RNA-Selective, Live Cell Imaging Probes for Studying Nuclear Structure and Function

Abstract

The higher-order structural organization of the cell nucleus reflects the underlying genome-wide transcriptional activity and macromolecular transport processes. To study the microscopic organization of RNA distribution within the nucleus, a combinatorial library of fluorescent styryl molecules was synthesized and screened for an in vitro RNA response and live cell nuclear imaging. Four different cell lines (HeLa, A549, 3T3, and 3T3-L1) were analyzed in terms of higher-order nuclear organization. We identified RNA-selective dyes with better imaging properties relative to commercially available SYTORNASelect dye; the selected dyes were also cell permeant, photostable, and well tolerated by the cells. Our dyes also had very good counterstain compatibility with Hoechst and DAPI, which could help to image the DNA distribution in relation to RNA distribution in live cells and therefore reveal different patterns of RNA-DNA colocalization.

Quantitative Structure‐Fluorescence Property Relationship Analysis of a Large BODIPY Library

“…[2][3][4] The diversity-oriented fluorescence library approach (DOFLA), a combinatorial approach which creates a diverse library of fluorophores by systematically varying the substituents attached to a core scaffold, has emerged as a general alternative in fluorophore design. [5] Such DOFLA-generated molecules have found wide applications as bioimaging sensors in a variety of analyses including those of DNA, [6] RNA, [7] nucleotides, [8] peptides, [9] proteins, [10][11][12] and polysaccharides, [13] thus demonstrating the universal applicability of this approach. They have also been used as living cell probes specific for subcellular organelles, [14] as well as cell-status markers.…”

Oxonium heterocyclic quinone in the synthesis of some cyanine dyes and their antimicrobial activity

“…Cyanine dyes also used as optical recording materials [9][10][11][12][13][14][15], in manufacturing of blue filter to laminate of an organic electroluminescent element, and color filter showed highly pure light emission [16] and antioxidants [17]. Cyanine dyes are colorant compounds used in staining of internal limiting membrane (ILM) [18] and used as fluorescent dyes in DNA detection [19][20][21][22][23]. Quinone derivatives are widely used as fungicides [24,25], and antibacterial agent [25][26][27][28][29].…”

Using measurements of muscle cell nuclear RNA with flow cytometry to improve assessment of larval condition of Walleye Pollock (Gadus chalcogrammus)

“…Most nRNA is contained in the nucleolus (Li et al, 2006), the site of ribosome biogenesis (Sirri et al, 2008), and ribosome production correlates with cellular growth (Caldarola et al, 2009). For many cell types grown in culture, nRNA content of G1 cells is highly variable, and a specifi c amount may be required for entry into the S phase (Darzynkiewicz et al, 1980;Piwnicka et al, 1983;Staiano-Coico et al, 1989).…”