Skip to main content
SpringerLink
Log in

Fluorescent Nucleic Acid Probes in Living Cells

  • Chapter
  • First Online:
DNA and RNA Nanobiotechnologies in Medicine: Diagnosis and Treatment of Diseases

Part of the book series: RNA Technologies ((RNATECHN))

  • 2094 Accesses

Abstract

During the last decade a variety of fluorescent probes have been developed that allow quantitative analysis of specific DNA and RNA sequences in biological samples. In combination with recently developed methods in fluorescence microscopy, this offers the unique opportunity to quantitatively study DNA and RNA content in fixed and living cells in response to cellular stimulation. This chapter is intended to supply the reader with an overview of relevant approaches for probing specific DNA and RNA sequences in biological samples with a focus on DNA hairpin probes. We follow this with discussion on the modes of cellular entry from the perspective of both viral and non-viral carriers. To conclude we elaborate on the key barriers that need to be overcome for successful transfer of DNA probes into living cells.

Anne Seefeld, Ganesh R. Kokil and Karnaker R. Tupally contributed equally to the manuscript.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Adams MD, Dubnick M, Kerlavage AR, Venter JC (1992) Sequence identification of 2,375 human brain genes. Nature 355:632–634

    PubMed  CAS  Google Scholar 

  • Aderem A, Underhill DM (1999) Mechanisms of phagocytosis in macrophages. Annu Rev Immunol 17:593–623

    PubMed  CAS  Google Scholar 

  • Alberts B, Johnson A, Lewis J et al (2002) The lipid bilayer. Molecular biology of the cell, 4th edn. Garland Science, New York, NY

    Google Scholar 

  • Altschul S (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    PubMed  CAS  Google Scholar 

  • Altschul SF, Gish W, Miller W et al (1990) Basic local alignment search tool. J Mol Biol 215: 403–410

    PubMed  CAS  Google Scholar 

  • Alwine JC, Kemp DJ, Stark GR (1977) Method for detection of specific RNAs in agarose gels by transfer to diazobenzyloxymethyl-paper and hybridization with DNA probes. Proc Natl Acad Sci USA 74:5350–5354

    PubMed  CAS  Google Scholar 

  • Ansari A, Kuznetsov SV, Shen Y (2001) Configurational diffusion down a folding funnel describes the dynamics of DNA hairpins. Proc Natl Acad Sci USA 98:7771–7776

    PubMed  CAS  Google Scholar 

  • Areschoug T, Gordon S (2009) Scavenger receptors: role in innate immunity and microbial pathogenesis. Cell Microbiol 11:1160–1169

    PubMed  CAS  Google Scholar 

  • Austin CP (2004) The impact of the completed human genome sequence on the development of novel therapeutics for human disease. Annu Rev Med 55:1–13

    PubMed  CAS  Google Scholar 

  • Bailey MR, Khokhlova VA, Sapozhnikov OA et al (2003) Physical mechanisms of the therapeutic effect of ultrasound (a review). Acoust Phys 49:369–388

    Google Scholar 

  • Bao S, Thrall BD, Miller DL (1997) Transfection of a reporter plasmid into cultured cells by sonoporation in vitro. Ultrasound Med Biol 23:953–959

    PubMed  CAS  Google Scholar 

  • Bareford LM, Swaan PW (2007) Endocytic mechanisms for targeted drug delivery. Adv Drug Deliv Rev 59:748–758

    PubMed  CAS  Google Scholar 

  • Barry E, Gesek F, Friedman P (1993) Introduction of antisense oligonucleotides into cells by permeabilization with streptolysin O. Biotechniques 15:1016

    PubMed  CAS  Google Scholar 

  • Bartlett JS, Samulski RJ, McCown TJ (1998) Selective and rapid uptake of adeno-associated virus type 2 in brain. Hum Gene Ther 9:1181–1186

    PubMed  CAS  Google Scholar 

  • Beaudette TT, Cohen JA, Bachelder EM et al (2009) Chemoselective ligation in the functionalization of polysaccharide-based particles. J Am Chem Soc 131:10360–10361

    PubMed  CAS  Google Scholar 

  • Behr J-P (1997) The proton sponge: a trick to enter cells the viruses did not exploit. Chimia 51:3

    Google Scholar 

  • Belting M, Sandgren S, Wittrup A (2005) Nuclear delivery of macromolecules: barriers and carriers. Adv Drug Deliv Rev 57:505–527

    PubMed  CAS  Google Scholar 

  • Berglund P, Sjoberg M, Garoff H et al (1993) Semliki Forest virus expression system: production of conditionally infectious recombinant particles. Biotechnology (N Y) 11:916–920

    CAS  Google Scholar 

  • Bertrand E, Chartrand P, Schaefer M et al (1998) Localization of ASH1 mRNA particles in living yeast. Mol Cell 2:437–445

    PubMed  CAS  Google Scholar 

  • Borst A, Box AT, Fluit AC (2004) False-positive results and contamination in nucleic acid amplification assays: suggestions for a prevent and destroy strategy. Eur J Clin Microbiol 23: 289–299

    CAS  Google Scholar 

  • Botelho RJ, Grinstein S (2011) Phagocytosis. Curr Biol 21:R533–R538

    PubMed  CAS  Google Scholar 

  • Boucrot E, Saffarian S, Zhang R, Kirchhausen T (2010) Roles of AP-2 in clathrin-mediated endocytosis. PLoS One 5:e10597

    PubMed  Google Scholar 

  • Boussif O, Lezoualc’h F, Zanta MA et al (1995) A versatile vector for gene and oligonucleotide transfer into cells in culture and in vivo: polyethylenimine. Proc Natl Acad Sci USA 92: 7297–7301

    PubMed  CAS  Google Scholar 

  • Brodsky FM, Chen CY, Knuehl C et al (2001) Biological basket weaving: formation and function of clathrin-coated vesicles. Annu Rev Cell Dev Biol 17:517–568

    PubMed  CAS  Google Scholar 

  • Budker V, Zhang G, Danko I et al (1998) The efficient expression of intravascularly delivered DNA in rat muscle. Gene Ther 5:272–276

    PubMed  CAS  Google Scholar 

  • Bureau MF, Naimi S, Torero Ibad R et al (2004) Intramuscular plasmid DNA electrotransfer: biodistribution and degradation. Biochim Biophys Acta 1676:138–148

    PubMed  CAS  Google Scholar 

  • Carmo-Fonseca M, Pepperkok R, Sproat BS et al (1991) In vivo detection of snRNP-rich organelles in the nuclei of mammalian cells. EMBO J 10:1863–1873

    PubMed  CAS  Google Scholar 

  • Chalfie M, Tu Y, Ghia E, Prasher DC (2007) Green fluorescent protein as a marker for gene expression. Int S Tech Pol Inn 52:1766–1767

    Google Scholar 

  • Chandy T, Sharma CP (1990) Chitosan–as a biomaterial. Biomater Artif Cells Artif Organs 18: 1–24

    PubMed  CAS  Google Scholar 

  • Chang DC, Reese TS (1990) Changes in membrane structure induced by electroporation as revealed by rapid-freezing electron microscopy. Biophys J 58:1–12

    PubMed  CAS  Google Scholar 

  • Chaudhuri G (1997) Scavenger receptor-mediated delivery of antisense mini-exon phosphorothioate oligonucleotide to Leishmania-infected macrophages. Selective and efficient elimination of the parasite. Biochem Pharmacol 53:385–391

    PubMed  CAS  Google Scholar 

  • Chen HH, Mack LM, Kelly R et al (1997) Persistence in muscle of an adenoviral vector that lacks all viral genes. Proc Natl Acad Sci USA 94:1645–1650

    PubMed  CAS  Google Scholar 

  • Cole NB, Lippincott-Schwartz J (1995) Organization of organelles and membrane traffic by microtubules. Curr Opin Cell Biol 7:55–64

    PubMed  CAS  Google Scholar 

  • Cole AJ, David AE, Wang J et al (2011) Polyethylene glycol modified, cross-linked starch-coated iron oxide nanoparticles for enhanced magnetic tumor targeting. Biomaterials 32:2183–2193

    PubMed  CAS  Google Scholar 

  • Conner SD, Schmid SL (2003) Regulated portals of entry into the cell. Nature 422:37–44

    PubMed  CAS  Google Scholar 

  • Daigle N, Ellenberg J (2007) LambdaN -GFP: an RNA reporter system for live-cell imaging. Nat Methods 4:633–636

    PubMed  CAS  Google Scholar 

  • Desjardins M (2003) ER-mediated phagocytosis: a new membrane for new functions. Nat Rev Immunol 3:280–291

    PubMed  CAS  Google Scholar 

  • Doherty GJ, McMahon HT (2008) Mediation, modulation, and consequences of membrane-cytoskeleton interactions. Annu Rev Biophys 37:65–95

    PubMed  CAS  Google Scholar 

  • Doherty GJ, McMahon HT (2009) Mechanisms of endocytosis. Annu Rev Biochem 78:857–902

    PubMed  CAS  Google Scholar 

  • Dunlap DD, Maggi A, Soria MR, Monaco L (1997) Nanoscopic structure of DNA condensed for gene delivery. Nucleic Acids Res 25:3095–3101

    PubMed  CAS  Google Scholar 

  • Dutta T, Jain NK, McMillan NAJ, Parekh HS (2010) Dendrimer nanocarriers as versatile vectors in gene delivery. Nanomedicine 6:25–34

    PubMed  CAS  Google Scholar 

  • Edelstein ML, Abedi MR, Wixon J, Edelstein RM (2004) Gene therapy clinical trials worldwide 1989-2004-an overview. J Gene Med 6:597–602

    PubMed  Google Scholar 

  • Edelstein ML, Abedi MR, Wixon J (2007) Gene therapy clinical trials worldwide to 2007–an update. J Gene Med 9:833–842

    PubMed  Google Scholar 

  • Eliyahu H, Siani S, Azzam T et al (2006) Relationships between chemical composition, physical properties and transfection efficiency of polysaccharide-spermine conjugates. Biomaterials 27: 1646–1655

    PubMed  CAS  Google Scholar 

  • Ellis J, Bernstein A (1989) Gene targeting with retroviral vectors: recombination by gene conversion into regions of nonhomology. Mol Cell Biol 9:1621–1627

    PubMed  CAS  Google Scholar 

  • Engelhardt JF, Ye X, Doranz B, Wilson JM (1994) Ablation of E2A in recombinant adenoviruses improves transgene persistence and decreases inflammatory response in mouse liver. Proc Natl Acad Sci USA 91:6196–6200

    PubMed  CAS  Google Scholar 

  • Favre D, Cherel Y, Provost N et al (2000) Hyaluronidase enhances recombinant adeno-associated virus (rAAV)-mediated gene transfer in the rat skeletal muscle. Gene Ther 7:1417–1420

    PubMed  CAS  Google Scholar 

  • Felgner PL, Gadek TR, Holm M et al (1987) Lipofection: a highly efficient, lipid-mediated DNA-transfection procedure. Proc Natl Acad Sci USA 84:7413–7417

    PubMed  CAS  Google Scholar 

  • Femino AM, Fay FS, Fogarty K, Singer RH (1998) Visualization of single RNA transcripts in situ. Science 280:585–590

    PubMed  CAS  Google Scholar 

  • Ferrara KW (2008) Driving delivery vehicles with ultrasound. Adv Drug Deliv Rev 60:1097–1102

    PubMed  CAS  Google Scholar 

  • Fischer D, Li Y, Ahlemeyer B et al (2003) In vitro cytotoxicity testing of polycations: influence of polymer structure on cell viability and hemolysis. Biomaterials 24:1121–1131

    PubMed  CAS  Google Scholar 

  • Fisher KJ, Kelley WM, Burda JF, Wilson JM (1996) A novel adenovirus-adeno-associated virus hybrid vector that displays efficient rescue and delivery of the AAV genome. Hum Gene Ther 7:2079–2087

    PubMed  CAS  Google Scholar 

  • Frenkel N, Singer O, Kwong AD (1994) Minireview: the herpes simplex virus amplicon—a versatile defective virus vector. Gene Ther 1(Suppl 1):S40–S46

    PubMed  Google Scholar 

  • Fusco D, Accornero N, Lavoie B et al (2003) Single mRNA molecules demonstrate probabilistic movement in living mammalian cells. Curr Biol 13:161–167

    PubMed  CAS  Google Scholar 

  • Gall JG, Pardue ML (1969) Formation and detection of RNA-DNA hybrid molecules in cytological preparations. Proc Natl Acad Sci USA 63:378–383

    PubMed  CAS  Google Scholar 

  • Goncalves C, Mennesson E, Fuchs R et al (2004) Macropinocytosis of polyplexes and recycling of plasmid via the clathrin-dependent pathway impair the transfection efficiency of human hepatocarcinoma cells. Mol Ther 10:373–385

    PubMed  CAS  Google Scholar 

  • Gordon JW, Ruddle FH (1983) Gene transfer into mouse embryos: production of transgenic mice by pronuclear injection. Methods Enzymol 101:411–433

    PubMed  CAS  Google Scholar 

  • Gordon JW, Scangos GA, Plotkin DJ et al (1980) Genetic transformation of mouse embryos by microinjection of purified DNA. Proc Natl Acad Sci USA 77:7380–7384

    PubMed  CAS  Google Scholar 

  • Gosselin MA, Guo W, Lee RJ (2001) Efficient gene transfer using reversibly cross-linked low molecular weight polyethylenimine. Bioconjug Chem 12:989–994

    PubMed  CAS  Google Scholar 

  • Guo J, Ju J, Turro NJ (2012) Fluorescent hybridization probes for nucleic acid detection. Anal Bioanal Chem 402:3115–3125

    PubMed  CAS  Google Scholar 

  • Gupa P, Hung C (1994) Magnetically controlled targeted chemotherapy. In: Willmott N, Daly JM (eds) Microspheres and regional cancer therapy. CRC, Boca Raton, FL

    Google Scholar 

  • Hamm-Alvarez SF (1998) Molecular motors and their role in membrane traffic. Adv Drug Deliv Rev 29:229–242

    PubMed  CAS  Google Scholar 

  • Hammer RE, Pursel VG, Rexroad CE Jr et al (1985) Production of transgenic rabbits, sheep and pigs by microinjection. Nature 315:680–683

    PubMed  CAS  Google Scholar 

  • Hanson GT, Hanson BJ (2008) Fluorescent probes for cellular assays. Comb Chem High Throughput Screen 11:505–513

    PubMed  CAS  Google Scholar 

  • Harui A, Suzuki S, Kochanek S, Mitani K (1999) Frequency and stability of chromosomal integration of adenovirus vectors. J Virol 73:6141–6146

    PubMed  CAS  Google Scholar 

  • Heller LC, Ugen K, Heller R (2005) Electroporation for targeted gene transfer. Expert Opin Drug Deliv 2:255–268

    PubMed  CAS  Google Scholar 

  • Herve F, Ghinea N, Scherrmann JM (2008) CNS delivery via adsorptive transcytosis. AAPS J 10:455–472

    PubMed  Google Scholar 

  • Hillaireau H, Couvreur P (2009) Nanocarriers’ entry into the cell: relevance to drug delivery. Cell Mol Life Sci 66:2873–2896

    PubMed  CAS  Google Scholar 

  • Hosseinkhani H, Aoyama T, Ogawa O, Tabata Y (2002) Liver targeting of plasmid DNA by pullulan conjugation based on metal coordination. J Control Release 83:287–302

    PubMed  CAS  Google Scholar 

  • Huang F, Khvorova A, Marshall W, Sorkin A (2004) Analysis of clathrin-mediated endocytosis of epidermal growth factor receptor by RNA interference. J Biol Chem 279:16657–16661

    PubMed  CAS  Google Scholar 

  • Jones AT (2007) Macropinocytosis: searching for an endocytic identity and role in the uptake of cell penetrating peptides. J Cell Mol Med 11:670–684

    PubMed  CAS  Google Scholar 

  • Juskowiak B (2011) Nucleic acid-based fluorescent probes and their analytical potential. Anal Bioanal Chem 399:3157–3176

    PubMed  CAS  Google Scholar 

  • Kaplan IM, Wadia JS, Dowdy SF (2005) Cationic TAT peptide transduction domain enters cells by macropinocytosis. J Control Release 102:247–253

    PubMed  CAS  Google Scholar 

  • Kay MA, Glorioso JC, Naldini L (2001) Viral vectors for gene therapy: the art of turning infectious agents into vehicles of therapeutics. Nat Med 7:33–40

    PubMed  CAS  Google Scholar 

  • Kerr MC, Teasdale RD (2009) Defining macropinocytosis. Traffic 10:364–371

    PubMed  CAS  Google Scholar 

  • Khalil IA, Kogure K, Akita H, Harashima H (2006a) Uptake pathways and subsequent intracellular trafficking in nonviral gene delivery. Pharmacol Rev 58:32–45

    PubMed  CAS  Google Scholar 

  • Khalil IA, Kogure K, Futaki S, Harashima H (2006b) High density of octaarginine stimulates macropinocytosis leading to efficient intracellular trafficking for gene expression. J Biol Chem 281:3544–3551

    PubMed  CAS  Google Scholar 

  • Kibria G, Hatakeyama H, Ohga N et al (2011) Dual-ligand modification of PEGylated liposomes shows better cell selectivity and efficient gene delivery. J Control Release 153:141–148

    PubMed  CAS  Google Scholar 

  • Kim HJ, Greenleaf JF, Kinnick RR et al (1996) Ultrasound-mediated transfection of mammalian cells. Hum Gene Ther 7:1339–1346

    PubMed  CAS  Google Scholar 

  • Kim TI, Seo HJ, Choi JS et al (2004) PAMAM-PEG-PAMAM: novel triblock copolymer as a biocompatible and efficient gene delivery carrier. Biomacromolecules 5:2487–2492

    PubMed  CAS  Google Scholar 

  • Kirchhausen T (2009) Imaging endocytic clathrin structures in living cells. Trends Cell Biol 19: 596–605

    PubMed  CAS  Google Scholar 

  • Kitchens KM, Foraker AB, Kolhatkar RB et al (2007) Endocytosis and interaction of poly (amidoamine) dendrimers with Caco-2 cells. Pharm Res 24:2138–2145

    PubMed  CAS  Google Scholar 

  • Kitchens KM, Kolhatkar RB, Swaan PW, Ghandehari H (2008) Endocytosis inhibitors prevent poly(amidoamine) dendrimer internalization and permeability across Caco-2 cells. Mol Pharm 5:364–369

    PubMed  CAS  Google Scholar 

  • Knemeyer JP, Marmé N, Sauer M (2000) Probes for detection of specific DNA sequences at the single-molecule level. Anal Chem 72:3717–3724

    PubMed  CAS  Google Scholar 

  • Koeberl DD, Alexander IE, Halbert CL et al (1997) Persistent expression of human clotting factor IX from mouse liver after intravenous injection of adeno-associated virus vectors. Proc Natl Acad Sci USA 94:1426–1431

    PubMed  CAS  Google Scholar 

  • Kopatz I, Remy JS, Behr JP (2004) A model for non-viral gene delivery: through syndecan adhesion molecules and powered by actin. J Gene Med 6:769–776

    PubMed  CAS  Google Scholar 

  • Kurata S, Tsukakoshi M, Kasuya T, Ikawa Y (1986) The laser method for efficient introduction of foreign DNA into cultured cells. Exp Cell Res 162:372–378

    PubMed  CAS  Google Scholar 

  • Kuriyama S, Tominaga K, Kikukawa M et al (1998) Inhibitory effects of human sera on adenovirus-mediated gene transfer into rat liver. Anticancer Res 18:2345–2351

    PubMed  CAS  Google Scholar 

  • Kuriyama N, Kuriyama H, Julin CM et al (2001) Protease pretreatment increases the efficacy of adenovirus-mediated gene therapy for the treatment of an experimental glioblastoma model. Cancer Res 61:1805–1809

    PubMed  CAS  Google Scholar 

  • Kwoh DY, Coffin CC, Lollo CP et al (1999) Stabilization of poly-L-lysine/DNA polyplexes for in vivo gene delivery to the liver. Biochim Biophys Acta 1444:171–190

    PubMed  CAS  Google Scholar 

  • Latz E, Schoenemeyer A, Visintin A et al (2004) TLR9 signals after translocating from the ER to CpG DNA in the lysosome. Nat Immunol 5:190–198

    PubMed  CAS  Google Scholar 

  • Liang P, Pardee AB (1992) Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science 257:967–971

    PubMed  CAS  Google Scholar 

  • Lin MT, Pulkkinen L, Uitto J, Yoon K (2000) The gene gun: current applications in cutaneous gene therapy. Int J Dermatol 39:161–170

    PubMed  CAS  Google Scholar 

  • Lionnet T, Czaplinski K, Darzacq X et al (2011) A transgenic mouse for in vivo detection of endogenous labeled mRNA. Nat Methods 8:165–170

    PubMed  CAS  Google Scholar 

  • Liu G, Molas M, Grossmann GA et al (2001) Biological properties of poly-L-lysine-DNA complexes generated by cooperative binding of the polycation. J Biol Chem 276:34379–34387

    PubMed  CAS  Google Scholar 

  • Lukacs GL, Haggie P, Seksek O et al (2000) Size-dependent DNA mobility in cytoplasm and nucleus. J Biol Chem 275:1625–1629

    PubMed  CAS  Google Scholar 

  • Lundstrom K, Boulikas T (2003) Viral and non-viral vectors in gene therapy: technology development and clinical trials. Technol Cancer Res Treat 2:471–486

    PubMed  CAS  Google Scholar 

  • Malafaya PB, Silva GA, Reis RL (2007) Natural-origin polymers as carriers and scaffolds for biomolecules and cell delivery in tissue engineering applications. Adv Drug Deliv Rev 59: 207–233

    PubMed  CAS  Google Scholar 

  • Manno CS, Chew AJ, Hutchison S et al (2003) AAV-mediated factor IX gene transfer to skeletal muscle in patients with severe hemophilia B. Blood 101:2963–2972

    PubMed  CAS  Google Scholar 

  • Marmé N, Friedrich A, Müller M et al (2006) Identification of single-point mutations in mycobacterial 16S rRNA sequences by confocal single-molecule fluorescence spectroscopy. Nucleic Acids Res 34:e90

    PubMed  Google Scholar 

  • McMahon HT, Boucrot E (2011) Molecular mechanism and physiological functions of clathrin-mediated endocytosis. Nat Rev Mol Cell Biol 12:517–533

    PubMed  CAS  Google Scholar 

  • Mechti N, Leonetti J, Clarenc J et al (1991) Nuclear location of synthetic oligonucleotides microinjected somatic cells: its implication in an antisense strategy. Nucleic Acids Symp Ser 24:147

    PubMed  CAS  Google Scholar 

  • Medina SH, El-Sayed ME (2009) Dendrimers as carriers for delivery of chemotherapeutic agents. Chem Rev 109:3141–3157

    PubMed  CAS  Google Scholar 

  • Mercer J, Helenius A (2009) Virus entry by macropinocytosis. Nat Cell Biol 11:510–520

    PubMed  CAS  Google Scholar 

  • Miller MW (2000) Gene transfection and drug delivery. Ultrasound Med Biol 26(Suppl 1):S59–S62

    PubMed  Google Scholar 

  • Miller DG, Adam MA, Miller AD (1990) Gene transfer by retrovirus vectors occurs only in cells that are actively replicating at the time of infection. Mol Cell Biol 10:4239–4242

    PubMed  CAS  Google Scholar 

  • Mir LM, Moller PH, Andre F, Gehl J (2005) Electric pulse-mediated gene delivery to various animal tissues. Adv Genet 54:83–114

    PubMed  CAS  Google Scholar 

  • Molenaar C, Marras SA, Slats JC et al (2001) Linear 2′ O-Methyl RNA probes for the visualization of RNA in living cells. Nucleic Acids Res 29:E89-9

    PubMed  Google Scholar 

  • Motley A, Bright NA, Seaman MN, Robinson MS (2003) Clathrin-mediated endocytosis in AP-2-depleted cells. J Cell Biol 162:909–918

    PubMed  CAS  Google Scholar 

  • Muzyczka N (1992) Use of adeno-associated virus as a general transduction vector for mammalian cells. Curr Top Microbiol Immunol 158:97–129

    PubMed  CAS  Google Scholar 

  • Nermut MV, Hockley DJ (1996) Comparative morphology and structural classification of retroviruses. Curr Top Microbiol Immunol 214:1–24

    PubMed  CAS  Google Scholar 

  • Neu M, Fischer D, Kissel T (2005) Recent advances in rational gene transfer vector design based on poly(ethylene imine) and its derivatives. J Gene Med 7:992–1009

    PubMed  CAS  Google Scholar 

  • Report NIH (2002) Assessment of adenoviral vector safety and toxicity: report of the National Institutes of Health Recombinant DNA Advisory Committee. Hum Gene Ther 13:3–13

    Google Scholar 

  • Nolte O, Müller M, Häfner B, Knemeyer J-P, Stöhr K, Wolfrum J, Hakenbeck R, Denapaite D, Schwarz-Finsterle J, Stein S, Schmitt E, Cremer C, Herten D-P, Hausmann M, Sauer M (2006) Novel singly labelled probes for identification of microorganisms, detection of antibiotic resistance genes and mutations, and tumor diagnosis (SMART PROBES). In: Popp J, Strehle M (eds) Biophotonics: visions for better health care. Wiley-VCH Verlag GmbH & Co, Weinheim. doi:10.1002/3527608842.ch4

    Google Scholar 

  • Ogris M, Brunner S, Schuller S et al (1999) PEGylated DNA/transferrin-PEI complexes: reduced interaction with blood components, extended circulation in blood and potential for systemic gene delivery. Gene Ther 6:595–605

    PubMed  CAS  Google Scholar 

  • Ozawa T, Natori Y, Sato M, Umezawa Y (2007) Imaging dynamics of endogenous mitochondrial RNA in single living cells. Nat Med 4:413–419

    CAS  Google Scholar 

  • Paige JS, Wu KY, Jaffrey SR (2011) RNA mimics of green fluorescent protein. Science 333:642–646. doi:10.1126/science.1207339

    PubMed  CAS  Google Scholar 

  • Paillasson S, Robert-Nicoud M, Ronot X (1996) Specific detection of RNA molecules by fluorescent in situ hybridization in living cells. Cell Biol Toxicol 12:359–361

    PubMed  CAS  Google Scholar 

  • Park MR, Han KO, Han IK et al (2005) Degradable polyethylenimine-alt-poly(ethylene glycol) copolymers as novel gene carriers. J Control Release 105:367–380

    PubMed  CAS  Google Scholar 

  • Park TG, Jeong JH, Kim SW (2006) Current status of polymeric gene delivery systems. Adv Drug Deliv Rev 58:467–486

    PubMed  CAS  Google Scholar 

  • Park HY, Buxbaum AR, Singer RH (2010) Single mRNA tracking in live cells. Methods Enzymol 472:387–406

    PubMed  CAS  Google Scholar 

  • Patil ML, Zhang M, Taratula O et al (2009) Internally cationic polyamidoamine PAMAM-OH dendrimers for siRNA delivery: effect of the degree of quaternization and cancer targeting. Biomacromolecules 10:258–266

    PubMed  CAS  Google Scholar 

  • Pedroso de Lima MC, Neves S, Filipe A et al (2003) Cationic liposomes for gene delivery: from biophysics to biological applications. Curr Med Chem 10:1221–1231

    PubMed  CAS  Google Scholar 

  • Pelkmans L (2005) Secrets of caveolae- and lipid raft-mediated endocytosis revealed by mammalian viruses. Biochim Biophys Acta 1746:295–304

    PubMed  CAS  Google Scholar 

  • Pelkmans L, Zerial M (2005) Kinase-regulated quantal assemblies and kiss-and-run recycling of caveolae. Nature 436:128–133

    PubMed  CAS  Google Scholar 

  • Pelkmans L, Burli T, Zerial M, Helenius A (2004) Caveolin-stabilized membrane domains as multifunctional transport and sorting devices in endocytic membrane traffic. Cell 118:767–780

    PubMed  CAS  Google Scholar 

  • Petersen H, Fechner PM, Martin AL et al (2002) Polyethylenimine-graft-poly(ethylene glycol) copolymers: influence of copolymer block structure on DNA complexation and biological activities as gene delivery system. Bioconjug Chem 13:845–854

    PubMed  CAS  Google Scholar 

  • Plank C, Anton M, Rudolph C et al (2003) Enhancing and targeting nucleic acid delivery by magnetic force. Expert Opin Biol Ther 3:745–758

    PubMed  CAS  Google Scholar 

  • Poste G, Papahadjopoulos D, Vail WJ (1976) Lipid vesicles as carriers for introducing biologically active materials into cells. Methods Cell Biol 14:33–71

    PubMed  CAS  Google Scholar 

  • Pucadyil TJ, Schmid SL (2009) Conserved functions of membrane active GTPases in coated vesicle formation. Science 325:1217–1220. doi:10.1126/science.1171004

    PubMed  CAS  Google Scholar 

  • Raj A, Van Den Bogaard P, Rifkin SA et al (2008) Imaging individual mRNA molecules using multiple singly labeled probes. Nat Methods 5:877–879

    PubMed  CAS  Google Scholar 

  • Reeves EP, Lu H, Jacobs HL et al (2002) Killing activity of neutrophils is mediated through activation of proteases by K+ flux. Nature 416:291–297

    PubMed  CAS  Google Scholar 

  • Rejman J, Bragonzi A, Conese M (2005) Role of clathrin- and caveolae-mediated endocytosis in gene transfer mediated by lipo- and polyplexes. Mol Ther 12:468–474

    PubMed  CAS  Google Scholar 

  • Ren Y, Savill J (1998) Apoptosis: the importance of being eaten. Cell Death Differ 5:563–568

    PubMed  CAS  Google Scholar 

  • Richter M, Iwata A, Nyhuis J et al (2000) Adeno-associated virus vector transduction of vascular smooth muscle cells in vivo. Physiol Genomics 2:117–127

    PubMed  CAS  Google Scholar 

  • Robinson MS (2004) Adaptable adaptors for coated vesicles. Trends Cell Biol 14:167–174

    PubMed  CAS  Google Scholar 

  • Sahay G, Alakhova DY, Kabanov AV (2010) Endocytosis of nanomedicines. J Control Release 145:182–195

    PubMed  CAS  Google Scholar 

  • Saiki RK, Gelfand DH, Stoffel S et al (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487–491

    PubMed  CAS  Google Scholar 

  • Sakurai K, Mizu M, Shinkai S (2001) Polysaccharide–polynucleotide complexes. 2. Complementary polynucleotide mimic behavior of the natural polysaccharide schizophyllan in the macromolecular complex with single-stranded RNA and DNA. Biomacromolecules 2:641–650

    PubMed  CAS  Google Scholar 

  • Santangelo PJ, Nix B, Tsourkas A, Bao G (2004) Dual FRET molecular beacons for mRNA detection in living cells. Nucleic Acids Res 32:e57

    PubMed  Google Scholar 

  • Sato T, Ishii T, Okahata Y (2001) In vitro gene delivery mediated by chitosan. Effect of pH, serum, and molecular mass of chitosan on the transfection efficiency. Biomaterials 22:2075–2080

    PubMed  CAS  Google Scholar 

  • Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467–470

    PubMed  CAS  Google Scholar 

  • Scherer F, Anton M, Schillinger U et al (2002) Magnetofection: enhancing and targeting gene delivery by magnetic force in vitro and in vivo. Gene Ther 9:102–109

    PubMed  CAS  Google Scholar 

  • Schillinger U, Brill T, Rudolph C et al (2005) Advances in magnetofection—magnetically guided nucleic acid delivery. J Magn Magn Mater 293:8

    Google Scholar 

  • Shav-Tal Y, Darzacq X, Shenoy SM et al (2004) Dynamics of single mRNPs in nuclei of living cells. Science 304:1797–1800. doi: 10.1126/science.1099754

    Google Scholar 

  • Shenk TE (1996) Adenoviridae: the viruses and their replication. In: Fields BN, Howley PMKDM (eds) Fields Virology, 3rd edn. Lippincott-Raven, Philadelphia, PA, pp 2114–2148

    Google Scholar 

  • Shin J, Shum P, Thompson DH (2003) Acid-triggered release via dePEGylation of DOPE liposomes containing acid-labile vinyl ether PEG-lipids. J Control Release 91:187–200

    PubMed  CAS  Google Scholar 

  • Shirahata Y, Ohkohchi N, Itagak H, Satomi S (2001) New technique for gene transfection using laser irradiation. J Investig Med 49:184–190

    PubMed  CAS  Google Scholar 

  • Sieczkarski SB, Whittaker GR (2002) Dissecting virus entry via endocytosis. J Gen Virol 83: 1535–1545

    PubMed  CAS  Google Scholar 

  • Sizovs A, McLendon PM, Srinivasachari S, Reineke TM (2010) Carbohydrate polymers for nonviral nucleic acid delivery. Top Curr Chem 296:131–190

    PubMed  CAS  Google Scholar 

  • Sonawane ND, Szoka FC Jr, Verkman AS (2003) Chloride accumulation and swelling in endosomes enhances DNA transfer by polyamine-DNA polyplexes. J Biol Chem 278: 44826–44831

    PubMed  CAS  Google Scholar 

  • Stöhr K, Häfner B, Nolte O et al (2005) Species-specific identification of mycobacterial 16S rRNA PCR amplicons using smart probes. Anal Chem 77:7195–7203

    PubMed  Google Scholar 

  • Suda T, Liu D (2007) Hydrodynamic gene delivery: its principles and applications. Mol Ther 15: 2063–2069

    PubMed  CAS  Google Scholar 

  • Summerford C, Samulski RJ (1998) Membrane-associated heparan sulfate proteoglycan is a receptor for adeno-associated virus type 2 virions. J Virol 72:1438–1445

    PubMed  CAS  Google Scholar 

  • Swanson JA (2008) Shaping cups into phagosomes and macropinosomes. Nat Rev Mol Cell Biol 9:639–649

    PubMed  CAS  Google Scholar 

  • Takei K, Haucke V (2001) Clathrin-mediated endocytosis: membrane factors pull the trigger. Trends Cell Biol 11:385–391

    PubMed  CAS  Google Scholar 

  • Thayer MV, Wu JY (2011) Purity analysis and impurities determination by AEX-HPLC. In: Bonillaand JV, Srivatsa GS (eds) Handbook of analysis of oligonucleotide and related products. CRC, Boca Raton, FL

    Google Scholar 

  • Thomas CE, Ehrhardt A, Kay MA (2003) Progress and problems with the use of viral vectors for gene therapy. Nat Rev Genet 4:346–358

    PubMed  CAS  Google Scholar 

  • Tilsner J, Flors C (2011) FIT for purpose: PNA-based probes enable mRNA imaging in living cells. Chembiochem 12:1007–1009

    PubMed  CAS  Google Scholar 

  • Traub LM (2009) Tickets to ride: selecting cargo for clathrin-regulated internalization. Nat Rev Mol Cell Biol 10:583–596

    PubMed  CAS  Google Scholar 

  • Traub LM (2011) Regarding the amazing choreography of clathrin coats. PLoS Biol 9:e1001037

    PubMed  CAS  Google Scholar 

  • Tsen SW, Wu CY, Meneshian A et al (2009) Femtosecond laser treatment enhances DNA transfection efficiency in vivo. J Biomed Sci 16:36

    PubMed  Google Scholar 

  • Tsuji A, Koshimoto H, Sato Y et al (2000) Direct observation of specific messenger RNA in a single living cell under a fluorescence microscope. Biophys J 78:3260–3274

    PubMed  CAS  Google Scholar 

  • Tsuji A, Sato Y, Hirano M et al (2001) Development of a time-resolved fluorometric method for observing hybridization in living cells using fluorescence resonance energy transfer. Biophys J 81:501–515

    PubMed  CAS  Google Scholar 

  • Tuthill TJ, Groppelli E, Hogle JM, Rowlands DJ (2010) Picornaviruses. Curr Top Microbiol Immunol 343:43–89

    PubMed  CAS  Google Scholar 

  • Tyagi S, Alsmadi O (2004) Imaging native beta-actin mRNA in motile fibroblasts. Biophys J 87: 4153–4162

    PubMed  CAS  Google Scholar 

  • Tyagi S, Marras SAE, Vet JAM, Kramer FR (1996) Molecular beacons: hybridization probes for detection of nucleic acids in homogeneous solutions. Nat Biotechnol 1–8

    Google Scholar 

  • Underhill DM, Ozinsky A, Hajjar AM et al (1999) The toll-like receptor 2 is recruited to macrophage phagosomes and discriminates between pathogens. Nature 401:811–815

    PubMed  CAS  Google Scholar 

  • Van der Aa MAEM, Huth US, Hafele SY et al (2007) Cellular uptake of cationic polymer-DNA complexes via caveolae plays a pivotal role in gene transfection in COS-7 cells. Pharm Res 24:1590–1598

    PubMed  CAS  Google Scholar 

  • Velculescu VE, Zhang L, Vogelstein B, Kinzler KW (1995) Serial analysis of gene expression. Int S Tech Pol Inn 270:484–487

    CAS  Google Scholar 

  • Verma IM (1990) Gene therapy. Sci Am 263(68–72):81–84

    Google Scholar 

  • Vorhies JS, Nemunaitis JJ (2009) Synthetic vs. natural/biodegradable polymers for delivery of shRNA-based cancer therapies. Methods Mol Biol 480:11–29

    PubMed  CAS  Google Scholar 

  • Wadia JS, Stan RV, Dowdy SF (2004) Transducible TAT-HA fusogenic peptide enhances escape of TAT-fusion proteins after lipid raft macropinocytosis. Nat Med 10:310–315

    PubMed  CAS  Google Scholar 

  • Walker RA, Sheetz MP (1993) Cytoplasmic microtubule-associated motors. Annu Rev Biochem 62:429–451

    PubMed  CAS  Google Scholar 

  • Walther W, Stein U, Siegel R et al (2005) Use of the nuclease inhibitor aurintricarboxylic acid (ATA) for improved non-viral intratumoral in vivo gene transfer by jet-injection. J Gene Med 7:477–485

    PubMed  CAS  Google Scholar 

  • Wang J, Lee IL, Lim WS et al (2004a) Evaluation of collagen and methylated collagen as gene carriers. Int J Pharm 279:115–126

    PubMed  CAS  Google Scholar 

  • Wang S, Joshi S, Lu S (2004b) Delivery of DNA to skin by particle bombardment. Methods Mol Biol 245:185–196

    PubMed  CAS  Google Scholar 

  • Wattendorf U, Coullerez G, Voros J et al (2008) Mannose-based molecular patterns on stealth microspheres for receptor-specific targeting of human antigen-presenting cells. Langmuir 24: 11790–11802

    PubMed  CAS  Google Scholar 

  • Wells DJ (2004) Gene therapy progress and prospects: electroporation and other physical methods. Gene Ther 11:1363–1369

    PubMed  CAS  Google Scholar 

  • Wolfert MA, Seymour LW (1998) Chloroquine and amphipathic peptide helices show synergistic transfection in vitro. Gene Ther 5:409–414

    PubMed  CAS  Google Scholar 

  • Wong K, Sun G, Zhang X et al (2006) PEI-g-chitosan, a novel gene delivery system with transfection efficiency comparable to polyethylenimine in vitro and after liver administration in vivo. Bioconjug Chem 17:152–158

    PubMed  CAS  Google Scholar 

  • Worgall S, Wolff G, Falck-Pedersen E, Crystal RG (1997) Innate immune mechanisms dominate elimination of adenoviral vectors following in vivo administration. Hum Gene Ther 8:37–44

    PubMed  CAS  Google Scholar 

  • Wu P, Phillips MI, Bui J, Terwilliger EF (1998) Adeno-associated virus vector-mediated transgene integration into neurons and other nondividing cell targets. J Virol 72:5919–5926

    PubMed  CAS  Google Scholar 

  • Yang JP, Huang L (1996) Direct gene transfer to mouse melanoma by intratumor injection of free DNA. Gene Ther 3:542–548

    PubMed  CAS  Google Scholar 

  • Yang S, May S (2008) Release of cationic polymer-DNA complexes from the endosome: a theoretical investigation of the proton sponge hypothesis. J Chem Phys 129:185105

    PubMed  Google Scholar 

  • Yang Y, Zhao L (2010) Sensitive fluorescent sensing for DNA assay. Trends Anal Chem 29: 980–1003

    CAS  Google Scholar 

  • Yang JJ, Chen YM, Kurokawa T et al (2010) Gene expression, glycocalyx assay, and surface properties of human endothelial cells cultured on hydrogel matrix with sulfonic moiety: effect of elasticity of hydrogel. J Biomed Mater Res A 95:531–542

    PubMed  Google Scholar 

  • Yi Y, Noh MJ, Lee KH (2011) Current advances in retroviral gene therapy. Curr Gene Ther 11: 218–228

    PubMed  CAS  Google Scholar 

  • Young LS, Searle PF, Onion D, Mautner V (2006) Viral gene therapy strategies: from basic science to clinical application. J Pathol 208:299–318

    PubMed  CAS  Google Scholar 

  • Zamore PD, Williamson JR, Lehmann R (1997) The Pumilio protein binds RNA through a conserved domain that defines a new class of RNA-binding proteins. RNA 3:1421–1433

    PubMed  CAS  Google Scholar 

  • Zeira E, Manevitch A, Khatchatouriants A et al (2003) Femtosecond infrared laser-an efficient and safe in vivo gene delivery system for prolonged expression. Mol Ther 8:342–350

    PubMed  CAS  Google Scholar 

  • Zhang G, Vargo D, Budker V et al (1997) Expression of naked plasmid DNA injected into the afferent and efferent vessels of rodent and dog livers. Hum Gene Ther 8:1763–1772

    PubMed  CAS  Google Scholar 

  • Zhang J, Campbell RE, Ting AY, Tsien RY (2002) Creating new fluorescent probes for cell biology. Nat Rev Mol Cell Biol 3:906–918

    PubMed  CAS  Google Scholar 

  • Zuker M, Mathews DH, Turner DH (1999) Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide, NATO ASI series. Kluwer, Dordrecht, pp 11–43

    Google Scholar 

Download references

Acknowledgement

We gratefully thank the Deutsche Forschungsgemeinschaft (DFG, EXC 81), BMBF (LungSys) and the DAAD for their financial support.

Author information

Authors and Affiliations

  1. Single-Molecule Spectroscopy, Cellnetworks Cluster and Physikalisch-Chemisches Institut, Heidelberg University, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany

    Anne Seefeld & Dirk-Peter Herten

  2. Pharmacy Australia Centre of Excellence, The University of Queensland, St Lucia, QLD, Australia

    Ganesh R. Kokil, Karnaker R. Tupally & Harendra S. Parekh

Authors
  1. Anne Seefeld
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ganesh R. Kokil
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Karnaker R. Tupally
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Harendra S. Parekh
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Dirk-Peter Herten
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Harendra S. Parekh or Dirk-Peter Herten .

Editor information

Editors and Affiliations

  1. Institute of Chemistry/Biochemistry, Free University Berlin, Thielallee 63, Berlin, 14195, Berlin, Germany

    Volker A. Erdmann

  2. Inst. Bioorganic Chemistry, PAN Poznan, ul. Z. Noskowskiego 12/14, Poznan, 61-704, Poland

    Jan Barciszewski

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Seefeld, A., Kokil, G.R., Tupally, K.R., Parekh, H.S., Herten, DP. (2013). Fluorescent Nucleic Acid Probes in Living Cells. In: Erdmann, V., Barciszewski, J. (eds) DNA and RNA Nanobiotechnologies in Medicine: Diagnosis and Treatment of Diseases. RNA Technologies. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-36853-0_12

Download citation

Publish with us

Policies and ethics

Search

Navigation