scholarly journals Mismatch discrimination of lipidated DNA and LNA-probes (LiNAs) in hybridization-controlled liposome assembly

2016 ◽  
Vol 14 (29) ◽  
pp. 6985-6995 ◽  
Author(s):  
Ulla Jakobsen ◽  
Stefan Vogel
Keyword(s):  
Dna And Rna ◽  
Rna Targets ◽  
Mismatch Discrimination

A comprehensive mismatch discrimination study of lipidated DNA and LNA-probes (LiNAs) in hybridization-controlled liposome assembly is presented and evaluated for different DNA and RNA targets.

2′-N-(Pyren-1-yl)acetyl-2′-Amino-α-L-LNA: Synthesis and Detection of Single Nucleotide Mismatches in DNA and RNA Targets

ChemBioChem ◽  
2007 ◽  
Vol 8 (10) ◽  
pp. 1122-1125 ◽  
Author(s):  
T. Santhosh Kumar ◽  
Jesper Wengel ◽  
Patrick J. Hrdlicka
Keyword(s):  
Single Nucleotide ◽  
Dna And Rna ◽  
Rna Targets

High Affinity Of Backbone-Modified α-Anomeric Oligodeoxynucleottoes For Dna And Rna Targets

1998 ◽  
Vol 17 (9-11) ◽  
pp. 1645-1649 ◽  
Author(s):  
A. Laurent ◽  
F. Debart ◽  
J.-C. Bologna ◽  
J.-J. Vasseur ◽  
B. Rayner
Keyword(s):  
High Affinity ◽  
Dna And Rna ◽  
Rna Targets

scholarly journals A programmable pAgo nuclease with universal guide and target specificity from the mesophilic bacterium Kurthia massiliensis

2021 ◽  
Author(s):  
Ekaterina Kropocheva ◽  
Anton Kuzmenko ◽  
Alexei A. Aravin ◽  
Daria Esyunina ◽  
Andrey Kulbachinskiy
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acid Detection ◽  
Bacterial Cells ◽  
Dna And Rna ◽  
Rna Targets ◽  
Wide Range ◽  
Mesophilic Bacterium ◽  
Strict Specificity ◽  
Programmable Nucleases

ABSTRACTArgonaute proteins are programmable nucleases that are found in both eukaryotes and prokaryotes and provide defense against invading genetic elements. Although some prokaryotic Argonautes (pAgos) were shown to recognize RNA targets in vitro, the majority of studied pAgos have strict specificity toward DNA, which limits their practical use in RNA-centric applications. Here, we describe a unique KmAgo nuclease from the mesophilic bacterium Kurthia massiliensis that can be programmed with either DNA or RNA guides and can precisely cleave both DNA and RNA targets. KmAgo preferentially binds 16-20 nt long 5′-phosphorylated guide molecules with no strict specificity for their sequence and is active in a wide range of temperatures. In bacterial cells, KmAgo is loaded with small DNAs with no obvious sequence preferences suggesting that it can uniformly target genomic sequences. Target cleavage by KmAgo depends on the formation of secondary structure indicating that KmAgo can be used for structural probing of RNA targets. Mismatches between the guide and target sequences greatly affect the efficiency and precision of target cleavage, depending on the mismatch position and the nature of the reacting nucleic acid. These properties of KmAgo open the way for its use for highly specific nucleic acid detection and cleavage.

“Parallel” and “Antiparallel Tail-Clamps” Increase the Efficiency of Triplex Formation with Structured DNA and RNA Targets

ChemBioChem ◽  
2005 ◽  
Vol 6 (6) ◽  
pp. 1034-1042 ◽  
Author(s):  
Anna Nadal ◽  
Ramon Eritja ◽  
Teresa Esteve ◽  
Maria Pla
Keyword(s):  
Triplex Formation ◽  
Dna And Rna ◽  
Rna Targets

scholarly journals DNA and RNA editing without sequence limitation using the flap endonuclease 1 guided by hairpin DNA probes

2020 ◽  
Vol 48 (20) ◽  
pp. e117-e117
Author(s):  
Kun Tian ◽  
Yongjian Guo ◽  
Bingjie Zou ◽  
Liang Wang ◽  
Yun Zhang ◽  
...  
Keyword(s):  
Rna Editing ◽  
Human Cells ◽  
Hairpin Dna ◽  
Flap Endonuclease 1 ◽  
Dna And Rna ◽  
Rna Targets ◽  
Single Base Mismatch ◽  
Compact Size

Abstract Here, we characterized a flap endonuclease 1 (FEN1) plus hairpin DNA probe (hpDNA) system, designated the HpSGN system, for both DNA and RNA editing without sequence limitation. The compact size of the HpSGN system make it an ideal candidate for in vivo delivery applications. In vitro biochemical studies showed that the HpSGN system required less nuclease to cleave ssDNA substrates than the SGN system we reported previously by a factor of ∼40. Also, we proved that the HpSGN system can efficiently cleave different RNA targets in vitro. The HpSGN system cleaved genomic DNA at an efficiency of ∼40% and ∼20% in bacterial and human cells, respectively, and knocked down specific mRNAs in human cells at a level of ∼25%. Furthermore, the HpSGN system was sensitive to the single base mismatch at the position next to the hairpin both in vitro and in vivo. Collectively, this study demonstrated the potential of developing the HpSGN system as a small, effective, and specific editing tool for manipulating both DNA and RNA without sequence limitation.

scholarly journals Optimization of Single-Base-Pair Mismatch Discrimination in Oligonucleotide Microarrays

2003 ◽  
Vol 69 (5) ◽  
pp. 2848-2856 ◽  
Author(s):  
Hidetoshi Urakawa ◽  
Said El Fantroussi ◽  
Hauke Smidt ◽  
James C. Smoot ◽  
Erik H. Tribou ◽  
...  
Keyword(s):  
Base Pair ◽  
Dna Microarrays ◽  
Perfect Match ◽  
Analytical Framework ◽  
Single Base ◽  
Dna And Rna ◽  
Base Pair Mismatch ◽  
Nonequilibrium Dissociation ◽  
Single Base Pair ◽  
Mismatch Discrimination

ABSTRACT The discrimination between perfect-match and single-base-pair-mismatched nucleic acid duplexes was investigated by using oligonucleotide DNA microarrays and nonequilibrium dissociation rates (melting profiles). DNA and RNA versions of two synthetic targets corresponding to the 16S rRNA sequences of Staphylococcus epidermidis (38 nucleotides) and Nitrosomonas eutropha (39 nucleotides) were hybridized to perfect-match probes (18-mer and 19-mer) and to a set of probes having all possible single-base-pair mismatches. The melting profiles of all probe-target duplexes were determined in parallel by using an imposed temperature step gradient. We derived an optimum wash temperature for each probe and target by using a simple formula to calculate a discrimination index for each temperature of the step gradient. This optimum corresponded to the output of an independent analysis using a customized neural network program. These results together provide an experimental and analytical framework for optimizing mismatch discrimination among all probes on a DNA microarray.

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