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Table 3 16S rRNA targeted DNA probe sequences, target sites and target taxa

From: In vitromodeling of host-parasite interactions: the 'subgingival' biofilm challenge of primary human epithelial cells

DNA Probe

Sequence (5' to 3')b

Site

% Forma-

mide

Target

Reference

EUB338

GCTGCCTCCCGTAGGAGT

338-55

30-50

All biofilm members

[52]

L-Act476-2

ATCCAGCTACCGTCAACC

476-93

25-40

A. naeslundii

This study

CAMP655

CATCTGCCTCTCCCTYAC

655-72

30

C. rectus

This study

Fnuc133c

GTTGTCCCTANCTGTGAGGC

133-52

30-40

F. nucleatum

This study

L-Pgin1006-2

GTTTTCACCATCMGTCATC

1006-24

30

P. gingivalis

This study

L-Pint649-2

CGTTGCGTGCACTCAAGTC

649-67

30-50

P. intermedia

This study

L-MIT446-2

ACACYCGTTCTTCTCTTACAA

446-66

25-50

S. oralis

This study

MIT447

CACYCGTTCTTCTCTTACA

447-65

25

S. oralis

[47]

L-Scoint172-2

CAGTAAATGTTCTTATGCGGTA

172-91

25-40

S. intermedius

This study

Tfor127

CTCTGTTGCGGGCAGGTTAC

127-46

30-40

T. forsythia

[44]

Tfor582

GCGGACTTAACAGCCCACCT

582-601

30-40

T. forsythia

[44]

L-Tlema738-2

GCGTCAATTATCTGCCGG

738-55

30

T. lecithinolythicum

This study

VEI217

AATCCCCTCCTTCAGTGA

217-34

25-50

V. dispar

[47]

  1. a Probes were labeled at the 5'-end with Cy3, Cy5, 6-carboxyfluorescein (FAM), or 6-carboxy-X-rhodamine (ROX). The designations of all probes containing locked-nucleic-acid (LNA) substitutions start with L-. b Bold printed characters indicate LNA substitutions [53]. LNA incorporated DNA probes (LNA/DNA probes) have been described to improve significantly FISH fluorescence intensity in comparison to conventional DNA probes with the same sequence [53]. Our data fully confirm these findings. Applied in FISH at 10-20% higher formamide concentration than the corresponding conventional DNA probe with dental plaque samples, we noticed no loss of specificity for any of the new LNA/DNA probes (data not shown).