Erratum to: Mismatch discrimination in fluorescent in situ hybridization using different types of nucleic acids (Applied Microbiology and Biotechnology, 10.1007/s00253-015-6389-4);Mismatch discrimination in fluorescent in situ hybridization using different types of nucleic acids

Applied Microbiology and Biotechnology

Volumn 99, Issue 9, 2015, Pages 3961-3969

  Silvia, Fontenete ^a,b   Joana, Barros ^a,c   Pedro, Madureira ^a,d   Céu, Figueiredo ^a,e   Jesper, Wengel ^b   Filipe, Azevedo Nuno ^a  

^a UNIVERSITY OF PORTO   (Portugal)

^b UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

^c INEB INSTITUTO DE ENGENHARIA BIOMÉDICA   (Portugal)

^d UNIVERSITY OF PORTO   (Portugal)

^e University of Porto   (Portugal)

Author keywords

FISH; Microbiology; Mismatch discrimination; Nucleic acids; Oligonucleotides

Indexed keywords

BINDING ENERGY; CHEMICAL MODIFICATION; DNA SEQUENCES; FISH; FLUORESCENCE; FLUORESCENCE MICROSCOPY; MICROBIOLOGY; MONOMERS; OLIGONUCLEOTIDES; RNA;

COMPLEMENTARY STRAND; FLUORESCENCE IN SITU HYBRIDIZATION; FLUORESCENT IN SITU HYBRIDIZATION; HELICOBACTER PYLORI; LOCKED NUCLEIC ACID; MISMATCH DISCRIMINATION; PEPTIDE NUCLEIC ACID; ROBUST RECOGNITION;

NUCLEIC ACIDS;

FLUORESCENT DYE; LOCKED NUCLEIC ACID; MONOMER; NUCLEIC ACID; OLIGONUCLEOTIDE; PEPTIDE NUCLEIC ACID; OLIGONUCLEOTIDE PROBE;

BACTERIUM; FLUORESCENCE; HYBRIDIZATION; NUCLEIC ACID; TEMPERATURE EFFECT;

ACCURACY; ANALYTIC METHOD; ARTICLE; BINDING AFFINITY; CHEMICAL MODIFICATION; DNA SEQUENCE; FLUORESCENCE IN SITU HYBRIDIZATION; HELICOBACTER; HELICOBACTER ACINONYCHIS; HELICOBACTER PYLORI; NONHUMAN; RNA SEQUENCE; BASE MISPAIRING; GENETICS; MOLECULAR DIAGNOSIS; OLIGONUCLEOTIDE PROBE; PROCEDURES; SENSITIVITY AND SPECIFICITY; TEMPERATURE;

HELICOBACTER ACINONYCHIS; HELICOBACTER PYLORI;

BASE PAIR MISMATCH; HELICOBACTER PYLORI; IN SITU HYBRIDIZATION, FLUORESCENCE; MOLECULAR DIAGNOSTIC TECHNIQUES; NUCLEIC ACIDS; OLIGONUCLEOTIDE PROBES; SENSITIVITY AND SPECIFICITY; TEMPERATURE;

EID: 84938201773     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-015-6568-3     Document Type: Erratum

References (48)

1. Almeida C, Azevedo NF, Bento JC, Cerca N, Ramos H, Vieira MJ, Keevil CW (2013) Rapid detection of urinary tract infections caused by Proteus spp. using PNA-FISH. Eur J Clin Microbiol Infect Dis 32(6):781–786
2. Amann RI, Binder BJ, Olson RJ, Chisholm SW, Devereux R, Stahl DA (1990) Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbiol 56(6):1919–1925
3. Buchardt O, Egholm M, Berg RH, Nielsen PE (1993) Peptide nucleic acids and their potential applications in biotechnology. Trends Biotechnol 11(9):384–386
4. Campbell MA, Wengel J (2011) Locked vs. unlocked nucleic acids (LNA vs. UNA): contrasting structures work towards common therapeutic goals. Chem Soc Rev 40(12):5680–5689
5. Celeda D, Aldinger K, Haar FM, Hausmann M, Durm M, Ludwig H, Cremer C (1994) Rapid fluorescence in situ hybridization with repetitive DNA probes: quantification by digital image analysis. Cytometry 17(1):13–25
6. Cerqueira L, Azevedo NF, Almeida C, Jardim T, Keevil CW, Vieira MJ (2008) DNA mimics for the rapid identification of microorganisms by fluorescence in situ hybridization (FISH). Int J Mol Sci 9(10):1944–1960
7. Cerqueira L, Fernandes RM, Ferreira RM, Carneiro F, Dinis-Ribeiro M, Figueiredo C, Keevil CW, Azevedo NF, Vieira MJ (2011) PNA-FISH as a new diagnostic method for the determination of clarithromycin resistance of Helicobacter pylori. BMC Microbiol 11:101
8. Cerqueira L, Fernandes RM, Ferreira RM, Oleastro M, Carneiro F, Brandao C, Pimentel-Nunes P, Dinis-Ribeiro M, Figueiredo C, Keevil CW, Vieira MJ, Azevedo NF (2013) Validation of a fluorescence in situ hybridization method using peptide nucleic acid probes for detection of Helicobacter pylori clarithromycin resistance in gastric biopsy specimens. J Clin Microbiol 51(6):1887–1893
9. Christensen U, Jacobsen N, Rajwanshi VK, Wengel J, Koch T (2001) Stopped-flow kinetics of locked nucleic acid (LNA)-oligonucleotide duplex formation: studies of LNA-DNA and DNA-DNA interactions. Biochem J 354(Pt 3):481–484
10. DeLong EF, Wickham GS, Pace NR (1989) Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science 243(4896):1360–1363
11. Eaton KA, Dewhirst FE, Radin MJ, Fox JG, Paster BJ, Krakowka S, Morgan DR (1993) Helicobacter acinonyx sp. nov., isolated from cheetahs with gastritis. Int J Syst Bacteriol 43(1):99–106
12. Filichev VV, Christensen UB, Pedersen EB, Babu BR, Wengel J (2004) Locked nucleic acids and intercalating nucleic acids in the design of easily denaturing nucleic acids: thermal stability studies. Chembiochem 5(12):1673–1679
13. Fontenete S, Guimaraes N, Leite M, Figueiredo C, Wengel J, Filipe Azevedo N (2013) Hybridization-based detection of Helicobacter pylori at human body temperature using advanced locked nucleic acid (LNA) probes. PLoS One 8(11):e81230
14. Fontenete S., N. Guimarães., J. Wengel, N.F. Azevedo (in press). Prediction of melting temperatures in fluorescence in situ hybridization (FISH) procedures using thermodynamic models. Crit Rev Biotechnol.
15. Guga P, Koziolkiewicz M (2011) Phosphorothioate nucleotides and oligonucleotides—recent progress in synthesis and application. Chem Biodivers 8(9):1642–1681
16. Guimaraes N, Azevedo NF, Figueiredo C, Keevil CW, Vieira MJ (2007) Development and application of a novel peptide nucleic acid probe for the specific detection of Helicobacter pylori in gastric biopsy specimens. J Clin Microbiol 45(9):3089–3094
17. Kaur H, Wengel J, Maiti S (2008) Thermodynamics of DNA-RNA heteroduplex formation: effects of locked nucleic acid nucleotides incorporated into the DNA strand. Biochemistry 47(4):1218–1227
18. Kempf VAJ, Trebesius K, Autenrieth IB (2000) Fluorescent in situ hybridization allows rapid identification of microorganisms in blood cultures. J Clin Microbiol 38(2):830–838
19. Kierzek E, Ciesielska A, Pasternak K, Mathews DH, Turner DH, Kierzek R (2005) The influence of locked nucleic acid residues on the thermodynamic properties of 2′-O-methyl RNA/RNA heteroduplexes. Nucleic Acids Res 33(16):5082–5093
20. Koshkin AA, Singh SK, Nielsen P, Rajwanshi VK, Kumar R, Meldgaard M, Olsen CE, Wengel J (1998) 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(14):3607–3630
21. Krimmer V, Merkert H, von Eiff C, Frosch M, Eulert J, Lohr JF, Hacker J, Ziebuhr W (1999) Detection of Staphylococcus aureus and Staphylococcus epidermidis in clinical samples by 16S rRNA-directed in situ hybridization. J Clin Microbiol 37(8):2667–2673
22. Kubota K, Ohashi A, Imachi H, Harada H (2006) Improved in situ hybridization efficiency with locked-nucleic-acid-incorporated DNA probes. Appl Environ Microbiol 72(8):5311–5317
23. Kumar R, Singh SK, Koshkin AA, Rajwanshi VK, Meldgaard M, Wengel J (1998) The first analogues of LNA (locked nucleic acids): phosphorothioate-LNA and 2′-thio-LNA. Bioorg Med Chem Lett 8(16):2219–2222
24. Langkjaer N, Pasternak A, Wengel J (2009) UNA (unlocked nucleic acid): a flexible RNA mimic that allows engineering of nucleic acid duplex stability. Bioorg Med Chem 17(15):5420–5425
25. Majlessi M, Nelson NC, Becker MM (1998) Advantages of 2′-O-methyl oligoribonucleotide probes for detecting RNA targets. Nucleic Acids Res 26(9):2224–2229
26. Marshall BRH, Annear DI, Goodwin CS, Pearman JW, Warren JR, Armstrong JA (1984) Original isolation of Campylobacter pyloridis from human gastric mucosa. Microbiol Lett 25:83–88
27. Matsumoto K, Nakata E, Tamura T, Saito I, Aizawa Y, Morii T (2013) A peptide nucleic acid (PNA) heteroduplex probe containing an inosine-cytosine base pair discriminates a single-nucleotide difference in RNA. Chemistry 19(16):5034–5040
28. Matthiesen SH, Hansen CM (2012) Fast and non-toxic in situ hybridization without blocking of repetitive sequences. PLoS One 7(7):e40675
29. Mishra S, Ghosh S, Mukhopadhyay R (2012) Ordered self-assembled locked nucleic acid (LNA) structures on gold(111) surface with enhanced single base mismatch recognition capability. Langmuir 28(9):4325–4333
30. Mishra S, Ghosh S, Mukhopadhyay R (2013) Maximizing mismatch discrimination by surface-tethered locked nucleic acid probes via ionic tuning. Anal Chem 85(3):1615–1623
31. Mook OR, Baas F, de Wissel MB, Fluiter K (2007) Evaluation of locked nucleic acid-modified small interfering RNA in vitro and in vivo. Mol Cancer Ther 6(3):833–843
32. Moreno Y, Ferrus MA, Alonso JL, Jimenez A, Hernandez J (2003) Use of fluorescent in situ hybridization to evidence the presence of Helicobacter pylori in water. Water Res 37(9):2251–2256
33. Obika S, Nanbu D, Hari Y, Morio K-I, In Y, Ishida T, Imanishi T (1997) Synthesis of 2′-O,4′-C-methyleneuridine and -cytidine. Novel bicyclic nucleosides having a fixed C3, −endo sugar puckering. Tetrahedron Lett 38(50):8735–8738
34. Owczarzy R, You Y, Moreira BG, Manthey JA, Huang L, Behlke MA, Walder JA (2004) Effects of sodium ions on DNA duplex oligomers: improved predictions of melting temperatures. Biochemistry 43(12):3537–3554
35. Owczarzy R, You Y, Groth CL, Tataurov AV (2011) Stability and mismatch discrimination of locked nucleic acid-DNA duplexes. Biochemistry 50(43):9352–9367
36. Pasternak A, Wengel J (2010) Thermodynamics of RNA duplexes modified with unlocked nucleic acid nucleotides. Nucleic Acids Res 38(19):6697–6706
37. Pasternak A, Wengel J (2011) Unlocked nucleic acid—an RNA modification with broad potential. Org Biomol Chem 9(10):3591–3597
38. Perlikova P, Karlsen KK, Pedersen EB, Wengel J (2014) Unlocked nucleic acids with a pyrene-modified uracil: synthesis, hybridization studies, fluorescent properties and i-motif stability. Chembiochem 15(1):146–156
39. Politz JC, Browne ES, Wolf DE, Pederson T (1998) Intranuclear diffusion and hybridization state of oligonucleotides measured by fluorescence correlation spectroscopy in living cells. Proc Natl Acad Sci U S A 95(11):6043–6048
40. Sadhu C, Dutta S, Gopinathan KP (1984) Influence of formamide on the thermal-stability of DNA. J Biosci 6(6):817–821
41. SantaLucia J Jr, Allawi HT, Seneviratne PA (1996) Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 35(11):3555–3562
42. Sekiguchi Y, Kamagata Y, Nakamura K, Ohashi A, Harada H (1999) Fluorescence in situ hybridization using 16S rRNA-targeted oligonucleotides reveals localization of methanogens and selected uncultured bacteria in mesophilic and thermophilic sludge granules. Appl Environ Microbiol 65(3):1280–1288
43. Stender H, Fiandaca M, Hyldig-Nielsen JJ, Coull J (2002) PNA for rapid microbiology. J Microbiol Methods 48(1):1–17
44. Tavares A, Inacio J, Melo-Cristino J, Couto I (2008) Use of fluorescence in situ hybridization for rapid identification of staphylococci in blood culture samples collected in a Portuguese hospital. J Clin Microbiol 46(9):3097–3100
45. Yan Y, Yan J, Piao X, Zhang T, Guan Y (2012) Effect of LNA- and OMeN-modified oligonucleotide probes on the stability and discrimination of mismatched base pairs of duplexes. J Biosci 37(2):233–241
46. Yilmaz LS, Noguera DR (2007) Development of thermodynamic models for simulating probe dissociation profiles in fluorescence in situ hybridization. Biotechnol Bioeng 96(2):349–363
47. Yilmaz LS, Okten HE, Noguera DR (2006) Making all parts of the 16S rRNA of Escherichia coli accessible in situ to single DNA oligonucleotides. Appl Environ Microbiol 72(1):733–744
48. You Y, Moreira BG, Behlke MA, Owczarzy R (2006) Design of LNA probes that improve mismatch discrimination. Nucleic Acids Res 34(8):e60