Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning

Applied and Environmental Microbiology

Volumn 67, Issue 2, 2001, Pages 880-887

  Qiu, X ^a   Wu, L ^a   Huang, H ^a   McDonel, P E ^a   Palumbo, A V ^a   Tiedje, J M ^a   Zhou, J ^a  

^a OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENDONUCLEASE; HETERODUPLEX; POLYACRYLAMIDE GEL; RIBOSOME RNA; TAQ POLYMERASE;

MICROBIOLOGY;

ARTICLE; ARTIFACT; CHIMERA; GENE AMPLIFICATION; GENE MUTATION; GRAM NEGATIVE BACTERIUM; GRAM POSITIVE BACTERIUM; MOLECULAR CLONING; NONHUMAN; POLYMERASE CHAIN REACTION; PROTEIN PURIFICATION; SPECIES DIFFERENCE;

ARTIFACTS; CLONING, MOLECULAR; DEOXYRIBONUCLEASE I; DNA-DIRECTED DNA POLYMERASE; ECOSYSTEM; GENES, RRNA; GRAM-POSITIVE BACTERIA; MUTATION; NUCLEIC ACID HETERODUPLEXES; POLYMERASE CHAIN REACTION; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; PROTEOBACTERIA; RECOMBINANT FUSION PROTEINS; RNA, RIBOSOMAL, 16S;

EID: 0035145056     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.67.2.880-887.2001     Document Type: Article

References (41)

1. A molecular technique for identification of bacteria using small subunit ribosomal RNA sequence
2. Molecular microbial diversity of an agricultural soil in Wisconsin
3. Molecular microbial diversity in soils from eastern Amazonia: Evidence for unusual microorganisms and microbial population shifts associated with deforestation
4. Chimeric cDNA clones: A novel PCR artifact
5. Deletion mutagenesis during polymerase chain reaction: Dependence on DNA polymerase
6. PCR fidelity of Pfu DNA polymerase and other thermostable DNA polymerase
7. Archaea in coastal marine environments
8. Archaeal means and extremes
9. Genetic relationships determined by a DNA heteroduplex mobility assay: Analysis of HIV-1 env genes
10. Microbial diversity in a hydrocarbon- and chlorinated-solvent-contaminated aquifer undergoing intrinsic bioremediation
11. High fidelity DNA synthesis by the Thermus aquaticus DNA polymerse
12. PAGE analysis of the heteroduplexes formed between PCR-amplified 16S rRNA genes: Estimation of sequence similarity and rDNA complexity
13. Phylogeny of the main bacterial 16S rRNA sequences in Drentse A grassland soils (the Netherlands)
14. Phylogenetic diversity of subsurface marine microbial communities from Atlantic and Pacific oceans
15. Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval
16. Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients
17. Impact of culture independent studies on the emerging phylogenetic view of bacterial diversity
18. Recognition of chimeric small-subunit ribosomal DNAs composed of genes from uncultivated microorganisms
19. Nonradioactive method to study genetic profiles of natural bacterial gommunities by PCR-single-strand-conformation polymorphism
20. Potential risks of gene amplification by PCR as determined by SSU rDNA analysis of a mixed culture of strict barophilic bacteria
21. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA
22. Heteroduplex resolution using T7 endonuclease I in microbial community analyses
23. Succession and convergence of biofilm communities in fixed-film reactors treating aromatic hydrocarbons in groundwater
24. DNA recombination during PCR
25. Estimation of diversity and community structure through restriction fragment length polymorphism distribution analysis of bacterial 16S rRNA genes from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii
26. Profiling of complex microbial populations by denaturing gradient gel etectrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA
27. Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis
28. DNA damage promotes jumping between templates during enzymatic amplification
29. Phylogenetic analysis of the hyperthermophilic pink filament community in Octopus Spring, Yellowstone National Park
30. Bacterial diversity in a soil sample from a subtropical Australian environment as determined by SSU rDNA analysis
31. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR
32. Kinetic bias in estimates of coastal picoplankton community structure obtained by measurements of small-subunit rRNA gene PCR amplicon length heterogeneity
33. The frequency of chimeric molecules as a consequence of PCR co-amplification of 16S rRNA genes from different bacterial species
34. Frequency of formation of chimeric molecules as a consequence of PCR coamplification of 16S rRNA genes from mixed bacterial genomes
35. 16S ribosomal DNA amplification for phylogenetic study
36. Detecting single base substitution as heteroduuplex polymorphisms
37. Determination of microbial diversity in environmental samples: Pitfalls of PCR-based rRNA analysis
38. Bacterial diversity of a Carolina bay as determined by 16S rRNA gene analysis: Confirmation of novel taxa
39. Phylogenetic analysis of a new group of denitrifiers capable of anaerobic growth on toluene: Description of Azoarcus tolulyticus sp. nov.
40. Phylogenetic diversity of a bacterial community determined from Siberian tundra soil DNA