scholarly journals Sandwich assay for mixed-sequence recognition of double-stranded DNA: Invader-based detection of targets specific to foodborne pathogens

2013 ◽  
Vol 49 (84) ◽  
pp. 9851 ◽  
Author(s):  
Benjamin Denn ◽  
Saswata Karmakar ◽  
Dale C. Guenther ◽  
Patrick J. Hrdlicka
Keyword(s):  
Foodborne Pathogens ◽  
Sandwich Assay ◽  
Sequence Recognition ◽  
Double Stranded Dna ◽  
Mixed Sequence

scholarly journals Mixed-Sequence Recognition of Double-Stranded DNA Using Enzymatically Stable Phosphorothioate Invader Probes

Molecules ◽  
2015 ◽  
Vol 20 (8) ◽  
pp. 13780-13793 ◽  
Author(s):  
Brooke Anderson ◽  
Saswata Karmakar ◽  
Patrick Hrdlicka
Keyword(s):  
Sequence Recognition ◽  
Double Stranded Dna ◽  
Mixed Sequence

scholarly journals Identification and Characterization of Second-Generation Invader Locked Nucleic Acids (LNAs) for Mixed-Sequence Recognition of Double-Stranded DNA

2013 ◽  
Vol 78 (19) ◽  
pp. 9560-9570 ◽  
Author(s):  
Sujay P. Sau ◽  
Andreas S. Madsen ◽  
Peter Podbevsek ◽  
Nicolai K. Andersen ◽  
T. Santhosh Kumar ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Second Generation ◽  
Sequence Recognition ◽  
Double Stranded Dna ◽  
Mixed Sequence ◽  
Locked Nucleic Acids ◽  
Identification And Characterization

Selective recognition of G-quadruplexes by a dimeric carbocyanine dye

RSC Advances ◽  
2016 ◽  
Vol 6 (90) ◽  
pp. 87400-87404 ◽  
Author(s):  
P. Chilka ◽  
P. R. Patlolla ◽  
B. Datta
Keyword(s):  
Selective Recognition ◽  
Dna Molecules ◽  
Double Stranded Dna ◽  
Mixed Sequence ◽  
Carbocyanine Dye ◽  
G Quadruplex

A novel dimeric carbocyanine dye is found to recognise G-quadruplex structures selectively compared to mixed sequence or double-stranded DNA molecules.

scholarly journals Folding and duplex formation in mixed sequence recognition-encoded m-phenylene ethynylene polymers

2021 ◽  
Author(s):  
Giulia Iadevaia ◽  
Jonathan A. Swain ◽  
Diego Núñez-Villanueva ◽  
Andrew D. Bond ◽  
Christopher A. Hunter
Keyword(s):  
Phenylene Ethynylene ◽  
One Pot ◽  
Sequence Recognition ◽  
Mixed Sequence ◽  
Duplex Formation

One pot oligomerisation reactions give access to families of oligomers that allow facile analysis of folding propensity and assessment of suitability for sequence-selective duplex formation.

scholarly journals The complete genome and comparative analysis of the phage phiC120 infecting multidrug-resistant Escherichia coli and Salmonella strains

2021 ◽  
Vol 11 (2) ◽  
Author(s):  
Luis Amarillas ◽  
Claudia Villicaña ◽  
Luis Lightbourn-Rojas ◽  
Arturo González-Robles ◽  
Josefina León-Félix
Keyword(s):  
Escherichia Coli ◽  
Comparative Analysis ◽  
Foodborne Pathogens ◽  
Complete Genome ◽  
Multidrug Resistant ◽  
Open Reading Frames ◽  
E Coli ◽  
Protein Levels ◽  
Double Stranded Dna ◽  
Genes Encoding

Abstract Phages infecting Salmonella and Escherichia coli are promising agents for therapeutics and biological control of these foodborne pathogens, in particular those strains with resistance to several antibiotics. In an effort to assess the potential of the phage phiC120, a virulent phage isolated from horse feces in Mexico, we characterized its morphology, host range and complete genome. Herein, we showed that phiC120 possesses strong lytic activity against several multidrug-resistant E. coli O157: H7 and Salmonella strains, and its morphology indicated that is a member of Myoviridae family. The phiC120 genome is double-stranded DNA and consists of 186,570 bp in length with a 37.6% G + C content. A total of 281 putative open reading frames (ORFs) and two tRNAs were found, where 150 ORFs encoded hypothetical proteins with unknown function. Comparative analysis showed that phiC120 shared high similarity at nucleotide and protein levels with coliphages RB69 and phiE142. Detailed phiC120 analysis revealed that ORF 94 encodes a putative depolymerase, meanwhile genes encoding factors associated with lysogeny, toxins, and antibiotic resistance were absent; however, ORF 95 encodes a putative protein with potential allergenic and pro-inflammatory properties, making needed further studies to guarantee the safety of phiC120 for human use. The characterization of phiC120 expands our knowledge about the biology of coliphages and provides novel insights supporting its potential for the development of phage-based applications to control unwanted bacteria.

Targeting of mixed sequence double-stranded DNA using pyrene-functionalized 2′-amino-α-l-LNA

2005 ◽  
pp. 4279 ◽  
Author(s):  
Patrick J. Hrdlicka ◽  
T. Santhosh Kumar ◽  
Jesper Wengel
Keyword(s):  
Double Stranded Dna ◽  
Mixed Sequence

scholarly journals Impact of non-nucleotidic bulges on recognition of mixed-sequence dsDNA by pyrene-functionalized Invader probes

2020 ◽  
Vol 18 (24) ◽  
pp. 4645-4655
Author(s):  
Dale C. Guenther ◽  
Raymond G. Emehiser ◽  
Allison Inskeep ◽  
Saswata Karmakar ◽  
Patrick J. Hrdlicka
Keyword(s):  
Specific Recognition ◽  
Double Stranded Dna ◽  
Mixed Sequence

Invader probes featuring non-nucleotidic bulges are energetically activated for highly specific recognition of complementary double-stranded DNA targets.

scholarly journals Recognition of double-stranded DNA using energetically activated duplexes with interstrand zippers of 1-, 2- or 4-pyrenyl-functionalized O2′-alkylated RNA monomers

2014 ◽  
Vol 12 (39) ◽  
pp. 7758-7773 ◽  
Author(s):  
Saswata Karmakar ◽  
Andreas S. Madsen ◽  
Dale C. Guenther ◽  
Bradley C. Gibbons ◽  
Patrick J. Hrdlicka
Keyword(s):  
Single Nucleotide ◽  
Double Stranded Dna ◽  
Mixed Sequence

Energetically activated double-stranded probes with interstrand arrangements of intercalator-functionalized nucleotides enable recognition of mixed-sequence DNA with single nucleotide fidelity.

Head-to-head comparison of LNA, MPγPNA, INA and Invader probes targeting mixed-sequence double-stranded DNA

2020 ◽  
Vol 18 (1) ◽  
pp. 56-65 ◽  
Author(s):  
Raymond G. Emehiser ◽  
Eric Hall ◽  
Dale C. Guenther ◽  
Saswata Karmakar ◽  
Patrick J. Hrdlicka
Keyword(s):  
Specific Recognition ◽  
Double Stranded Dna ◽  
Mixed Sequence ◽  
Modified Dna ◽  
Dna Strands

Double-stranded (ds) Invader and INA probes allow for efficient and specific recognition of mixed-sequence dsDNA targets, whereas recognition is less efficient and specific with single-stranded LNA-modified DNA strands and fully modified MPγPNAs.

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