In Vitro Selection and Characterization of DNA Aptamers to a Small Molecule Target

2017 ◽  
Vol 9 (4) ◽  
pp. 233-268 ◽  
Author(s):  
Annamaria Ruscito ◽  
Erin M. McConnell ◽  
Anna Koudrina ◽  
Ranganathan Velu ◽  
Christopher Mattice ◽  
...  
Keyword(s):  
Small Molecule ◽  
In Vitro Selection ◽  
Dna Aptamers

scholarly journals In vitro selection and characterization of cellulose-binding DNA aptamers

2007 ◽  
Vol 35 (19) ◽  
pp. 6378-6388 ◽  
Author(s):  
B. J. Boese ◽  
R. R. Breaker
Keyword(s):  
In Vitro Selection ◽  
Dna Aptamers ◽  
Cellulose Binding

In Vitro Selection of DNA Aptamers for a Small-Molecule Porphyrin by Gold Nanoparticle-Based SELEX

2019 ◽  
Vol 87 (7-8) ◽  
pp. 231-239 ◽  
Author(s):  
Wenjing Li ◽  
Yu Luo ◽  
Tian Gao ◽  
Luyan Yang ◽  
Jine Wang ◽  
...  
Keyword(s):  
Gold Nanoparticle ◽  
Small Molecule ◽  
In Vitro Selection ◽  
Dna Aptamers ◽  
Selection Of

In vitro selection and characterization of DNA aptamers recognizing chloramphenicol

2011 ◽  
Vol 155 (4) ◽  
pp. 361-369 ◽  
Author(s):  
Jaytry Mehta ◽  
Bieke Van Dorst ◽  
Elsa Rouah-Martin ◽  
Wouter Herrebout ◽  
Marie-Louise Scippo ◽  
...  
Keyword(s):  
In Vitro Selection ◽  
Dna Aptamers

In vitro selection and characterization of single stranded DNA aptamers for luteolin: A possible recognition tool

2018 ◽  
Vol 549 ◽  
pp. 72-79 ◽  
Author(s):  
Jinan Tuma Sabah ◽  
Razauden Mohamed Zulkifli ◽  
Shafinaz Shahir ◽  
Farediah Ahmed ◽  
Mohammed Rafiq Abdul Kadir ◽  
...  
Keyword(s):  
In Vitro Selection ◽  
Dna Aptamers ◽  
Single Stranded Dna

scholarly journals In vitro selection of l-DNA aptamers that bind a structured d-RNA molecule

2020 ◽  
Vol 48 (4) ◽  
pp. 1669-1680 ◽  
Author(s):  
Sougata Dey ◽  
Jonathan T Sczepanski
Keyword(s):  
In Vitro Selection ◽  
Rna Binding ◽  
Rna Aptamers ◽  
Dna Aptamers ◽  
Binding Properties ◽  
Rna Molecules ◽  
Dna And Rna ◽  
Selection Of

Abstract The development of structure-specific RNA binding reagents remains a central challenge in RNA biochemistry and drug discovery. Previously, we showed in vitro selection techniques could be used to evolve l-RNA aptamers that bind tightly to structured d-RNAs. However, whether similar RNA-binding properties can be achieved using aptamers composed of l-DNA, which has several practical advantages compared to l-RNA, remains unknown. Here, we report the discovery and characterization of the first l-DNA aptamers against a structured RNA molecule, precursor microRNA-155, thereby establishing the capacity of DNA and RNA molecules of the opposite handedness to form tight and specific ‘cross-chiral’ interactions with each other. l-DNA aptamers bind pre-miR-155 with low nanomolar affinity and high selectivity despite the inability of l-DNA to interact with native d-RNA via Watson–Crick base pairing. Furthermore, l-DNA aptamers inhibit Dicer-mediated processing of pre-miRNA-155. The sequence and structure of l-DNA aptamers are distinct from previously reported l-RNA aptamers against pre-miR-155, indicating that l-DNA and l-RNA interact with the same RNA sequence through unique modes of recognition. Overall, this work demonstrates that l-DNA may be pursued as an alternative to l-RNA for the generation of RNA-binding aptamers, providing a robust and practical approach for targeting structured RNAs.

In Vitro Selection and Characterization of DNA Aptamers Specific for Phospholamban

2009 ◽  
Vol 329 (1) ◽  
pp. 57-63 ◽  
Author(s):  
Yoshie Tanaka ◽  
Takeshi Honda ◽  
Kenji Matsuura ◽  
Yoshihiro Kimura ◽  
Makoto Inui
Keyword(s):  
In Vitro Selection ◽  
Dna Aptamers

PENGEMBANGAN TEKNOLOGI SELEKSI IN VITRO BERULANG (REPEAT CYCLING–IN VITRO SELECTION) TOLERAN STRES KEKERINGAN UNTUK PERBAIKAN MUTU GENETIK DAN PRODUKSI TANAMAN KEDELAI BERMIKORIZA

2017 ◽  
Vol 1 (1) ◽  
pp. 74-84
Author(s):  
Ahmad Riduan ◽  
Rainiyati Rainiyati ◽  
Yulia Alia
Keyword(s):  
Arbuscular Mycorrhizae ◽  
In Vitro Selection ◽  
Soil Samples ◽  
Single Spore ◽  
Isolation And Characterization ◽  
Single Spore Culture ◽  
Spore Culture ◽  
Glomus Sp

Every plant rhizospheres in any ecosystem there are various living microorganisms including Arbuscular Mycorrhizae Fungi (AMF).  An isolation and characterization is required to investigate the species or type of the AMF. This research was aimed at studying the isolation and characterization of AMF sporulation in soybean rhizospheres in Jambi Province. The results of evaluation on soil samples before trapping showed that there are spores from three genus of AMF twelve types Glomus , two types Acaulospora and one type of Enthrophospora.  Following single spore culture in soybean rhizosphere, 5 spore types were obtained:  Glomus sp-1, Glomus sp-4, Glomus sp-7, Glomus sp-8 Glomus sp-10.

Engineering DNA aptamers and DNA enzymes with fluorescence-signaling properties

2004 ◽  
Vol 76 (7-8) ◽  
pp. 1547-1561 ◽  
Author(s):  
R. Nutiu ◽  
Shirley Mei ◽  
Zhongjie Liu ◽  
Y. Li
Keyword(s):  
Dna Sequences ◽  
Rational Design ◽  
In Vitro Selection ◽  
Random Sequence ◽  
Pair Potential ◽  
Dna Aptamers ◽  
Dna Molecules ◽  
Dna Enzymes ◽  
Fluorescence Signaling

Single-stranded DNA molecules with ligand-binding ability and catalytic function, referred to as DNA aptamers and DNA enzymes, respectively, are special DNA sequences isolated from random-sequence DNA libraries by “in vitro selection”. These two new classes of artificial DNA molecules have the potential of being used as molecular tools in a variety of innovative applications ranging from biosensing to gene regulation. Our laboratory is interested in engineering fluorescence-signaling DNA aptamers and DNA enzymes that can be widely exploited for detection-directed applications. In this article, we will first discuss our recent efforts on the rational design of a new class of signaling aptamers denoted “structure- switching signaling aptamers”, which report target binding by switching structures from DNA/DNA duplex to DNA/target complex. We will then describe the in vitro selection of fluorescence-signaling DNA enzymes that exhibit a synchronized catalysis-signaling capability by cleaving a chimeric RNA/DNA substrate at the lone RNA linkage surrounded by closely spaced fluorophore-quencher pair. Potential utilities of these signaling DNA molecules will also be discussed.

scholarly journals In Vitro Selection and Characterization of Hepatitis C Virus Serine Protease Variants Resistant to an Active-Site Peptide Inhibitor

2003 ◽  
Vol 77 (6) ◽  
pp. 3669-3679 ◽  
Author(s):  
Caterina Trozzi ◽  
Linda Bartholomew ◽  
Alessandra Ceccacci ◽  
Gabriella Biasiol ◽  
Laura Pacini ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Serine Protease ◽  
In Vitro Selection ◽  
Three Dimensional ◽  
Host Cells ◽  
Dimensional Structure ◽  
In Vitro Systems

ABSTRACT The hepatitis C virus (HCV) serine protease is necessary for viral replication and represents a valid target for developing new therapies for HCV infection. Potent and selective inhibitors of this enzyme have been identified and shown to inhibit HCV replication in tissue culture. The optimization of these inhibitors for clinical development would greatly benefit from in vitro systems for the identification and the study of resistant variants. We report the use HCV subgenomic replicons to isolate and characterize mutants resistant to a protease inhibitor. Taking advantage of the replicons' ability to transduce resistance to neomycin, we selected replicons with decreased sensitivity to the inhibitor by culturing the host cells in the presence of the inhibitor and neomycin. The selected replicons replicated to the same extent as those in parental cells. Sequence analysis followed by transfection of replicons containing isolated mutations revealed that resistance was mediated by amino acid substitutions in the protease. These results were confirmed by in vitro experiments with mutant enzymes and by modeling the inhibitor in the three-dimensional structure of the protease.

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