Unlocked Nucleic Acids with a Pyrene‐Modified Uracil: Synthesis, Hybridization Studies, Fluorescent Properties and i‐Motif Stability

Perlíková, Pavla; Karlsen, Kasper K.; Pedersen, Erik B.; Wengel, Jesper

doi:10.1002/cbic.201300567

Cited by 22 publications

(18 citation statements)

References 49 publications

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“…It was shown that UNA monomers modulate i-motif stability in a position-depending manner whereas no structural changes were observed in any case. In addition, 5-(pyren-1-yl)uracilyl UNA monomers were found to destabilize an i-motif structure at pH 5.2, both under molecular crowding and non-crowding conditions 125 .…”

Section: Effects Of Chemical Modifications On the Stabilitymentioning

confidence: 98%

Fundamental aspects of the nucleic acid i-motif structures

et al. 2014

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Section: Effects Of Chemical Modifications On the Stabilitymentioning

confidence: 98%

Fundamental aspects of the nucleic acid i-motif structures

et al. 2014

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“…For example, the insertion of pyrene-attached 2′-deoxyadenosine nucleotide ( Py A) at 5′-end led to prominent increase of T m (+11.4°C) at pH 4.0 that was caused by the stacking interaction between Py A and the terminal hemiprotonated C–C base pair ( 38 ). However other pyrene-containing non-nucleotide inserts, uracil UNA monomer ( 39 ) and TINA ( 40 ), within the loop region were shown to destabilize iM. In turn, different porphyrin-containing nucleotide and non-nucleotide derivatives were placed into the fragment of the sequence that did not participate in iM core formation, and they provoked strong stabilization (average T m was 53°C, whereas T m of the unmodified sequence was <25°C) at pH 5.0 owing to porphyrin–porphyrin interactions ( 41 ).…”

Section: Introductionmentioning

confidence: 99%

i-Clamp phenoxazine for the fine tuning of DNA i-motif stability

Цветков

Zatsepin

Belyaev

et al. 2018

Nucleic Acids Research

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Non-canonical DNA structures are widely used for regulation of gene expression, in DNA nanotechnology and for the development of new DNA-based sensors. I-motifs (iMs) are two intercalated parallel duplexes that are held together by hemiprotonated C-C base pairs. Previously, iMs were used as an accurate sensor for intracellular pH measurements. However, iM stability is moderate, which in turn limits its in vivo applications. Here, we report the rational design of a new substituted phenoxazine 2′-deoxynucleotide (i-clamp) for iM stabilization. This residue contains a C8-aminopropyl tether that interacts with the phosphate group within the neighboring chain without compromising base pairing. We studied the influence of i-clamp on pH-dependent stability for intra- and intermolecular iM structures and found the optimal positions for modification. Two i-clamps on opposite strands provide thermal stabilization up to 10–11°C at a pH of 5.8. Thus, we developed a new modification that shows significant iM-stabilizing effect both at strongly and mildly acidic pH and increases iM transition pH values. i-Clamp can be used for tuning iM-based pH probes or assembling extra stable iM structures for various applications.

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“…The thermal denaturation studies were performed following published protocols (Christensen et al 2001;Perlikova et al 2014). Melting curves of fully complementary and of one-mismatchcontaining oligonucleotide duplexes were recorded on a PerkinElmer LAMBDA 35 UV/Vis spectrometer equipment with a PTP 6 (Peltier Temperature Programmer) element (Massachusetts, USA).…”

Section: Thermal Denaturation Studiesmentioning

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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Unlocked Nucleic Acids with a Pyrene‐Modified Uracil: Synthesis, Hybridization Studies, Fluorescent Properties and i‐Motif Stability

Cited by 22 publications

References 49 publications

Fundamental aspects of the nucleic acid i-motif structures

Fundamental aspects of the nucleic acid i-motif structures

i-Clamp phenoxazine for the fine tuning of DNA i-motif stability

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

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