Erratum to: Evaluation of locked nucleic acids for signal enhancement of oligonucleotide probes for microalgae immobilised on solid surfaces(J Appl Phycol, 10.1007/s10811-008-9399-0);Evaluation of locked nucleic acids for signal enhancement of oligonucleotide probes for microalgae immobilised on solid surfaces

Journal of Applied Phycology

Volumn 21, Issue 6, 2009, Pages 657-668

  Diercks, Sonja ^a   Gescher, Christine ^a   Metfies, Katja ^b   Medlin, Linda K ^c  

^a ALFRED WEGENER INSTITUTE FOR POLAR AND MARINE RESEARCH   (Germany)

^b INSTITUTE OF MATERIALS RESEARCH   (Germany)

^c LABORATOIRE ARAGO   (France)

Author keywords

Locked nucleic acids; Microalgae; Microarray; Oligonucleotide probes; Sandwich hybridisation

Indexed keywords

EID: 77349117337     PISSN: 09218971     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10811-010-9612-9     Document Type: Erratum

References (67)

1. Braasch DA, Corey DR (2001) Locked nucleic acid (LNA): fine-tuning the recognition of DNA and RNA. Chem Biol 8: 1-87.
2. Chou L-S, Meadows C, Wittwer CT, Lyon E (2005) Unlabeled oligonucleotide probes modified with locked nucleic acids for improved mismatch discrimination in genotyping by melting analysis. BioTechniques 39: 644-647.
3. DeRisi JL, Iyer VR, Brown PO (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278: 680-686.
4. Diercks S, Metfies K, Medlin LK (2008a) Molecular probe sets for the detection of toxic algae for use in sandwich hybridisation formats. J Plankt Res 30: 439-448.
5. Diercks S, Metfies K, Medlin LK (2008b) Colorimetric detection of the toxic dinoflagellate Alexandrium minutum using sandwich hybridization in a microtiter plate assay. Harmful Algae 7: 137-145.
6. Diercks S, Metfies K, Medlin LK (2008c) Development and adaptation of a multiprobe biosensor for the use in a semi-automated device for the detection of toxic algae. Biosens Bioelectron 23: 1527-1533.
7. Eppley RW, Holmes RW, Strickland JDH (1967) Sinking rates of marine phytoplankton measured with a fluorometer. J Exp Mar Biol Ecol 1: 191-208.
8. Gagnon S, Bourbeau D, Levesque RC (1996) Secondary structures and features of the 18S, 5. 8S and 26S ribosomal RNAs from the apicomplexan parasite Toxoplasma gondii. Gene 173: 129-135.
9. Gescher C, Metfies K, Medlin LK (2007) The ALEX CHIP-Development of a DNA chip for identification and monitoring of Alexandrium. Harmful Algae 7: 485-494.
10. Gescher C, Metfies K, Frickenhaus S, Knefelkamp B, Wiltshire KH, Medlin LK (2008) Feasibility of assessing the community composition of Prasinophytes at the Helgoland Roads sampling site with a DNA microarray. Appl Env Microbiol 74: 5305-5316.
11. Graves DJ (1999) Powerful tools for genetic analysis come of age. Trends Biotechnol 17: 127-134.
12. Groben R, Medlin L (2005) In Situ hybridization of phytoplankton using fluorescently labeled rRNA probes. Methods in Enzymology. In: Zimmer EAS, Roalson EH (ed) Molecular Evolution: Producing the Biochemical Data Academic Press, NY, pp 299-310.
13. Groben R, John U, Eller G, Lange M, Medlin LK (2004) Using fluorescently-labelled rRNA probes for hierarchical estimation of phytoplankton diversity-a mini-review. Nova Hedwigia 79: 313-320.
14. Guillou L, Chrétiennot-Dinet M-J, Medlin LK, Claustre H, Loiseaux-De Goer S, Vaulot D (1999) Bolidomonas: A new genus with two species belonging to a new algal class, the Bolidophyceae (Heterokonta). J Phycol 35: 368-381.
15. Howley PM, Israel MA, Law M, Martin MA (1979) A rapid method for detecting and mapping homology between heterologous DNAs. J BiolChem 254: 4876-4883.
16. Hummelshoj L, Ryder LP, Madsen HO, Poulsen LK (2005) Locked nucleic acid inhibits amplification of contaminating DNA in real-time PCR. BioTechniques 38: 605-610.
17. Jacobsen N, Bentzen J, Meldgaard M, Jakobsen MH, Fenger M, Kauppinen S, Skouv J (2002a) LNA-enhanced detection of single nucleotide polymorphisms in the apolipoprotein E. Nucl Acids Res 30: e100.
18. Jacobsen N, Fenger M, Bentzen J, Rasmussen SL, Jakobsen MH, Fenstholt J, Skouv J (2002b) Genotyping of the apolipoprotein B R3500Q mutation using immobilized locked nucleic acid capture probes. Clin Chem 48: 657-660.
19. Kappel K, Westernhagen HV, Blohm DH (2003) Microarray-based identification of eggs and larvae from fish species common in the North Sea, Dechema Chip-Technology Meeting, Frankfurt, Germany.
20. Kauppinen S, Nielsen PS, Mouritzen P, Nielsen AT, Vissing H, Møller S, Ramsing NB (2003) LNA Microarrays in Genomics. Pharma Genomics 24-32.
21. Keller MD, Selvin RC, Claus W, Guillard RRL (1987) Media for the culture of oceanic ultraphytoplankton. J Phycol 23: 633-338.
22. Ki J-S, Han M-S (2006) A low-density oligonucleotide array study for parallel detection of harmful algal species using hybridization of consensus PCR products of LSU rDNA D2 domain. Biosens Bioelectr 21: 1812-1821.
23. Kim C-J, Sako Y (2005) Molecular identification of toxic Alexandrium tamiyavanichii (Dinophyceae) using two DNA probes. Harmful Algae 4: 984-991.
24. Kloosterman WP, Wienholds E, De Bruijn E, Kauppinen S, Plasterk RHA (2006) In situ detection of miRNAs in animal embryos using LNA-modified oligonucleotide probes. Nature Methods 3: 27-29.
25. Kongsbak L (2002) LNA: fine-tuning of primers and probes. LNA 01: 1.
26. Koshkin AA, Rajwanshi VK, Wengel J (1998a) Novel convenient syntheses of LNA [2. 2. 1]bicyclo nucleosides. Tet Lett 39: 4381-4384.
27. Koshkin AA, Singh SK, Nielsen P, Rajwanshi VK, Kumar R, Meldgaard M, Olsen CE, Wengel J (1998b) LNA (locked nucleic acids): synthesis of the adenine, cytosine, guanine, 5-methylcytosine, thymine and uracil bicyclonucleoside monomers, oligomerisation, and unprecedented nucleic acid recognition. Tetrahedron 54: 3607-3630.
28. Kubota K, Ohashi A, Imachi H, Harada H (2006) Improved in situ hybridization efficiency with locked-nucleic-acid-incorporated DNA probes. Appl Env Microbiol 72: 5311-5317.
29. Lehner A, Loy A, Behr T, Gaenge H, Ludwig W, Wagner M, Schleifer K-H (2005) Oligonucleotide microarray for identification of Enterococcus species. FEMS Microbiol Lett 246: 133-142.
30. Lim EL, Amaral LA, Caron DA, Delong EF (1993) Application of rRNA-based probes for observing marine nanoplanktonic protists. Appl Env Microbiol 59: 1647-1655.
31. Lockhart DJ (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotechnology 14: 1675-1680.
32. Loy A, Lehner A, Lee N, Adamczyk J, Meier H, Ernst J, Schleifer K-H, Wagner M (2002) Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of Sulfate-reducing prokaryotes in the environment. Appl Env Microbiol 68: 5064-5081.
33. Loy A, Schulz C, Lucker S, Schopfer-Wendels A, Stoecker K, Baranyi C, Lehner A, Wagner M (2005) 16S rRNA Gene-based oligonucleotide microarray for environmental monitoring of the betaproteobacterial Order "Rhodocyclales". Appl Env Microbiol 71: 1373-1386.
34. Medlin LK, Elwood HJ, Stickel S, Sogin ML (1988) The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene 71: 491-499.
35. Medlin LK, Metfies K, Mehl H, Wiltshire KH, Valentin K (2006) Picoeukaryotic plankton diversity at the Helgoland time series site as assessed by three molecular methods. Microb Ecol 52: 53-71.
36. Metfies K, Medlin LK (2004) DNA microchips for phytoplankton: the fluorescent wave of the future. Nova Hedwigia 79: 321-327.
37. Metfies K, Medlin LK (2005) Ribosomal RNA probes and microarrays: Their potential use in assessing microbial biodiversity. In Zimmer EA Roalson EH (eds) Methods in Enzymology, Molecular Evolution: Producing the Biochemical Data Academic, NY, pp 258-278.
38. Metfies K, Medlin LK (2008) Feasibility of transferring fluorescent in situ hybridization probes to an 18S rRNA gene Phylochip and mapping of signal intensities. Appl Env Microbiol 74: 2814-2821.
39. Metfies K, Huljic S, Lange M, Medlin LK (2005) Electrochemical detection of the toxic dinoflagellate Alexandrium ostenfeldii with a DNA-biosensor. Biosens Bioelect 20: 1349-1357.
40. Metfies K, Berzano M, Gualerzi C, Muyzer G, Medlin LK (2006) Meeting report: molecular ecology workshop. Detection of microbial biodiversity in environmental samples, Camerino, Italy, September 19-21, 2005. Protist 157: 247-250.
41. Metfies K, Berzano M, Mayer C, Roosken P, Gualerzi C, Medlin LK, Muyzer G (2007) An optimised protocol for the identification of diatoms, flagellated algae and pathogenic protozoa with phylochips. Mol Ecol Notes 7: 925-936.
42. Metfies K, Borsutzki P, Gescher C, Medlin LK, Frickenhaus S (2008) PhylochipAnalyzer-A program for analyzing hierachical probe-sets. Molec Ecol Res 8: 99-102.
43. Montresor M, John U, Beran A, Medlin LK (2004) Alexandrium tamutum sp. nov. (Dinophyceae): a new nontoxic species in the genus Alexandrium. J Phycol 40: 398-411.
44. Nielsen PS, Kauppinen S (2002) The use of LNA Oligonucleotide Microarrays provides superior sensitivity and specificity in expression profiling. LNA 17: 1-3.
45. Niemeyer CM, Blohm D (1999) DNA Microarrays. Angewandte Chemie International Edition, 38: 2865-2869.
46. Obika S, Nanbu D, Hari Y, Andoh J-I, Morio K-I, Doi T, Imanishi T (1998) Stability and structural features of the duplexes containing nucleoside analogues with a fixed N-type conformation, 2′-O, 4′-C-methyleneribonucleosides. Tet Lett 39: 5401-5404.
47. Parekh-Olmedo H, Drury M, Kmiec EB (2002) Targeted nucleotide exchange in Saccharomyces cerevisiae directed by short oligonucleotides containing locked nucleic acids. Chem Biol 9: 1073-1084.
48. Peplies J, Glockner FO, Amann R (2003) Optimization strategies for DNA microarray-based detection of bacteria with 16S rRNA-targeting oligonucleotide probes. Appl Env Microbiol 69: 1397-1407.
49. Peplies J, Glockner FO, Amann R, Ludwig W (2004a) Comparative sequence analysis and oligonucleotide probe design based on 23S rRNA genes of alpha proteobacteria from North Sea bacterioplankton. Syst Appl Microbiol 27: 573-580.
50. Peplies J, Lau SCK, Pernthaler J, Amann R, Glockner FO (2004b) Application and validation of DNA microarrays for the 16S rRNA-based analysis of marine bacterioplankton. Env Microbiol 6: 638-645.
51. Peplies J, Lachmund C, Glockner FO, Manz W (2006) A DNA microarray platform based on direct detection of rRNA for characterization of freshwater sediment-related prokaryotic communities. Appl Env Microbiol 72: 4829-4838.
52. Scholin CA, Herzog M, Sogin M, Anderson DM (1994) Identification of group- and strain-specific genetic markers for the globally distributed Alexandrium (Dinophyceae). 2. Sequence analysis of a fragment of the LSU rRNA gene. J Phycol 30: 999-1011.
53. Scholin CA, Buck KR, Britschgi T, Cangelosi G, Chavez FP (1996) Identification of Pseudo-nitzschia australis (Bacillariophyceae) using rRNA-targeted probes in whole cell and sandwich hybridization formats. Phycologia 35: 190-197.
54. Scholin CA, Miller P, Buck KR, Chavez FP, Harris P, Haydock P, Howard J, Cangelosi G (1997) Detection and quantification of Pseudo nitzschia australis in cultured and natural populations using LNA rRNA-targeted probes. Limnol Oceanogr 42: 1265-1272.
55. Silahtaroglu AN, Tommerup N, Vissing H (2003) FISHing with locked nucleic acids (LNA): evaluation of different LNA/DNA mixmers. Molec Cellular Probes 17: 165-169.
56. Silahtaroglu AN, Pfundheller HM, Koshkin AA, Tommerup N, Kauppinen S (2004) LNA-modified oligonucleotides are highly efficient as FISH probes. Cytogenetic and Genome Res 107: 32-37.
57. Simon N, Campbell E, Ornolfsdottir E, Groben R, Guillou L, Lange M, Medlin LK (2000) Oligonucleotide probes for the identification of three algal groups by dot blot and fluorescent whole-cell hybridization. J Eukaryot Microbiol 47: 76-84.
58. Singh SK, Koshkin AA, Wengel J, Nielsen P (1998) LNA (locked nucleic acids): synthesis and high-affinity nucleic acid recognition. Chem Comm 4: 455-456.
59. Sun Z, Zhou L, Zeng H, Chen Z, Zhu H (2007) Multiplex locked nucleic acid probes for analysis of hepatitis B virus mutants using real-time PCR. Genomics 89: 151-159.
60. Tyrrell JV, Connell LB, Scholin CA (2002) Monitoring for Heterosigma akashiwo using a sandwich hybridization assay. Harmful Algae 1: 205-214.
61. Ugozzoli LA, Latorra D, Pucket R, Arar K, Hamby K (2004) Real-time genotyping with oligonucleotide probes containing locked nucleic acids. Anal Biochem 324: 143-152.
62. Vester B, Wengel J (2004) LNA (Locked Nucleic Acid): high-affinity targeting of complementary RNA and DNA. Biochem 43: 13233-13241.
63. Vester B, Lundberg LB, Sørensen MD, Babu BR, Douthwaite S, Wengel J (2004) Improved RNA cleavage by LNAzyme derivatives of DNAzymes. Biochem Soc Trans 32: 37-40.
64. Vester B, Hansen L, Bo Lundberg L, Babu BR, Sorensen M, Wengel J, Douthwaite S (2006) Locked nucleoside analogues expand the potential of DNAzymes to cleave structured RNA targets. BMC Mol Biol 7: 19.
65. Wienholds E, Kloosterman WP, Miska E, Alvarez-Saavedra E, Berezikov E, De Bruijn E, Horvitz HR, Kauppinen S, Plasterk RHA (2005) MicroRNA expression in zebrafish embryonic development. Science 309: 310-311.
66. Ye RW, Wang T, Bedzyk L, Croker KM (2001) Applications of DNA microarrays in microbial systems. J Microbiol Meth 47: 257-272.
67. You M, Moreira BG, Behlke MA, Owczarzy R (2006) Design of LNA probes that improve mismatch discrimination. Nucleic Acids Res 34: e60.