Site-specific functionalization of RNA molecules by an unnatural base pair transcription system via click chemistry

2012 ◽  
Vol 48 (88) ◽  
pp. 10835 ◽  
Author(s):  
Takumi Ishizuka ◽  
Michiko Kimoto ◽  
Akira Sato ◽  
Ichiro Hirao
Keyword(s):  
Click Chemistry ◽  
Base Pair ◽  
Site Specific ◽  
Rna Molecules ◽  
Transcription System

scholarly journals PCR Amplification and Transcription for Site-Specific Labeling of Large RNA Molecules by a Two-Unnatural-Base-Pair System

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Michiko Kimoto ◽  
Rie Yamashige ◽  
Shigeyuki Yokoyama ◽  
Ichiro Hirao
Keyword(s):  
Base Pair ◽  
Pcr Amplification ◽  
Base Pairs ◽  
Dna Templates ◽  
Site Specific ◽  
Rna Molecules ◽  
Transcription System ◽  
Rna Transcripts ◽  
Pcr Method ◽  
Functional Components

For the site-specific labeling and modification of RNA by genetic alphabet expansion, we developed a PCR and transcription system using two hydrophobic unnatural base pairs: 7-(2-thienyl)-imidazo[4,5-b]pyridine (Ds) and 2-nitro-4-propynylpyrrole (Px) as a third pair for PCR amplification andDsand pyrrole-2-carbaldehyde (Pa) for the incorporation of functional components as modifiedPabases into RNA by T7 transcription. To prepareDs-containing DNA templates with long chains, theDs-Pxpair was utilized in a fusion PCR method, by which we demonstrated the synthesis of 282-bp DNA templates containingDsat specific positions. Using theseDs-containing DNA templates and a biotin-linkedPasubstrate (Biotin-PaTP) as a modifiedPabase, 260-mer RNA transcripts containing Biotin-Paat a specific position were generated by T7 RNA polymerase. This two-unnatural-base-pair system, combining theDs-PxandDs-Papairs with modifiedPasubstrates, provides a powerful tool for the site-specific labeling and modification of desired positions in large RNA molecules.

Site-specific fluorescent probing of RNA molecules by unnatural base-pair transcription for local structural conformation analysis

2010 ◽  
Vol 5 (7) ◽  
pp. 1312-1323 ◽  
Author(s):  
Yasushi Hikida ◽  
Michiko Kimoto ◽  
Shigeyuki Yokoyama ◽  
Ichiro Hirao
Keyword(s):  
Base Pair ◽  
Conformation Analysis ◽  
Site Specific ◽  
Rna Molecules ◽  
Structural Conformation

scholarly journals Site-Specific Incorporation of Functional Components into RNA by an Unnatural Base Pair Transcription System

Molecules ◽  
2012 ◽  
Vol 17 (3) ◽  
pp. 2855-2876 ◽  
Author(s):  
Nobuyuki Morohashi ◽  
Michiko Kimoto ◽  
Akira Sato ◽  
Rie Kawai ◽  
Ichiro Hirao
Keyword(s):  
Base Pair ◽  
Site Specific ◽  
Transcription System ◽  
Functional Components

A modified dinucleotide for site-specific RNA-labelling by transcription priming and click chemistry

2014 ◽  
Vol 50 (11) ◽  
pp. 1313-1316 ◽  
Author(s):  
Ayan Samanta ◽  
André Krause ◽  
Andres Jäschke
Keyword(s):  
Click Chemistry ◽  
Site Specific

scholarly journals Supercoiling and looping promote DNA base accessibility and coordination among distant sites

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jonathan M. Fogg ◽  
Allison K. Judge ◽  
Erik Stricker ◽  
Hilda L. Chan ◽  
Lynn Zechiedrich
Keyword(s):  
Mechanical Stress ◽  
Genomic Instability ◽  
Base Pair ◽  
Base Pairing ◽  
Complex Interplay ◽  
Site Specific ◽  
Torsional Strain ◽  
Dna Base ◽  
Dna Backbone ◽  
Negative Supercoiling

AbstractDNA in cells is supercoiled and constrained into loops and this supercoiling and looping influence every aspect of DNA activity. We show here that negative supercoiling transmits mechanical stress along the DNA backbone to disrupt base pairing at specific distant sites. Cooperativity among distant sites localizes certain sequences to superhelical apices. Base pair disruption allows sharp bending at superhelical apices, which facilitates DNA writhing to relieve torsional strain. The coupling of these processes may help prevent extensive denaturation associated with genomic instability. Our results provide a model for how DNA can form short loops, which are required for many essential processes, and how cells may use DNA loops to position nicks to facilitate repair. Furthermore, our results reveal a complex interplay between site-specific disruptions to base pairing and the 3-D conformation of DNA, which influences how genomes are stored, replicated, transcribed, repaired, and many other aspects of DNA activity.

Site-Specific Surface Functionalization via Microchannel Cantilever Spotting (µCS): Comparison between Azide-Alkyne and Thiol-Alkyne Click Chemistry Reactions

Small ◽  
2018 ◽  
Vol 14 (21) ◽  
pp. 1800131 ◽  
Author(s):  
Seyed Mohammad Mahdi Dadfar ◽  
Sylwia Sekula-Neuner ◽  
Uwe Bog ◽  
Vanessa Trouillet ◽  
Michael Hirtz
Keyword(s):  
Specific Surface ◽  
Click Chemistry ◽  
Surface Functionalization ◽  
Site Specific

Polymer Pen Lithography (PPL)-Induced Site-Specific Click Chemistry for the Formation of Functional Glycan Arrays

Small ◽  
2012 ◽  
Vol 8 (13) ◽  
pp. 2000-2005 ◽  
Author(s):  
Shudan Bian ◽  
Jiajun He ◽  
Kevin B. Schesing ◽  
Adam B. Braunschweig
Keyword(s):  
Click Chemistry ◽  
Site Specific ◽  
Polymer Pen Lithography

scholarly journals Site‐specific Bioconjugation and Convergent Click Chemistry Enhances Antibody–Chromophore Conjugate Binding Efficiency

2020 ◽  
Vol 96 (3) ◽  
pp. 596-603 ◽  
Author(s):  
Amissi Sadiki ◽  
Eric M. Kercher ◽  
Haibin Lu ◽  
Ryan T. Lang ◽  
Bryan Q. Spring ◽  
...  
Keyword(s):  
Click Chemistry ◽  
Site Specific
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