scholarly journals Flavylium Dye as pH-Tunable Fluorescent and CD Probe for Double-Stranded DNA and RNA

Chemosensors ◽  
2020 ◽  
Vol 8 (4) ◽  
pp. 129
Author(s):  
Ivo Crnolatac ◽  
Letícia Giestas ◽  
Gordan Horvat ◽  
António Jorge Parola ◽  
Ivo Piantanida
Keyword(s):  
Steady State ◽  
Detection Limit ◽  
Rna Secondary Structure ◽  
Binding Affinities ◽  
Cationic Form ◽  
Rna Detection ◽  
Time Resolved ◽  
Dna And Rna ◽  
Double Stranded Dna ◽  
Acidic Conditions

The interaction of 4′-(N,N-dimethylamino)-6-hydroxyflavylium cation with double stranded (ds-) DNA/RNA was studied by UV/Vis spectrophotometry, circular dichroism (CD), and also steady-state and time-resolved emission spectroscopies at neutral and weakly acidic conditions. At pH 5, the studied molecule, in its flavylium cationic form, showed considerable binding affinities (5 < logKs < 6) for all ds-DNA/RNA, contrary to chalcones forms (dominant at pH 7), which did not show binding to polynucleotides. Flavylium cation intercalated into ds-DNAs at variance to dominant groove aggregation within ds-RNA, which was reported by RNA-specific bisignate induced CD spectrum (ICD) bands. The intrinsically negligible fluorescence of flavylium was strongly increased upon the addition of DNA or RNA, whereby both the fluorescence intensity and emission lifetimes of complexes differed considerably: the strongest emission increase was observed for AU-RNA (detection limit estimated to 10 nM) followed by AT-DNAs and the much weaker effect of GC-DNAs. Both fluorescence sensitivity on the ds-DNA/RNA secondary structure and sequence-selective ICD bands make the flavylium–chalcones system an intriguing pH-switchable new probe for distinguishing between various polynucleotide sequences.

scholarly journals The structural plasticity of nucleic acid duplexes revealed by WAXS and MD

2021 ◽  
Vol 7 (17) ◽  
pp. eabf6106
Author(s):  
Weiwei He ◽  
Yen-Lin Chen ◽  
Lois Pollack ◽  
Serdal Kirmizialtin
Keyword(s):  
Structural Diversity ◽  
Conformational Ensemble ◽  
Structural Variations ◽  
Dna And Rna ◽  
X Ray Scattering ◽  
Double Stranded Dna ◽  
Binding Partners ◽  
Rna Duplexes ◽  
Dynamics Simulations ◽  
Integrate Solution

Double-stranded DNA (dsDNA) and RNA (dsRNA) helices display an unusual structural diversity. Some structural variations are linked to sequence and may serve as signaling units for protein-binding partners. Therefore, elucidating the mechanisms and factors that modulate these variations is of fundamental importance. While the structural diversity of dsDNA has been extensively studied, similar studies have not been performed for dsRNA. Because of the increasing awareness of RNA’s diverse biological roles, such studies are timely and increasingly important. We integrate solution x-ray scattering at wide angles (WAXS) with all-atom molecular dynamics simulations to explore the conformational ensemble of duplex topologies for different sequences and salt conditions. These tightly coordinated studies identify robust correlations between features in the WAXS profiles and duplex geometry and enable atomic-level insights into the structural diversity of DNA and RNA duplexes. Notably, dsRNA displays a marked sensitivity to the valence and identity of its associated cations.

scholarly journals Ground- and excited-state characteristics in photovoltaic polymer N2200

RSC Advances ◽  
2021 ◽  
Author(s):  
Guanzhao Wen ◽  
Xianshao Zou ◽  
Rong Hu ◽  
Jun Peng ◽  
Zhifeng Chen ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Excited State ◽  
Steady State ◽  
Excited States ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Time Dependent ◽  
Functional Theory ◽  
Time Resolved ◽  
Dependent Density

Ground- and excited-states properties of N2200 have been studied by steady-state and time-resolved spectroscopies as well as time-dependent density functional theory calculations.

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