Genomes and Genes
Summary: A group of ribonucleotides (up to 12) in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.
- Hornung V, Ellegast J, Kim S, Brzózka K, Jung A, Kato H, et al. 5'-Triphosphate RNA is the ligand for RIG-I. Science. 2006;314:994-7 pubmed
- Threlfall R, Torres A, Krivenko A, Gait M, Caruthers M. Synthesis and biological activity of phosphonoacetate- and thiophosphonoacetate-modified 2'-O-methyl oligoribonucleotides. Org Biomol Chem. 2012;10:746-54 pubmed publisherChimeric 2'-O-methyl oligoribonucleotides (2'-OMe ORNs) containing internucleotide linkages which were modified with phosphonoacetate (PACE) or thiophosphonoacetate (thioPACE) were prepared by solid-phase synthesis...
- Yang J, Hakansson K. Fragmentation of oligoribonucleotides from gas-phase ion-electron reactions. J Am Soc Mass Spectrom. 2006;17:1369-1375 pubmed publisher..We found that the ECD fragmentation patterns of the oligoribonucleotides A6, C6, and CGGGGC are nucleobase dependent, suggesting that cleavage proceeds following electron capture ..
- Haeberli P, Berger I, Pallan P, Egli M. Syntheses of 4'-thioribonucleosides and thermodynamic stability and crystal structure of RNA oligomers with incorporated 4'-thiocytosine. Nucleic Acids Res. 2005;33:3965-75 pubmed..Incorporation of 4'-thiocytidines into oligoribonucleotides improved the thermal stability of the corresponding duplexes by approximately 1 degrees C per modification, ..
- Pav O, Kóšiová I, Barvik I, Pohl R, Budesinsky M, Rosenberg I. Synthesis of oligoribonucleotides with phosphonate-modified linkages. Org Biomol Chem. 2011;9:6120-6 pubmed publisherSolid phase synthesis of phosphonate-modified oligoribonucleotides using 2'-O-benzoyloxymethoxymethyl protected monomers is presented in both 3'?5' and 5'?3' directions...
- Kaukinen U, Lonnberg H, PERAKYLA M. Stabilisation of the transition state of phosphodiester bond cleavage within linear single-stranded oligoribonucleotides. Org Biomol Chem. 2004;2:66-73 pubmed..on the stability of the transition state (TS) of phosphodiester bond cleavage within linear single-stranded oligoribonucleotides has been studied in order to better understand why the reactivity of some phosphodiester bonds is enhanced ..
- Niittymäki T, Kaukinen U, Virta P, Mikkola S, Lonnberg H. Preparation of azacrown-functionalized 2'-O-methyl oligoribonucleotides, potential artificial RNases. Bioconjug Chem. 2004;15:174-84 pubmed..The 3'- and intrachain-tethered conjugates have been shown to cleave as their Zn(II) chelate complementary oligoribonucleotide sequences. ..
- Xiong Y, Schroeder K, Greenbaum N, Hendrickson C, Marshall A. Improved mass analysis of oligoribonucleotides by 13C, 15N double depletion and electrospray ionization FT-ICR mass spectrometry. Anal Chem. 2004;76:1804-9 pubmed..The abrupt onset and high magnitude of the monoisotopic species promise to facilitate accurate mass measurement of RNA's. ..
- Hobartner C, Rieder R, Kreutz C, Puffer B, Lang K, Polonskaia A, et al. Syntheses of RNAs with up to 100 nucleotides containing site-specific 2'-methylseleno labels for use in X-ray crystallography. J Am Chem Soc. 2005;127:12035-45 pubmed..We point out that the approach documented here has been the chemical basis for the very recent structure determination of the Diels-Alder ribozyme which represents the first novel RNA fold that has been solved via its Se-derivatives. ..
- Malathi K, Paranjape J, Ganapathi R, Silverman R. HPC1/RNASEL mediates apoptosis of prostate cancer cells treated with 2',5'-oligoadenylates, topoisomerase I inhibitors, and tumor necrosis factor-related apoptosis-inducing ligand. Cancer Res. 2004;64:9144-51 pubmed..These findings indicate that RNase L integrates and amplifies apoptotic signals generated during treatment of prostate cancer cells with 2-5A, Topo I inhibitors, and TRAIL. ..
- Chworos A, Severcan I, Koyfman A, Weinkam P, Oroudjev E, Hansma H, et al. Building programmable jigsaw puzzles with RNA. Science. 2004;306:2068-72 pubmed..It demonstrates that fully addressable materials based on RNA can be synthesized and provides insights into self-assembly processes involving large populations of RNA molecules. ..
- Küpfer P, Leumann C. The chemical stability of abasic RNA compared to abasic DNA. Nucleic Acids Res. 2007;35:58-68 pubmed..Thus abasic RNA is significantly more stable than abasic DNA. The higher stability of abasic RNA is discussed in the context of its potential biological role. ..
- Song M, Kiledjian M. 3' Terminal oligo U-tract-mediated stimulation of decapping. RNA. 2007;13:2356-65 pubmed..These data suggest that following post-transcriptional oligo uridylation of an mRNA or mRNA fragment, the U-tract has the capacity to specifically stimulate 5' end decapping to expedite mRNA decay. ..
- Oberstrass F, Auweter S, Erat M, Hargous Y, Henning A, Wenter P, et al. Structure of PTB bound to RNA: specific binding and implications for splicing regulation. Science. 2005;309:2054-7 pubmed..Thus, PTB will induce RNA looping when bound to two separated pyrimidine tracts within the same RNA. This leads to structural models for how PTB functions as an alternative-splicing repressor. ..
- Abelian A, Walsh A, Lentzen G, Aboul ela F, Gait M. Targeting the A site RNA of the Escherichia coli ribosomal 30 S subunit by 2'-O-methyl oligoribonucleotides: a quantitative equilibrium dialysis binding assay and differential effects of aminoglycoside antibiotics. Biochem J. 2004;383:201-8 pubmed..ribosomal subunits from Escherichia coli with a set of overlapping, complementary OMe (2'-O-methyl) 10-mer oligoribonucleotides. An equilibrium dialysis technique was applied to measure dissociation constants of these oligonucleotides...
- Akabayov B, Lee S, Akabayov S, Rekhi S, Zhu B, Richardson C. DNA recognition by the DNA primase of bacteriophage T7: a structure-function study of the zinc-binding domain. Biochemistry. 2009;48:1763-73 pubmed publisher..Thus the zinc in the ZBD may act as a charge modulation indicator for the surrounding sulfur atoms necessary for recognition of specific DNA sequences...
- Lan T, Putta M, Wang D, Dai M, Yu D, Kandimalla E, et al. Synthetic oligoribonucleotides-containing secondary structures act as agonists of Toll-like receptors 7 and 8. Biochem Biophys Res Commun. 2009;386:443-8 pubmed publisher..In the present study, we have designed and synthesized phosphorothioate oligoribonucleotides (ORNs) with self-complementary sequences that form duplex structures with either 3'- or 5'-overhanging ..
- Finger L, Trantirek L, Johansson C, Feigon J. Solution structures of stem-loop RNAs that bind to the two N-terminal RNA-binding domains of nucleolin. Nucleic Acids Res. 2003;31:6461-72 pubmed..These results show that a disordered NRE consensus sequence is not a prerequisite for nucleolin RBD12 binding. ..
- Mullen T, Marzluff W. Degradation of histone mRNA requires oligouridylation followed by decapping and simultaneous degradation of the mRNA both 5' to 3' and 3' to 5'. Genes Dev. 2008;22:50-65 pubmed publisher..RNAi experiments demonstrate that both the exosome and 5'-to-3' decay pathway components are required for degradation, and individual histone mRNAs are then degraded simultaneously 5' to 3' and 3' to 5'. ..
- Saneyoshi H, Seio K, Sekine M. A general method for the synthesis of 2'-O-cyanoethylated oligoribonucleotides having promising hybridization affinity for DNA and RNA and enhanced nuclease resistance. J Org Chem. 2005;70:10453-60 pubmedreaction: see text] An effective method for the synthesis of 2'-O-cyanoethylated oligoribonucleotides as a new class of 2'-O-modified RNAs was developed...
- Corn J, Pease P, Hura G, Berger J. Crosstalk between primase subunits can act to regulate primer synthesis in trans. Mol Cell. 2005;20:391-401 pubmed publisher..Our data suggest that the replisome may cooperatively use multiple primases and this conformational switch to control initiation frequency, processivity, and ultimately, Okazaki fragment synthesis...
- Heil F, Hemmi H, Hochrein H, Ampenberger F, Kirschning C, Akira S, et al. Species-specific recognition of single-stranded RNA via toll-like receptor 7 and 8. Science. 2004;303:1526-9 pubmed..These data suggest that ssRNA represents a physiological ligand for TLR7 and TLR8. ..
- Tromp J, Schürch S. Gas-phase dissociation of oligoribonucleotides and their analogs studied by electrospray ionization tandem mass spectrometry. J Am Soc Mass Spectrom. 2005;16:1262-8 pubmedb>Oligoribonucleotides (RNA) and modified oligonucleotides were subjected to low-energy collision-induced dissociation in a hybrid quadrupole time-of-flight mass spectrometer to investigate their fragmentation pathways...
- Lee S, Richardson C. Acidic residues in the nucleotide-binding site of the bacteriophage T7 DNA primase. J Biol Chem. 2005;280:26984-91 pubmed publisherDNA primases catalyze the synthesis of oligoribonucleotides to initiate lagging strand DNA synthesis during DNA replication...
- Owczarzy R, You Y, Moreira B, Manthey J, Huang L, Behlke M, et al. Effects of sodium ions on DNA duplex oligomers: improved predictions of melting temperatures. Biochemistry. 2004;43:3537-54 pubmed..The results are discussed in the context of counterion condensation theory. ..
- Mörking P, Dallagiovanna B, Foti L, Garat B, Picchi G, Umaki A, et al. TcZFP1: a CCCH zinc finger protein of Trypanosoma cruzi that binds poly-C oligoribonucleotides in vitro. Biochem Biophys Res Commun. 2004;319:169-77 pubmed..We report here the functional expression of a recombinant tcZFP1, and the relative affinity and stability of the specific complexes formed between the protein and synthetic oligoribonucleotides containing C-rich sequences.
- Küpfer P, Leumann C. Photochemically induced RNA and DNA abasic sites. Nucleosides Nucleotides Nucleic Acids. 2007;26:1177-80 pubmed..blocks were synthesized that can easily be deprotected by UV light to reveal natural abasic sites in oligoribonucleotides as well as in oligodeoxyribonucleotides...
- Christensen U. Thermodynamic and kinetic characterization of duplex formation between 2'-O, 4'-C-methylene-modified oligoribonucleotides, DNA and RNA. Biosci Rep. 2007;27:327-33 pubmed..Introduction of a few LNA's thus may be a better strategy, than using full length LNA's to obtain an oligonucleotide that markedly increases the strength of duplexes formed with the complementary DNA and RNA. ..
- Filichev V, Vester B, Hansen L, Abdel Aal M, Babu B, Wengel J, et al. Enhanced inhibition of transcription start by targeting with 2'-OMe pentaribonucleotides comprising locked nucleic acids and intercalating nucleic acids. Chembiochem. 2005;6:1181-4 pubmed
- Lutay A, Zenkova M, Vlassov V. Nonenzymatic recombination of RNA: possible mechanism for the formation of novel sequences. Chem Biodivers. 2007;4:762-7 pubmed
- Rao H, Sawant A, Tanpure A, Srivatsan S. Posttranscriptional chemical functionalization of azide-modified oligoribonucleotides by bioorthogonal click and Staudinger reactions. Chem Commun (Camb). 2012;48:498-500 pubmed publisher..This postsynthetic labeling protocol is robust and modular, and offers an alternative access to RNA labeled with biophysical probes. ..
- Legiewicz M, Yarus M. A more complex isoleucine aptamer with a cognate triplet. J Biol Chem. 2005;280:19815-22 pubmed..Among the important nucleotides is a conserved isoleucine anticodon, supporting the escaped triplet theory, which posits a stereochemical genetic code originating in RNA amino acid binding sites. ..
- Kato Y, Minakawa N, Komatsu Y, Kamiya H, Ogawa N, Harashima H, et al. New NTP analogs: the synthesis of 4'-thioUTP and 4'-thioCTP and their utility for SELEX. Nucleic Acids Res. 2005;33:2942-51 pubmed..With these successful results in hand, we attempted the selection of thioRNA aptamers to human alpha-thrombin using thioUTP and thioCTP, and found a thioRNA aptamer with high binding affinity (K(d) = 4.7 nM). ..
- Hobartner C, Micura R. Chemical synthesis of selenium-modified oligoribonucleotides and their enzymatic ligation leading to an U6 SnRNA stem-loop segment. J Am Chem Soc. 2004;126:1141-9 pubmed..This includes the synthesis of a novel 2'-Se-methylcytidine phosphoramidite 11 and its incorporation into oligoribonucleotides by solid-phase synthesis...
- Lan T, Dai M, Wang D, Zhu F, Kandimalla E, Agrawal S. Toll-like receptor 7 selective synthetic oligoribonucleotide agonists: synthesis and structure-activity relationship studies. J Med Chem. 2009;52:6871-9 pubmed publisher..In conclusion, we have designed and synthesized novel SIMRA compounds that selectively act as agonists of TLR7. ..
- Huang T, Kharlamova A, Liu J, McLuckey S. Ion trap collision-induced dissociation of multiply deprotonated RNA: c/y-ions versus (a-B)/w-ions. J Am Soc Mass Spectrom. 2008;19:1832-40 pubmed publisher..Therefore, base loss from low charge state oligonucleotide anions, in which protonation of one or more bases via intramolecular proton transfer can occur, may also be stabilized in RNA anions relative to corresponding DNA anions. ..
- Thakur C, Xu Z, Wang Z, Novince Z, Silverman R. A convenient and sensitive fluorescence resonance energy transfer assay for RNase L and 2',5' oligoadenylates. Methods Mol Med. 2005;116:103-13 pubmed..The RNA probe used in the FRET assay was designed based on a region of respiratory syncytial genomic RNA. We demonstrate the utility of our FRET assay with several novel biostable analogs of 2-5A. ..
- Schlee M, Roth A, Hornung V, Hagmann C, Wimmenauer V, Barchet W, et al. Recognition of 5' triphosphate by RIG-I helicase requires short blunt double-stranded RNA as contained in panhandle of negative-strand virus. Immunity. 2009;31:25-34 pubmed publisher..for 5' triphosphate oligoribonucleotide synthesis and found that synthetic single-stranded 5' triphosphate oligoribonucleotides were unable to bind and activate RIG-I...
- Kierzek E, Ciesielska A, Pasternak K, Mathews D, Turner D, Kierzek R. The influence of locked nucleic acid residues on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexes. Nucleic Acids Res. 2005;33:5082-93 pubmed..Internal mismatches with LNA nucleotides significantly destabilize duplexes with RNA. ..
- Sekine M, Oeda Y, Iijima Y, Taguchi H, Ohkubo A, Seio K. Synthesis and hybridization properties of 2'-O-methylated oligoribonucleotides incorporating 2'-O-naphthyluridines. Org Biomol Chem. 2011;9:210-8 pubmed publisher..building blocks, these 2'-O-aryluridine derivatives were incorporated into 2'-O-methylated oligoribonucleotides. Incorporation of five 2'-O-(2-naphthyl)uridines into a 2'-O-methylated RNA sense strand significantly ..
- Arzumanov A, Stetsenko D, Malakhov A, Reichelt S, Sørensen M, Babu B, et al. A structure-activity study of the inhibition of HIV-1 Tat-dependent trans-activation by mixmer 2'-O-methyl oligoribonucleotides containing locked nucleic acid (LNA), alpha-L-LNA, or 2'-thio-LNA residues. Oligonucleotides. 2003;13:435-53 pubmed..Thus, OMe/LNA mixmers are powerful reagents for use as steric block inhibitors of gene expression regulated by protein-RNA interactions within HeLa cell nuclei. ..
- Hölzl G, Oberacher H, Pitsch S, Stutz A, Huber C. Analysis of biological and synthetic ribonucleic acids by liquid chromatography-mass spectrometry using monolithic capillary columns. Anal Chem. 2005;77:673-80 pubmed..The method was applied to the analysis of synthetic oligoribonucleotides, transfer RNAs, and ribosomal RNA...
- Puffer B, Moroder H, Aigner M, Micura R. 2'-Methylseleno-modified oligoribonucleotides for X-ray crystallography synthesized by the ACE RNA solid-phase approach. Nucleic Acids Res. 2008;36:970-83 pubmed..We additionally report on their incorporation into oligoribonucleotides including deprotection and purification...
- Li F, Pallan P, Maier M, Rajeev K, Mathieu S, Kreutz C, et al. Crystal structure, stability and in vitro RNAi activity of oligoribonucleotides containing the ribo-difluorotoluyl nucleotide: insights into substrate requirements by the human RISC Ago2 enzyme. Nucleic Acids Res. 2007;35:6424-38 pubmed..Beyond potential improvements in the efficacy of oligoribonucleotides, chemical modification may also provide insight into the mechanism of mRNA downregulation mediated by the ..
- Slepenkov S, Darzynkiewicz E, Rhoads R. Stopped-flow kinetic analysis of eIF4E and phosphorylated eIF4E binding to cap analogs and capped oligoribonucleotides: evidence for a one-step binding mechanism. J Biol Chem. 2006;281:14927-38 pubmed..investigated the interaction of both eIF4E and phosphorylated eIF4E (eIF4E(P)) with cap analogs and capped oligoribonucleotides by stopped-flow kinetics...
- Küpfer P, Leumann C. Synthesis, base pairing properties and trans-lesion synthesis by reverse transcriptases of oligoribonucleotides containing the oxidatively damaged base 5-hydroxycytidine. Nucleic Acids Res. 2011;39:9422-32 pubmed publisher..The properties of this RNA damage is discussed in the context of its putative biological function. ..
- Hannoush R, Damha M. Remarkable stability of hairpins containing 2',5'-linked RNA loops. J Am Chem Soc. 2001;123:12368-74 pubmed..Furthermore, they may be particularly useful as structural motifs for synthetic ribozymes and nucleic acid "aptamers". ..
- Gordon P, Piccirilli J. Metal ion coordination by the AGC triad in domain 5 contributes to group II intron catalysis. Nat Struct Biol. 2001;8:893-8 pubmed
- Adamiak D, Rypniewski W, Milecki J, Adamiak R. The 1.19 A X-ray structure of 2'-O-Me(CGCGCG)(2) duplex shows dehydrated RNA with 2-methyl-2,4-pentanediol in the minor groove. Nucleic Acids Res. 2001;29:4144-53 pubmed..Intrusion of MPD into the minor groove of 2'-O-Me(CGCGCG)(2) is discussed with respect to RNA dehydration, a prerequisite of Z-RNA formation. ..
- Kaukinen U, Lyytikäinen S, Mikkola S, Lonnberg H. The reactivity of phosphodiester bonds within linear single-stranded oligoribonucleotides is strongly dependent on the base sequence. Nucleic Acids Res. 2002;30:468-74 pubmed..Duplex formation at the 3'- and/or 5'-side of the scissile bond was also studied and observed to be strongly rate retarding. The origin of the high sensitivity of phosphodiester bonds to the molecular environment is discussed. ..
- Vickers T, Wyatt J, Freier S. Effects of RNA secondary structure on cellular antisense activity. Nucleic Acids Res. 2000;28:1340-7 pubmed..We also show that potency of oligonucleotides can be improved by altering chemistry to increase affinity for the mRNA target even in a region that is highly structured. ..