the anticancer alkaloid sanguinarine to double stranded RNAs: insights into the structural and energetics aspects. Mol Biosyst. 2010;6:1265-76 pubmed publisher..poly(G). These results further advance our understanding on the binding of small molecules that are specific binders to double stranded RNA sequences. ..
- Kubota N, Ebihara T, Matsumoto M, Gando S, Seya T. IL-6 and IFN-alpha from dsRNA-stimulated dendritic cells control expansion of regulatory T cells. Biochem Biophys Res Commun. 2010;391:1421-6 pubmed publisher..These data suggest that the balance of IL-6 and IFN-alpha in the region of RNA virus infection may determine the number of peripheral Treg, which affects the effective immune responses against viruses. ..
- Shin M, Levin B, Kim H, Kim H, Lee I, Cho D, et al. Profiling of length heteroplasmies in the human mitochondrial DNA control regions from blood cells in the Korean population. Electrophoresis. 2006;27:1331-40 pubmed..This result supports the possibility that a severe frameshift in the 303-315 poly-C tract may also cause the impairment of mtDNA replication in hematopoietic tissue. ..
- Chen J, You Y, Chen J, Huang T, Kuo C. Organization and promoter analysis of the zebrafish (Danio rerio) interferon gene. DNA Cell Biol. 2005;24:641-50 pubmed..These results indicate that the interferon promoter is active in a tissue-specific manner, and suggest that the interferon promoter plays an important role in virus resistance during teleost growth. ..
- Hsieh Y, Huang B, Liu C, Liu C. NaDDBS as a dispersion agent for multiwalled carbon nanotubes in capillary EKC separation of nucleotides. Electrophoresis. 2010;31:3288-95 pubmed..The system has been used to separate oligonucleotides, and to analyze nucleotides in a complex matrix sample. ..
- de Los Santos Alvarez P, Lobo Castañón M, Miranda Ordieres A, Tuñón Blanco P. Voltammetric determination of underivatized oligonucleotides on graphite electrodes based on their oxidation products. Anal Chem. 2002;74:3342-7 pubmed..Moreover, the adsorbed oxidized oligonucleotide shows electrocatalytic activity toward the oxidation of NADH. The capability of the new method to detect DNA hybridization is discussed. ..
- Malinovskii V, Nussbaumer A, Haner R. Oligopyrenotides: chiral nanoscale templates for chromophore assembly. Angew Chem Int Ed Engl. 2012;51:4905-8 pubmed publisher..The cationic porphyrin meso-tetrakis(1-methylpyridin-4-yl)porphyrin interacts with the helical polymers in a similar way as with poly(dA:dT). ..
- Wu C, Yin P, Hung W, Li A, Li S, Chi C, et al. Mitochondrial DNA mutations and mitochondrial DNA depletion in gastric cancer. Genes Chromosomes Cancer. 2005;44:19-28 pubmed..018). Our results suggest that somatic mtDNA mutations and mtDNA depletion occur in gastric cancer and that mtDNA depletion is involved in carcinogenesis and/or cancer progression of gastric carcinoma. ..
- Munakata H, Imai H, Nakagawa S, Osada A, Uemori Y. Water-soluble porphyrins appending platinum(II) complexes as binders for synthetic nucleic acid polymers. Chem Pharm Bull (Tokyo). 2003;51:614-5 pubmed..UV-vis spectral data suggested that these porphyrins bind to the nucleic acids by coordinative and Coulomb interactions. ..
- Dinguirard N, Yoshino T. Potential role of a CD36-like class B scavenger receptor in the binding of modified low-density lipoprotein (acLDL) to the tegumental surface of Schistosoma mansoni sporocysts. Mol Biochem Parasitol. 2006;146:219-30 pubmed..Inhibition of sporocyst growth also indicates a potential involvement of this SR homologue in some aspect of larval growth and/or development. ..
- Kennedy T, Maclean J, Liu J. Blue emitting gold nanoclusters templated by poly-cytosine DNA at low pH and poly-adenine DNA at neutral pH. Chem Commun (Camb). 2012;48:6845-7 pubmed publisher..Blue fluorescent gold nanoclusters were prepared in the presence of poly-cytosine DNAs at low pH and poly-adenine at neutral pH using citrate as the reducing agent; various buffer conditions affecting the synthesis have been explored. ..
- Hung W, Lin J, Lee L, Wu C, Tseng L, Yin P, et al. Tandem duplication/triplication correlated with poly-cytosine stretch variation in human mitochondrial DNA D-loop region. Mutagenesis. 2008;23:137-42 pubmed publisher..These observations suggest that the occurrence of the tandem duplication/triplication in mtDNA D-loop is not specific for cancer tissues, but highly associated with the poly-C length variations around np 568. ..
- Neff A, Lee J, Wilusz J, Tian B, Wilusz C. Global analysis reveals multiple pathways for unique regulation of mRNA decay in induced pluripotent stem cells. Genome Res. 2012;22:1457-67 pubmed publisher..Overall, our results highlight the importance of post-transcriptional control in pluripotent cells and identify miRNAs and RNA-binding proteins whose activity may coordinately control expression of a wide range of genes in iPS cells. ..
- Seifried S, Bjornson K, von Hippel P. Structure and assembly of the Escherichia coli transcription termination factor rho and its interactions with RNA. II. Physical chemical studies. J Mol Biol. 1991;221:1139-51 pubmed..Fluorescence and sedimentation studies show the association steps to be sensitive to salt concentration. Consistent with earlier work, we find that assembly to the hexameric state is driven by RNA binding. ..
- Rieder E, Bunch T, Brown F, Mason P. Genetically engineered foot-and-mouth disease viruses with poly(C) tracts of two nucleotides are virulent in mice. J Virol. 1993;67:5139-45 pubmed
- Ashkenasy N, Sanchez Quesada J, Bayley H, Ghadiri M. Recognizing a single base in an individual DNA strand: a step toward DNA sequencing in nanopores. Angew Chem Int Ed Engl. 2005;44:1401-4 pubmed
- Zarudnaya M, Samijlenko S, Potyahaylo A, Hovorun D. Structural transitions in polycytidylic acid: proton buffer capacity data. Nucleosides Nucleotides Nucleic Acids. 2002;21:125-37 pubmed..This reaction causes cooperative dissociation of the poly(C) double helices. The second narrow peak reflects the dissociation process. ..
- Rodriguez M, Moussaoui M, Benito A, Cuchillo C, Nogués M, Vilanova M. Human pancreatic ribonuclease presents higher endonucleolytic activity than ribonuclease A. Arch Biochem Biophys. 2008;471:191-7 pubmed publisher..These residues may reinforce the strength of a non-catalytic secondary phosphate binding (p2) or, alternatively, constitute a new non-catalytic phosphate binding subsite (p3). ..
- Huang J, Ficorilli N, Hartley C, Wilcox R, Weiss M, Studdert M. Equine rhinitis B virus: a new serotype. J Gen Virol. 2001;82:2641-5 pubmed..It is suggested that P313/75 can be classified as a new serotype of the genus Erbovirus, tentatively named ERBV2. Seroepidemiological data indicate that ERBV2 infection of horses may be common (24%) in Australia. ..
- Jin B, Ahn J, Ko J, Wang W, Han S, Kim S. Effect of the position and number of positive charges on the intercalation and stacking of porphyrin to poly[d(G-C)2], poly[d(A-T)2], and native DNA. J Phys Chem B. 2008;112:15875-82 pubmed publisher..Conversely, CD and LDr characteristics of both trans- and cis-BMPyP-DNA complexes resembled those that complexed with poly[d(A-T)2] at a high [porphyrin]/[DNA] ratio, suggesting that both porphyrins were stacked along the DNA stem. ..
- Expert Bezançon A, Le Caer J, Marie J. Heterogeneous nuclear ribonucleoprotein (hnRNP) K is a component of an intronic splicing enhancer complex that activates the splicing of the alternative exon 6A from chicken beta-tropomyosin pre-mRNA. J Biol Chem. 2002;277:16614-23 pubmed..hnRNP I (PTB) was also found associated with the strong enhancer sequences. Its function in the splicing of exon 6A is discussed. ..
- Gu L, Wang Y. Nanopore single-molecule detection of circulating microRNAs. Methods Mol Biol. 2013;1024:255-68 pubmed publisher..This concise protocol describes how to device a protein nanopore to quantify target miRNAs in RNA extraction, and discusses at the end the advantages, challenges, and broad impact of the nanopore approach for miRNA detection. ..
- Hattori M, Frazier J, Miles H. Poly(8-aminoguanylic acid): formation of ordered self-structures and interaction with poly(cytidylic acid). Biochemistry. 1975;14:5033-45 pubmed..The properties of the ordered structures are interpreted in terms of a strong tendency of the 8-amino group to form a third interbase hydrogen bond, when this possibility is not prevented by high pH. ..
- Mekata T, Sudhakaran R, Okugawa S, Inada M, Kono T, Sakai M, et al. A novel gene of tumor necrosis factor ligand superfamily from kuruma shrimp, Marsupenaeus japonicus. Fish Shellfish Immunol. 2010;28:571-8 pubmed publisher..These observations suggest that MjTNF plays a role in the innate immune defense in kuruma shrimp. The discovery of shrimp TNF will allow a more complete and concrete understanding of shrimp inflammatory responses. ..
- Potter Perigo S, Johnson P, Evanko S, Chan C, Braun K, Wilkinson T, et al. Polyinosine-polycytidylic acid stimulates versican accumulation in the extracellular matrix promoting monocyte adhesion. Am J Respir Cell Mol Biol. 2010;43:109-20 pubmed publisher..These results highlight an important role for versican in the hyaluronan-dependent binding of monocytes to the ECM of lung fibroblasts stimulated with polyinosine-polycytidylic acid. ..
- Thomson A, Cahill C, Cho H, Kassachau K, Epis M, Bridges K, et al. The acute box cis-element in human heavy ferritin mRNA 5'-untranslated region is a unique translation enhancer that binds poly(C)-binding proteins. J Biol Chem. 2005;280:30032-45 pubmed..The regulated association of H-ferritin mRNA with the poly(C)-binding proteins suggests a novel role for these proteins in ferritin translation and iron homeostasis in human liver. ..
- Arora K, Prabhakar N, Chand S, Malhotra B. Ultrasensitive DNA hybridization biosensor based on polyaniline. Biosens Bioelectron. 2007;23:613-20 pubmed..Compared to direct electrochemical oxidation of guanine, hybridization detection using MB results in the enhanced detection limit by about 100 times. These DNA immobilized PANI electrodes have hybridization response time of about 60 s. ..
- Hasegawa T, Fujisawa T, Numata M, Matsumoto T, Umeda M, Karinaga R, et al. Schizophyllans carrying oligosaccharide appendages as potential candidates for cell-targeted antisense carrier. Org Biomol Chem. 2004;2:3091-8 pubmed..beta-lactoside-appended schizophyllan enhanced an antisense activity in hepatocytes which express lactoside-binding proteins on their cell surfaces. ..
- Magulick J, Beerbom M, Schlaf R. Comparison of ribonucleic acid homopolymer ionization energies and charge injection barriers. J Phys Chem B. 2006;110:15973-81 pubmed..Comparison with earlier results on cytidine and adenosine RNA homopolymers (poly rC, poly rA) indicates significant ionization energy and charge injection barrier differences between purines and pyrimidines. ..
- Xiang T, Goss D, Diem M. Strategies for the computation of infrared CD and absorption spectra of biological molecules: ribonucleic acids. Biophys J. 1993;65:1255-61 pubmed..We find that observed band shapes are generally well reproduced by these models, particularly if care is taken to determine the direction of the vibrational dipole transition moments accurately. ..
- Zhu M, Xu L, Chen X, Ma Z, Wang H, Ng T. A novel ribonuclease with HIV-1 reverse transcriptase inhibitory activity from the edible mushroom Hygrophorus russula. Appl Biochem Biotechnol. 2013;170:219-30 pubmed publisher..It exerted the highest RNase activity on poly C and poly U. The Michaelis constant (K(m)) value of the RNase on yeast tRNA was 3...
- Pastro L, Smircich P, Pérez Díaz L, Duhagon M, Garat B. Implication of CA repeated tracts on post-transcriptional regulation in Trypanosoma cruzi. Exp Parasitol. 2013;134:511-8 pubmed publisher..Altogether, these results suggest the involvement of polyCA as a signal in gene expression regulation in T. cruzi. ..
- Martin L, Neal Z, McBride M, Palmenberg A. Mengovirus and encephalomyocarditis virus poly(C) tract lengths can affect virus growth in murine cell culture. J Virol. 2000;74:3074-81 pubmed..The characterized cultures should provide excellent tools for molecular study of poly(C) tract-mediated virulence. ..
- Toyoda H, Franco D, Fujita K, Paul A, Wimmer E. Replication of poliovirus requires binding of the poly(rC) binding protein to the cloverleaf as well as to the adjacent C-rich spacer sequence between the cloverleaf and the internal ribosomal entry site. J Virol. 2007;81:10017-28 pubmed..These data reveal a new essential function of the spacer between the CL and the IRES in poliovirus proliferation. ..