2-Aminopurine Fluorescence as a Probe of Local RNA Structure and Dynamics and Global Folding

2015 ◽  
pp. 99-124 ◽  
Author(s):  
Michael J. Rau ◽  
Kathleen B. Hall
Keyword(s):  
Rna Structure ◽  
Structure And Dynamics

RNA structure and dynamics: A base pairing perspective

2013 ◽  
Vol 113 (2) ◽  
pp. 264-283 ◽  
Author(s):  
Sukanya Halder ◽  
Dhananjay Bhattacharyya
Keyword(s):  
Rna Structure ◽  
Base Pairing ◽  
Structure And Dynamics

scholarly journals 4-Cyanoindole-2′-deoxyribonucleoside as a Dual Fluorescence and Infrared Probe of DNA Structure and Dynamics

Molecules ◽  
2019 ◽  
Vol 24 (3) ◽  
pp. 602 ◽  
Author(s):  
Ismail A. Ahmed ◽  
Arusha Acharyya ◽  
Christina M. Eng ◽  
Jeffrey M. Rodgers ◽  
William F. DeGrado ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Rna Structure ◽  
High Throughput Screening ◽  
Local Environment ◽  
Spectroscopic Properties ◽  
Site Specific ◽  
Structure And Dynamics ◽  
High Fluorescence ◽  
Fluorescence Quencher ◽  
A Site

Unnatural nucleosides possessing unique spectroscopic properties that mimic natural nucleobases in both size and chemical structure are ideally suited for spectroscopic measurements of DNA/RNA structure and dynamics in a site-specific manner. However, such unnatural nucleosides are scarce, which prompts us to explore the utility of a recently found unnatural nucleoside, 4-cyanoindole-2′-deoxyribonucleoside (4CNI-NS), as a site-specific spectroscopic probe of DNA. A recent study revealed that 4CNI-NS is a universal nucleobase that maintains the high fluorescence quantum yield of 4-cyanoindole and that among the four natural nucleobases, only guanine can significantly quench its fluorescence. Herein, we further show that the C≡N stretching frequency of 4CNI-NS is sensitive to the local environment, making it a useful site-specific infrared probe of oligonucleotides. In addition, we demonstrate that the fluorescence-quencher pair formed by 4CNI-NS and guanine can be used to quantitatively assess the binding affinity of a single-stranded DNA to the protein system of interest via fluorescence spectroscopy, among other applications. We believe that this fluorescence binding assay is especially useful as its potentiality allows high-throughput screening of DNA–protein interactions.

scholarly journals Back Cover: Regio-Selective Chemical-Enzymatic Synthesis of Pyrimidine Nucleotides Facilitates RNA Structure and Dynamics Studies ({JABT} 30/2014)

ChemBioChem ◽  
2014 ◽  
Vol 15 (11) ◽  
pp. 1688-1688
Author(s):  
Luigi J. Alvarado ◽  
Regan M. LeBlanc ◽  
Andrew P. Longhini ◽  
Sarah C. Keane ◽  
Niyati Jain ◽  
...  
Keyword(s):  
Enzymatic Synthesis ◽  
Rna Structure ◽  
Pyrimidine Nucleotides ◽  
Back Cover ◽  
Structure And Dynamics ◽  
Selective Chemical

scholarly journals Probing RNA Structure and Dynamics in the HIV‐1 5′ UTR using Ensemble and Single Molecule Approaches

2018 ◽  
Vol 32 (S1) ◽  
Author(s):  
Karin Musier‐Forsyth ◽  
Benjamin Brigham ◽  
Jonathan Kitzrow ◽  
Joshua‐Paolo C. Reyes ◽  
James Munro
Keyword(s):  
Single Molecule ◽  
Rna Structure ◽  
Structure And Dynamics ◽  
Hiv 1
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