scholarly journals Oligonucleotides containing a piperazino-modified 2′-amino-LNA monomer exhibit very high duplex stability and remarkable nuclease resistance

2015 ◽  
Vol 51 (19) ◽  
pp. 4024-4027 ◽  
Author(s):  
Chenguang Lou ◽  
Birte Vester ◽  
Jesper Wengel
Keyword(s):  
Complementary Dna ◽  
Dna And Rna ◽  
Duplex Stability ◽  
Nuclease Resistance ◽  
Exonucleolytic Degradation ◽  
Very High

Incorporation of a novel piperazino-modified 2′-amino-LNA monomer (PipLNA-T) into oligonucleotides leads to a pronounced affinity increase against complementary DNA and RNA and a strong stabilising effect against 3′-exonucleolytic degradation.

scholarly journals Fundamental aspects of the interaction of propidium diiodide with nuclei acids studied in a model system of polyacrylamide films.

1981 ◽  
Vol 29 (8) ◽  
pp. 929-936 ◽  
Author(s):  
J Tas ◽  
G Westerneng
Keyword(s):  
Staining Method ◽  
Model System ◽  
Appreciable Amount ◽  
Optimal Conditions ◽  
Binding Ability ◽  
Qualitative And Quantitative ◽  
Dna And Rna ◽  
Linear Relationships ◽  
The Stability ◽  
Very High

Qualitative and quantitative aspects of the fluorescent propidium diiodide (PI) staining method have been investigated with model films of polyacrylamide gel incorporated with DNA, RNA, and other macromolecular compounds. PI was found to bind specifically to DNA and RNA, most probably by intercalation into double-stranded regions. Proteins, glycogen, and glycosaminoglycans did not show fluorescence after PI staining. Optimal conditions for dye binding and differentiation have been defined. The stability of nucleic acid-PI complexes, as present in model films, was shown to be very high in distilled water, while dissociation rapidly occurred in ionic media. Linear relationships were found between the fluorescence intensity of bound PI and both the thickness of the model films and the amount of DNA or RNA incorporated. The presence of histone protein bound ionically to DNA did not influence the fluorescent PI binding ability in any appreciable amount.

Synthesis and thermal stabilities of oligonucleotides containing 2′-O,4′-C-methylene bridged nucleic acid with a phenoxazine base

2017 ◽  
Vol 15 (38) ◽  
pp. 8145-8152 ◽  
Author(s):  
Yuki Kishimoto ◽  
Akane Fujii ◽  
Osamu Nakagawa ◽  
Tetsuya Nagata ◽  
Takanori Yokota ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Binding Affinities ◽  
Thermal Stabilities ◽  
Complementary Dna ◽  
Dna And Rna

BNAP-modified ODNs showed higher binding affinities toward complementary DNA and RNA as compared to ODNs bearing 2′,4′-BNA/LNA with 5-methylcytosine or 2′-deoxyribonucleoside with phenoxazine.

Thermodynamic and Kinetic Characterization of Duplex Formation between 2′-O, 4′-C-Methylene-modified Oligoribonucleotides, DNA and RNA

2007 ◽  
Vol 27 (6) ◽  
pp. 327-333 ◽  
Author(s):  
Ulla Christensen
Keyword(s):  
Nucleic Acid ◽  
Full Length ◽  
Locked Nucleic Acid ◽  
Complementary Dna ◽  
High Affinity ◽  
Thermodynamics And Kinetics ◽  
Dna And Rna ◽  
Reaction Thermodynamics ◽  
Duplex Formation

2′-O,4′-C-methylene-linked ribonucleotide derivatives, named LNA (locked nucleic acid) and BNA (bridged nucleic acid) are nucleic acid analogoues that have shown high-affinity recognition of DNA and RNA, and the employment of LNA oligomers for antisense activity, gene regulation and nucleic acid diagnostics seems promising. Here we show kinetic and thermodynamic results on the interaction of a series of 10 bases long LNA–DNA mixmers, gabmers as well as full length LNA's with the complementary DNA, RNA and LNA oligonucleotides in the presence and absence of 10 mM Mg2+- ions. Our results show no significant differences in the reaction thermodynamics and kinetics between the LNA species, only a tendency to stronger duplex formation with the gabmer and mixmer. 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.

Lipophilic 2′-O-Acetal Ester RNAs: Synthesis, Thermal Duplex Stability, Nuclease Resistance, Cellular Uptake, and siRNA Activity after Spontaneous Naked Delivery

ChemBioChem ◽  
2016 ◽  
Vol 17 (21) ◽  
pp. 2054-2062 ◽  
Author(s):  
Annabelle Biscans ◽  
Jean-Rémi Bertrand ◽  
Josephine Dubois ◽  
Jacqueline Rüger ◽  
Jean-Jacques Vasseur ◽  
...  
Keyword(s):  
Cellular Uptake ◽  
Duplex Stability ◽  
Nuclease Resistance

Hybridization properties of oligoarabinonucleotides

1994 ◽  
Vol 72 (3) ◽  
pp. 909-918 ◽  
Author(s):  
Paul Apostolos Giannaris ◽  
Masad José Damha
Keyword(s):  
Solid Phase ◽  
Stable Complex ◽  
Mobility Shift ◽  
Complementary Dna ◽  
Melting Temperatures ◽  
Snake Venom Phosphodiesterase ◽  
Dna And Rna ◽  
Negative Effect ◽  
Gel Mobility Shift ◽  
Rna Complexes

3′-Phosphoramidite derivatives of arabinocytidine, arabinoadenosine, and arabinouridine were prepared and used for the solid-phase synthesis of oligoarabinonucleotides (arabinonucleic acid, or ANA). Thermal denaturation analysis and gel mobility shift assays were used to investigate the interaction between ANA and complementary DNA and RNA. In general, the ANA/DNA and ANA/RNA complexes exhibited melting temperatures comparable to those of the corresponding DNA/DNA and DNA/RNA complexes. Thus the inversion of stereochemistry at the C2′ of ribonucleotides does not have a negative effect on interaction with natural sequences. In fact, in complexes with poly dT, oligoarabinoadenylates displayed greater hybridization affinity than oligoriboadenylates. In summary, we observed that (i) ara(Ap)7A interacted favourably with poly rU and poly dT, (ii) ara(Cp)7C formed a stable complex with poly rG; (iii) ara(Up)7U did not bind with complementary poly rA; and (iv) the mixed oligoarabinonucleotide ara(UCU UCC CUC UCC C) formed complexes with complementary DNA and RNA. Hybridization was observed between the phosphorothioatelinked arabinoadenylate ara(Aps)7A and poly rU and poly dT; however, this binding was weaker than that between the phosphorothioate-linked deoxyriboadenylate d(Aps)7A and poly rU and poly dT. Both ara(Aps)7A and its deoxy analog d(Aps)7A displayed significant and similar resistance to digestion by snake venom phosphodiesterase.

scholarly journals Studies on the interactions of Ag(i) with DNA and their implication on the DNA-templated synthesis of silver nanoclusters and on the interaction with complementary DNA and RNA sequences

RSC Advances ◽  
2021 ◽  
Vol 11 (15) ◽  
pp. 9029-9042
Author(s):  
Alejandra de la Hoz ◽  
Alba Navarro ◽  
Anna Aviñó ◽  
Ramon Eritja ◽  
Raimundo Gargallo
Keyword(s):  
Secondary Structure ◽  
Dna Sequence ◽  
Analytical Signal ◽  
Silver Nanoclusters ◽  
Fluorescent Properties ◽  
Rna Sequences ◽  
Complementary Dna ◽  
Templated Synthesis ◽  
Dna And Rna ◽  
Hybridization Reaction

Variables affecting the fluorescent properties of DNA-stabilized silver nanoclusters are studied. The secondary structure of the AgNC-stabilizing DNA sequence dramatically affects the analytical signal behind the hybridization reaction.

scholarly journals Highly specific enrichment of rare nucleic acids using Thermus thermophilus Argonaute

2018 ◽  
Author(s):  
Jinzhao Song ◽  
Jorrit W. Hegge ◽  
Michael G. Mauk ◽  
Neha Bhagwat ◽  
Jacob E. Till ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Thermus Thermophilus ◽  
Wild Type ◽  
Single Nucleotide ◽  
Blood Samples ◽  
Complementary Dna ◽  
Enzymatic Amplification ◽  
Dna And Rna ◽  
Rare Alleles

ABSTRACTCharacterization of disease-associated, cell-free nucleic acids (liquid biopsy) provides a powerful, minimally-invasive means for early detection, genotyping, and personalized therapy; but is challenged by alleles of interest differing by single nucleotide from and residing among large abundance of wild-type alleles. We describe a new multiplexed enrichment assay, dubbed NAVIGATER, that utilizes short nucleic acid-guided endonucleases Argonaute (Ago), derived from the bacterium Thermus thermophilus (TtAgo), to specifically cleave complementary DNA and RNA while sparing alleles having single nucleotide mismatches with the guides. NAVIGATER greatly increases the fractions of rare alleles of interest in samples and enhances sensitivity of downstream procedures such ddPCR, sequencing, and clamped enzymatic amplification. We demonstrate 60-fold enrichment of KRAS G12D in blood samples from pancreatic cancer patients and detection of KRAS, EGFR, and BRAF mutants with XNA-PCR at 0.01% fraction.

Triazole- and Tetrazole-Bridged Nucleic Acids: Synthesis, Duplex Stability, Nuclease Resistance, and in Vitro and in Vivo Antisense Potency

2016 ◽  
Vol 82 (1) ◽  
pp. 12-24 ◽  
Author(s):  
Yasunori Mitsuoka ◽  
Tsuyoshi Yamamoto ◽  
Akira Kugimiya ◽  
Reiko Waki ◽  
Fumito Wada ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Duplex Stability ◽  
Nuclease Resistance
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