LNA (Locked Nucleic Acids): Synthesis of the adenine, cytosine, guanine, 5-methylcytosine, thymine and uracil bicyclonucleoside monomers, oligomerisation, and unprecedented nucleic acid recognition

Koshkin, Alexei A.; Singh, Sanjay K.; Nielsen, P. H.; Rajwanshi, Vivek K.; Kumar, Ravindra; Meldgaard, Michael; Olsen, Carl Erik; Wengel, Jesper

doi:10.1016/s0040-4020(98)00094-5

Cited by 946 publications

(849 citation statements)

References 29 publications

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“…But in general, it would be necessary to solve the bacterial-cell-penetration problem before such materials would be worth exploring as potential antibiotics. Nevertheless, significant improvements may be possible in levels of inhibition of in vitro translation by exploration of the incorporation of tighter-binding analogues that maintain an RNA-like conformation, such as LNAs (locked nucleic acids) [43,44]. This might allow even stronger binding to the A site on ribosomes or ribosomal subunits.…”

Section: Discussionmentioning

confidence: 99%

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

Abelian

Walsh

Lentzen

et al. 2004

Biochemical Journal

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The bacterial ribosome comprises 30 S and 50 S ribonucleoprotein subunits, contains a number of binding sites for known antibiotics and is an attractive target for selection of novel antibacterial agents. On the 30 S subunit, for example, the A site (aminoacyl site) close to the 3′-end of 16 S rRNA is highly important in the decoding process. Binding by some aminoglycoside antibiotics to the A site leads to erroneous protein synthesis and is lethal for bacteria. We targeted the A site on purified 30 S 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. We show that there is a single high-affinity region, spanning from A1493 to C1510 (Kd, 29–130 nM), flanked by two lower-affinity regions, within a span from U1485 to G1516 (Kd, 310–4300 nM). Unexpectedly, addition of the aminoglycoside antibiotic paromomycin (but not hygromycin B) caused a dose-dependent increase of up to 7.5-fold in the binding of the highest affinity 10-mer 1493 to 30 S subunits. Oligonucleotides containing residues complementary to A1492 and/or A1493 showed particularly marked stimulation of binding by paromomycin. The results are consistent with high-resolution structures of antibiotic binding to the A site and with greater accessibility of residues of A1492 and A1493 upon paromomycin binding. 10-mer 1493 binding is thus a probe of the conformational switch to the ‘closed’ conformation triggered by paromomycin that is implicated in the discrimination by 30 S subunits of cognate from non-cognate tRNA and the translational misreading caused by paromomycin. Finally, we show that OMe oligonucleotides targeted to the A site are moderately good inhibitors of in vitro translation and that there is a limited correlation of inhibition activity with binding strength to the A site.

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Section: Discussionmentioning

confidence: 99%

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

Abelian

Walsh

Lentzen

et al. 2004

Biochemical Journal

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“…The detection of microorganisms by FISH has significantly changed with the introduction of several types of synthetic oligonucleotides that possess a higher capacity of discrimination and affinity towards complementary sequences (Buchardt et al 1993;Obika et al 1997;Koshkin et al 1998;Majlessi et al 1998;Guimaraes et al 2007;Guga and Koziolkiewicz 2011). Therefore, it is very important to discuss which type of nucleic acid mimics is more suitable for each specific situation, such as the recognition of mismatches.…”

Section: Discussionmentioning

confidence: 99%

Mismatch discrimination in fluorescent in situ hybridization using different types of nucleic acids

Fontenete

Barros

Madureira

et al. 2015

Appl Microbiol Biotechnol

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In the past few years, several researchers have focused their attention on nucleic acid mimics due to the increasing necessity of developing a more robust recognition of DNA or RNA sequences. Fluorescence in situ hybridization (FISH) is an example of a method where the use of these novel nucleic acid monomers might be crucial to the success of the analysis. To achieve the expected accuracy in detection, FISH probes should have high binding affinity towards their complementary strands and discriminate effectively the noncomplementary strands. In this study, we investigate the effect of different chemical modifications in fluorescent probes on their ability to successfully detect the complementary target and discriminate the mismatched base pairs by FISH. To our knowledge, this paper presents the first study where this analysis is per-formed with different types of FISH probes directly in biological targets, Helicobacter pylori and Helicobacter acinonychis. This is also the first study where unlocked nucleic acids (UNA) were used as chemistry modification in oligonucleotides for FISH methodologies. The effectiveness in detecting the specific target and in mismatch discrimination appears to be improved using locked nucleic acids 2 (LNA)/2′-O-methyl RNA (2′OMe) or peptide nucleic acid (PNA) in comparison to LNA/DNA, LNA/UNA, or DNA probes. Further, the use of LNA modifications together with 2′OMe monomers allowed the use of shorter fluorescent probes and increased the range of hybridization temperatures at which FISH would work.

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“…1) contains a ribose ring which is locked by a O2'-C4'-methylene linkage, imposing conformational restriction to adopt an N-type sugar puckering. [2][3][4][5]10 Structural investigation of LNA oligonucleotides by NMR spectroscopy revealed their similarities with natural nucleic acid duplexes, and confirmed the RNA mimicking structures adopted by LNA. 11,12 LNA offers key properties needed for successful therapeutic exploitation of oligonucleotides, including (1) unprecedented binding affinity towards RNA (and DNA), (2) excellent base pairing specificity, (3) high bio-stability (resistance towards nucleolytic degradation, (4) low toxicity (at least for many LNA oligonucleotides) in animals and (5) convenient chemistry for manufacturing and modification.…”

Section: Introductionmentioning

confidence: 69%

“…Among the numerous modifications known, LNA has shown broad usefulness within chemical biology. [2][3][4][5][6][7][8][9] LNA: Structural Features and Key Properties LNA ( Fig. 1) contains a ribose ring which is locked by a O2'-C4'-methylene linkage, imposing conformational restriction to adopt an N-type sugar puckering.…”

Section: Introductionmentioning

confidence: 99%

Locked nucleic acid as a novel class of therapeutic agents

Veedu¹,

Wengel²

2009

RNA Biology

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108

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LNA (Locked Nucleic Acids): Synthesis of the adenine, cytosine, guanine, 5-methylcytosine, thymine and uracil bicyclonucleoside monomers, oligomerisation, and unprecedented nucleic acid recognition

Cited by 946 publications

References 29 publications

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

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

Mismatch discrimination in fluorescent in situ hybridization using different types of nucleic acids

Locked nucleic acid as a novel class of therapeutic agents

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