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Locked Nucleic Acid (locked + nucleic_acid)
Selected AbstractsSequence-specific inhibition of RNA polymerase III-dependent transcription using Zorro locked nucleic acid (LNA)THE JOURNAL OF GENE MEDICINE, Issue 1 2008Rongbin Ge Abstract Background RNA polymerase III (pol III)-dependent transcripts are involved in many fundamental activities in a cell, such as splicing and protein synthesis. They also regulate cell growth and influence tumor formation. During recent years vector-based systems for expression of short hairpin (sh) RNA under the control of a pol III promoter have been developed as gene-based medicines. Therefore, there is an increasing interest in means to regulate pol III-dependent transcription. Recently, we have developed a novel anti-gene molecule ,Zorro LNA (Locked Nucleic Acid)', which simultaneously hybridizes to both strands of super-coiled DNA and potently inhibits RNA polymerase II-derived transcription. We have now applied Zorro LNA in an attempt to also control U6 promoter-driven expression of shRNA. Methods In this study, we constructed pshluc and pshluc2BS plasmids, in which U6 promoter-driven small hairpin RNA specific for luciferase gene (shluc) was without or with Zorro LNA binding sites, respectively. After hybridization of Zorro LNA to pshluc2BS, the LNA-bound plasmid was cotransfected with pEGFPluc into mammalian cells and into a mouse model. In cellular experiments, cotransfection of unhybridized pshluc2BS, Zorro LNA and pEGFPluc was also performed. Results The results showed that the Zorro LNA construct efficiently inhibited pol III-dependent transcription as an anti-gene reagent in a cellular context, including in vivo in a mouse model. Conclusions Thus, this new form of gene silencer ,Zorro LNA' could potentially serve as a versatile regulator of pol III-dependent transcription, including various forms of shRNAs. Copyright © 2007 John Wiley & Sons, Ltd. [source] Methylphosphonate LNA: A Locked Nucleic Acid with a Methylphosphonate Linkage.CHEMINFORM, Issue 17 2003Anne Lauritsen Abstract For Abstract see ChemInform Abstract in Full Text. [source] ChemInform Abstract: The Adenine Derivative of ,-L-LNA (,-L-ribo Configured Locked Nucleic Acid): Synthesis and High-Affinity Hybridization Towards DNA, RNA, LNA and ,-L-LNA Complementary Sequences.CHEMINFORM, Issue 48 2001Anders E. Haakansson Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source] Energetic aspects of locked nucleic acids quadruplex association and dissociationBIOPOLYMERS, Issue 6 2006Luigi Petraccone Abstract The design of modified nucleic acid aptamers is improved by considering thermodynamics and kinetics of their association/dissociation processes. Locked Nucleic Acids (LNA) is a promising class of nucleic acid analogs. In this work the thermodynamic and kinetic properties of a LNA quadruplex formed by the TGGGT sequence, containing only conformationally restricted LNA residues, are reported and compared to those of 2,-OMe-RNA (O-RNA) and DNA quadruplexes. The thermodynamic analysis indicates that the sugar-modified quadruplexes (LNA and O-RNA) are stabilized by entropic effects. The kinetic analysis shows that LNA and O-RNA quadruplexes are characterized by a slower dissociation and a faster association with respect to DNA quadruplex. Interestingly, the LNA quadruplex formation process shows a second-order kinetics with respect to single strand concentration and has a negative activation energy. To explain these data, a mechanism for tetramer formation with two intermediate states was proposed. © 2006 Wiley Periodicals, Inc. Biopolymers 83: 584,594, 2006 This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Crystallization and preliminary X-ray diffraction data of an LNA 7-mer duplex derived from a ricin aptamerACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 9 2009Charlotte Förster Locked nucleic acids (LNAs) are modified nucleic acids which contain a modified sugar such as , - d -2,- O,4,- C methylene-bridged ribofuranose or other sugar derivatives in LNA analogues. The ,- d -2,- O,4,- C methylene ribofuranose LNAs in particular possess high stability and melting temperatures, which makes them of interest for stabilizing the structure of different nucleic acids. Aptamers, which are DNAs or RNAs targeted against specific ligands, are candidates for substitution with LNAs in order to increase their stability. A 7-mer helix derived from the terminal part of an aptamer that was targeted against ricin was chosen. The ricin aptamer originally consisted of natural RNA building blocks and showed high affinity in ricin binding. For future stabilization of the aptamer, the terminal helix has been constructed as an `all-locked' LNA and was successfully crystallized in order to investigate its structural properties. Optimization of crystal growth succeeded by the use of different metal salts as additives, such as CuCl2, MgCl2, MnCl2, CaCl2, CoCl2 and ZnSO4. Preliminary X-ray diffraction data were collected and processed to 2.8,Å resolution. The LNA crystallized in space group P65, with unit-cell parameters a = 50.11, b = 50.11, c = 40.72,Å. The crystals contained one LNA helix per asymmetric unit with a Matthews coefficient of 3.17,Å3,Da,1, which implies a solvent content of 70.15%. [source] Ultraviolet resonance Raman spectroscopy of locked single-stranded oligo(dA) reveals conformational implications of the locked ribose in LNAJOURNAL OF RAMAN SPECTROSCOPY, Issue 9 2009Stanislav O. Konorov Abstract We report here the first UV resonance Raman spectroscopic (UVRRS) study on locked nucleic acid (LNA) oligomers. Locking a base in nucleic acid (NA) oligomers produces a conformational change in the glycosyl bond between backbone and base. We present evidence of this change in LNAs when compared to their natural analogs using UVRRS. Wavenumber downshifts and peak amplitude increases, especially of the ,1481 cm,1 peak that is a spectral marker for part of the glycosyl bond, correlate with the fraction of locked bases when single-stranded oligomers incorporating up to three locked bases were examined. By varying the position of the locked base within a fixed length sequence, we conclude that one, or at most two bases, on either side of the lock is affected. We further conclude from these data, and previously published reports, that the conformation of LNA is determined by imidazole,imidazole and pyrimidine,pyrimidine repulsion and imidazole,pyrimidine attraction in contrast to dispersion attraction-dependent aggregation in the B conformation of DNA. Copyright © 2009 John Wiley & Sons, Ltd. [source] Highly Fluorescent Conjugated Pyrenes in Nucleic Acid Probes: (Phenylethynyl)pyrenecarbonyl-Functionalized Locked Nucleic AcidsCHEMISTRY - A EUROPEAN JOURNAL, Issue 35 2008Irina Abstract In recent years, fluorescently labeled oligonucleotides have become a widely used tool in diagnostics, DNA sequencing, and nanotechnology. The recently developed (phenylethynyl)pyrenes are attractive dyes for nucleic acid labeling, with the advantages of long-wave emission relative to the parent pyrene, high fluorescence quantum yields, and the ability to form excimers. Herein, the synthesis of six (phenylethynyl)pyrene-functionalized locked nucleic acid (LNA) monomers M1,M6 and their incorporation into DNA oligomers is described. Multilabeled duplexes display higher thermal stabilities than singly modified analogues. An increase in the number of phenylethynyl substituents attached to the pyrene results in decreased binding affinity towards complementary DNA and RNA and remarkable bathochromic shifts of absorption/emission maxima relative to the parent pyrene fluorochrome. This bathochromic shift leads to the bright fluorescence colors of the probes, which differ drastically from the blue emission of unsubstituted pyrene. The formation of intra- and interstrand excimers was observed for duplexes that have monomers M1,M6 in both complementary strands and in numerous single-stranded probes. If more phenylethynyl groups are inserted, the detected excimer signals become more intense. In addition, (phenylethynyl)pyrenecarbonyl,LNA monomers M4, M5, and M6 proved highly useful for the detection of single mismatches in DNA/RNA targets. [source] Crystallization and X-ray diffraction analysis of an `all-locked' nucleic acid duplex derived from a tRNASer microhelixACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2009Katja Behling Modified nucleic acids are of great interest with respect to their nuclease resistance and enhanced thermostability. In therapeutical and diagnostic applications, such molecules can substitute for labile natural nucleic acids that are targeted against particular diseases or applied in gene therapy. The so-called `locked nucleic acids' contain modified sugar moieties such as 2,- O,4,- C -methylene-bridged ,- d -ribofuranose and are known to be very stable nucleic acid derivatives. The structure of locked nucleic acids in single or multiple LNA-substituted natural nucleic acids and in LNA,DNA or LNA,RNA heteroduplexes has been well investigated, but the X-ray structure of an `all-locked' nucleic acid double helix has not been described to date. Here, the crystallization and X-ray diffraction data analysis of an `all-locked' nucleic acid helix, which was designed as an LNA originating from a tRNASer microhelix RNA structure, is presented. The crystals belonged to space group C2, with unit-cell parameters a = 77.91, b = 40.74, c = 30.06,Å, , = 91.02°. A high-resolution and a low-resolution data set were recorded, with the high-resolution data showing diffraction to 1.9,Å resolution. The crystals contained two double helices per asymmetric unit, with a Matthews coefficient of 2.48,Å3,Da,1 and a solvent content of 66.49% for the merged data. [source] | ||||||||||