title: 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.
authors.affiliation: Department of Chemistry, New York University, New York, New York 10003, USA.
authors.forename: Qian
authors.initials: Q
authors.lastname: Li
authors.forename: Yunkyung
authors.initials: Y
authors.lastname: Kim
authors.forename: Joshua
authors.initials: J
authors.lastname: Namm
authors.forename: Amita
authors.initials: A
authors.lastname: Kulkarni
authors.forename: Gus R
authors.initials: GR
authors.lastname: Rosania
authors.forename: Young-Hoon
authors.initials: YH
authors.lastname: Ahn
authors.forename: Young-Tae
authors.initials: YT
authors.lastname: Chang
mesh_terms: D000818:Animals; D002460:Cell Line; D002467:Cell Nucleus / Q000737:chemistry / Q000235:genetics* / Q000502:physiology*; D002470:Cell Survival; D004396:Coloring Agents / Q000032:analysis / Q000737:chemistry; D004247:DNA / Q000032:analysis / Q000235:genetics / Q000378:metabolism; D003851:Deoxyribonucleases / Q000378:metabolism; D006801:Humans; D007211:Indoles; D051379:Mice; D015335:Molecular Probes / Q000032:analysis* / Q000235:genetics*; D015394:Molecular Structure; D012313:RNA / Q000032:analysis / Q000235:genetics / Q000378:metabolism*; D012260:Ribonucleases / Q000378:metabolism; D012996:Solutions; D013194:Staining and Labeling / Q000379:methods*; D013379:Substrate Specificity
chemical_list: D004396:Coloring Agents; D007211:Indoles; D015335:Molecular Probes; D012996:Solutions; C007293:DAPI; D012313:RNA; D004247:DNA; D003851:Deoxyribonucleases; D012260:Ribonucleases