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Xiong Y, McQuistan TJ, Stanek JW, Summerton JE, Mata JE, Squier TC. Detection of unique Ebola virus oligonucleotides using fluorescently-labeled phosphorodiamidate morpholino oligonucleotide probe pairs. Anal Biochem 2018; 557:84-90. [PMID: 30030994 DOI: 10.1016/j.ab.2018.07.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 07/12/2018] [Indexed: 12/22/2022]
Abstract
Here we identify a low-cost diagnostic platform using fluorescently-labeled phosphorodiamidate morpholino oligonucleotide (PMO) probe pairs, which upon binding target oligonucleotides undergo fluorescence resonance energy transfer (FRET). Using a target oligonucleotide derived from the Ebola virus (EBOV), we have derivatized PMO probes with either Alexa Fluor488 (donor) or tetramethylrhodamine (acceptor). Upon EBOV target oligonulceotide binding, observed changes in FRET between PMO probe pairs permit a 25 pM lower limit of detection; there is no off-target binding within a complex mixture of nucleic acids and other biomolecules present in human saliva. Equivalent levels of FRET occur using PMO probe pairs for single or double stranded oligonucleotide targets. High-affinity binding is retained under low-ionic strength conditions that disrupt oligonucleotide secondary structures (e.g., stem-loop structures), ensuring reliable target detection. Under these low-ionic strength conditions, rates of PMO probe binding to target oligonucleotides are increased 3-fold relative to conventional high-ionic strength conditions used for nucleic acid hybridization, with half-maximal binding occurring within 10 min. Our results indicate an ability to use PMO probe pairs to detect clinically relevant levels of EBOV and other oligonucleotide targets in complex biological samples without the need for nucleic acid amplification, and open the possibility of population screening that includes assays for the genomic integration of DNA based copies of viral RNA.
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Affiliation(s)
- Yijia Xiong
- Department of Basic Medical Sciences, Western University of Health Sciences, 200 Mullins Drive, Lebanon, OR, 97355, United States
| | - Tammie J McQuistan
- Department of Basic Medical Sciences, Western University of Health Sciences, 200 Mullins Drive, Lebanon, OR, 97355, United States
| | - James W Stanek
- Department of Basic Medical Sciences, Western University of Health Sciences, 200 Mullins Drive, Lebanon, OR, 97355, United States
| | - James E Summerton
- Gene Tools, LLC, One Summerton Way, Philomath, OR, 97370, United States
| | - John E Mata
- Department of Basic Medical Sciences, Western University of Health Sciences, 200 Mullins Drive, Lebanon, OR, 97355, United States; Takena Technologies Inc, 405 West First Street, Albany, OR, 97321, United States
| | - Thomas C Squier
- Department of Basic Medical Sciences, Western University of Health Sciences, 200 Mullins Drive, Lebanon, OR, 97355, United States.
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2
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Wang Q, Chen L, Long Y, Tian H, Wu J. Molecular beacons of xeno-nucleic acid for detecting nucleic acid. Theranostics 2013; 3:395-408. [PMID: 23781286 PMCID: PMC3677410 DOI: 10.7150/thno.5935] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 04/10/2013] [Indexed: 12/24/2022] Open
Abstract
Molecular beacons (MBs) of DNA and RNA have aroused increasing interest because they allow a continuous readout, excellent spatial and temporal resolution to observe in real time. This kind of dual-labeled oligonucleotide probes can differentiate between bound and unbound DNA/RNA in homogenous hybridization with a high signal-to-background ratio in living cells. This review briefly summarizes the different unnatural sugar backbones of oligonucleotides combined with fluorophores that have been employed to sense DNA/RNA. With different probes, we epitomize the fundamental understanding of driving forces and these recognition processes. Moreover, we will introduce a few novel and attractive emerging applications and discuss their advantages and disadvantages. We also highlight several perspective probes in the application of cancer therapeutics.
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Wu YT, Liao JD, Lin JI, Lu CC. Determination of the optimized conditions for coupling oligonucleotides with 16-mercaptohexadecanoic acid chemically adsorbed upon Au. Bioconjug Chem 2007; 18:1897-904. [PMID: 17970584 DOI: 10.1021/bc700217n] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A specific 5'-modified amino group oligonucleotide (Primer 1), 15-mers in length, is selectively coupled with the carboxyl terminated 16-mercaptohexadecanoic acid (MHDA) chemically adsorbed on Au and subsequently hybridized with Antisense Primer. The amide-coupling process is of significance to create an intermediate structure for the purpose of adding Primer 1, while the hybridization reaction is relevant to various diagnostic purposes to determine the presence in nucleic acids for a target sequence. In this work, the coupling setting was particularly emphasized by varying commonly used temperatures and pH values with a definite concentration of coupling agents (i.e., 10 mM). The recombination with analogous hybridization treatment was investigated using high resolution X-ray photoelectron spectroscopy and a 75 degrees grazing angle Fourier transform infrared spectrometer. On the basis of the spectroscopic studies, the optimized conditions for the coupling process that is also correlated with the molecular density of subsequent hybridization process on MHDA/Au have been proposed at 37 degrees C and a pH value of 4.5. Therefore, it is pertinent to intensify the joining of short-chain DNA strands by complementary base pairing in diagnostic applications such as the identification of single nucleotide polymorphisms.
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Affiliation(s)
- Yi-Te Wu
- Department of Materials Science and Engineering, Center for Micro/Nano Science and Technology, National Cheng Kung University, Tainan, Taiwan
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Ashtari P, He X, Wang K, Gong P. An efficient method for recovery of target ssDNA based on amino-modified silica-coated magnetic nanoparticles. Talanta 2005; 67:548-54. [PMID: 18970204 PMCID: PMC7111873 DOI: 10.1016/j.talanta.2005.06.043] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper, an improved recovery method for target ssDNA using amino-modified silica-coated magnetic nanoparticles (ASMNPs) is reported. This method takes advantages of the amino-modified silica-coated magnetic nanoparticles prepared using water-in-oil microemulsion technique, which employs amino-modified silica as the shell and iron oxide as the core of the magnetic nanoparticles. The nanoparticles have a silica surface with amino groups and can be conjugated with any desired bio-molecules through many existing amino group chemistry. In this research, a linear DNA probe was immobilized onto nanoparticles through streptavidin conjugation using covalent bonds. A target ssDNA(I) (5'-TMR-CGCATAGGGCCTCGTGATAC-3') has been successfully recovered from a crude sample under a magnet field through their special recognition and hybridization. A designed ssDNA fragment of severe acute respiratory syndrome (SARS) virus at a much lower concentration than the target ssDNA(I) was also recovered with high efficiency and good selectivity.
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Affiliation(s)
| | | | - Kemin Wang
- Biomedical Engineering Center, State Key Laboratory of Chemo/Biosensing and Chemometrics, Institute of Life Science and Biological Technology, Hunan University & Engineering Research Center for Bio-Nanotechnology of Hunan Province, Changsha 410082, PR China
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Lowe M, Spiro A, Zhang YZ, Getts R. Multiplexed, particle-based detection of DNA using flow cytometry with 3DNA dendrimers for signal amplification. Cytometry A 2005; 60:135-44. [PMID: 15290714 DOI: 10.1002/cyto.a.20021] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
BACKGROUND Complex mixtures of DNA may be found in environmental and medical samples. There is a need for techniques that can measure low concentrations of target DNAs. For a multiplexed, flow cytometric assay, we show that the signal-to-noise ratio for fluorescence detection may be increased with the use of 3DNA dendrimers. A single fluorescent DNA molecule per bead could be detected with conventional flow cytometry instrumentation. METHODS The analyte consisted of single-stranded (ss) DNA amplicons that were hybridized to capture probes on the surface of fluorescent polystyrene microspheres (beads) and initially labeled with streptavidin-R-phycoerythrin (single-step labeling). These beads have a low reporter fluorescence background and high efficiency of DNA hybridization. The DNA/SA-RPE complex was then labeled with 3DNA dendrimers and SA-RPE. The bead complexes were detected with a Luminex 100 flow cytometer. Bead standards were developed to convert the intensity to the number of SA-RPE labels per bead and the number of dendrimers per bead. RESULTS The dendrimer assay resulted in 10-fold fluorescence amplification compared with single-step SA-RPE labeling. Based on concentration curves of pure target ss-amplicons, the signal-to-noise ratio of the dendrimer assay was greater by a factor of 8.5 over single-step SA-RPE labeling. The dendrimer assay was tested on 16S ribosomal DNA amplified from filter retentates of contaminated groundwater. Multiplexed detection of a single dendrimer-labeled DNA molecule per bead was demonstrated. CONCLUSIONS Multiplexed detection of DNA hybridization on a single molecule level per bead was achieved with conventional flow cytometry instrumentation. This assay is useful for detecting target DNAs at low concentrations.
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Affiliation(s)
- Mary Lowe
- Physics Department, Loyola College in Maryland, Baltimore, Maryland 21210, USA.
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Platonova GA, Tennikova TB. Chromatographic investigation of macromolecular affinity interactions. J Chromatogr A 2005; 1065:75-81. [PMID: 15782953 DOI: 10.1016/j.chroma.2004.10.073] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
High-performance monolithic disk affinity chromatography was applied to the investigation of formation of complexes between (1) complementary polyriboadenylic and polyribouridylic acids, e.g. poly(A) and poly(U), respectively, (2) poly(A) and synthetic polycation poly(allylamine), pAA. Polyriboadenylic acid and poly(allylamine) were immobilized on macroporous disks (CIM disks). Quantitative parameters of affinity interactions between macromolecules were established using frontal analysis at different flow rates.
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Affiliation(s)
- Galina A Platonova
- Institute of Macromolecular Compounds, Russian Academy of Sciences, St Petersburg 199004, Russia
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Platonova GA, Tennikova TB. Affinity processes realized on high-flow-through methacrylate-based macroporous monoliths. J Chromatogr A 2005; 1065:19-28. [PMID: 15782946 DOI: 10.1016/j.chroma.2004.12.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The technology for preparation of rigid macroporous polymers suggested in the late 1980s has become a powerful instrument for the development of a novel scientific and practical field. At present, monolithic stationary phases are widely used in the processes of bioseparation (chromatography), bioconversion (enzyme reactors) as well as in other processes based on interphase mass distribution (for example, solid phase peptide and oligonucleotide synthesis). Bioaffinity modes of suggested dynamic methods are very promising for their use in different analytical processes (immunological, ecological, medical and other types of analytical monitoring), preparative isolation of blood proteins such as myoglobin, hemoglobin, immunoglobulins, etc. and also recombinant products directly from cell supernatants or lysates. For the first time, it has been shown that bioaffinity pairing with participation of immobilized on carefully designed rigid supports is very fast and the whole process of affinity separation can be realized within second time scale. The principle of bioaffinity recognition is generaly at the construction of biological reactors (for example, enzyme reactors). Improved kinetics of biocatalized reactions is explained by a minimal influence on the surface of the used sorbent. Very perspective field is the use of discussed monoliths for solid phase chemical synthesis of fragments of biological macromolecules (peptides and oligonucleotides). Several examples of these applications will be presented and discussed.
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Affiliation(s)
- Galina A Platonova
- Institute of Macromolecular Compounds, Russian Academy of Sciences, St Petersburg 199 004, Russia
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Pokorski JK, Witschi MA, Purnell BL, Appella DH. (S,S)-trans-cyclopentane-constrained peptide nucleic acids. a general backbone modification that improves binding affinity and sequence specificity. J Am Chem Soc 2005; 126:15067-73. [PMID: 15548003 DOI: 10.1021/ja046280q] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Replacing the ethylenediamine portion of aminoethylglycine peptide nucleic acids (aegPNAs) with one or more (S,S)-trans-cyclopentane diamine units significantly increases binding affinity and sequence specificity to complementary DNA, making these modified PNAs ideal for use as nucleic acid probes in genomic analysis. The synthesis and study of this new class of PNAs (tcypPNAs) is described in which trans-cyclopentane diamine has been incorporated into several positions, and in varying number, within PNA backbones of mixed-base sequences.
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Affiliation(s)
- Jonathan K Pokorski
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
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9
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Nielsen PE. The many faces of PNA. Int J Pept Res Ther 2005. [DOI: 10.1007/s10989-005-4860-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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10
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Abstract
Peptide nucleic acids (PNA) are deoxyribonucleic acid (DNA) mimics with a pseudopeptide backbone. PNA is an extremely good structural mimic of DNA (or of ribonucleic acid [RNA]), and PNA oligomers are able to form very stable duplex structures with Watson-Crick complementary DNA and RNA (or PNA) oligomers, and they can also bind to targets in duplex DNA by helix invasion. Therefore, these molecules are of interest in many areas of chemistry, biology, and medicine, including drug discovery, genetic diagnostics, molecular recognition, and the origin of life. Recent progress in studies of PNA properties and applications is reviewed.
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Affiliation(s)
- Peter E Nielsen
- Center for Biomolecular Recognition, IMBG, The Panum Institute, University of Copenhagen, Blegdamsvej 3C, Copenhagen DK-2200N, Denmark.
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11
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12
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Bruckner-Lea CJ, Tsukuda T, Dockendorff B, Follansbee JC, Kingsley MT, Ocampo C, Stults JR, Chandler DP. Renewable microcolumns for automated DNA purification and flow-through amplification: from sediment samples through polymerase chain reaction. Anal Chim Acta 2002. [DOI: 10.1016/s0003-2670(01)01438-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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Li Y, Jin T, Liu K. Synthesis and binding affinity of a chiral PNA analogue. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2001; 20:1705-21. [PMID: 11580196 DOI: 10.1081/ncn-100105906] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The synthesis of a chiral peptide nucleic acid (PNA), which is composed of N-aminoethyl-cis-4-nucleobase-L-proline units, was described. The chiral PNA monomers containing all four nucleobases (A. T, C and G) were steroselectively prepared. The x-ray diffraction data from a single crystal confirmed the configuration of a key intermediate. Binding activity of the oligomers with their complementary DNA targets was also investigated.
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Affiliation(s)
- Y Li
- Beijing Institute of Pharmacology & Toxicology, China
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Gilar M, Bouvier ES, Compton BJ. Advances in sample preparation in electromigration, chromatographic and mass spectrometric separation methods. J Chromatogr A 2001; 909:111-35. [PMID: 11269513 DOI: 10.1016/s0021-9673(00)01108-0] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The quality of sample preparation is a key factor in determining the success of analysis. While analysis of pharmaceutically important compounds in biological matrixes has driven forward the development of sample clean-up procedures in last 20 years, today's chemists face an additional challenge: sample preparation and analysis of complex biochemical samples for characterization of genotypic or phenotypic information contained in DNA and proteins. This review focuses on various sample pretreatment methods designed to meet the requirements for the analysis of biopolymers and small drugs in complex matrices. We discuss the advances in development of solid-phase extraction (SPE) sorbents, on-line SPE, membrane-based sample preparation, and sample clean-up of biopolymers prior to their analysis by mass spectrometry.
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Affiliation(s)
- M Gilar
- Waters Corp., Milford, MA 01757, USA.
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Nielsen PE. Peptide nucleic acid: a versatile tool in genetic diagnostics and molecular biology. Curr Opin Biotechnol 2001; 12:16-20. [PMID: 11167067 DOI: 10.1016/s0958-1669(00)00170-1] [Citation(s) in RCA: 174] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
During the past ten years, the DNA mimic peptide nucleic acid has inspired the development of a variety of hybridisation-based methods for detection, quantification, purification and characterisation of nucleic acids. Most of these methods have taken advantage of the very favourable DNA and RNA hybridisation properties of peptide nucleic acids combined with the unique properties and opportunities offered by peptide chemistry. Within the past year, significant progress in in situ hybridisation technology has been achieved, which has resulted, in particular, in reliable and sensitive methods for detection of bacteria in clinical samples, as well as in environmental samples. Furthermore, applications of the polymerase chain reaction clamping method have been expanded, and novel ways of exploiting complexes of peptide nucleic acids with double-stranded DNA, such as double duplex invasion complexes and PD loops, have been developed.
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Affiliation(s)
- P E Nielsen
- Center for Biomolecular Recognition, Department for Biochemistry and Genetics, Laboratory B, The Panum Institute, Blegdamsvej 3c, DK-2200 N Copenhagen, Denmark
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Chandler DP, Stults JR, Cebula S, Schuck BL, Weaver DW, Anderson KK, Egholm M, Brockman FJ. Affinity purification of DNA and RNA from environmental samples with peptide nucleic acid clamps. Appl Environ Microbiol 2000; 66:3438-45. [PMID: 10919804 PMCID: PMC92168 DOI: 10.1128/aem.66.8.3438-3445.2000] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Bispeptide nucleic acids (bis-PNAs; PNA clamps), PNA oligomers, and DNA oligonucleotides were evaluated as affinity purification reagents for subfemtomolar 16S ribosomal DNA (rDNA) and rRNA targets in soil, sediment, and industrial air filter nucleic acid extracts. Under low-salt hybridization conditions (10 mM NaPO(4), 5 mM disodium EDTA, and 0.025% sodium dodecyl sulfate [SDS]) a PNA clamp recovered significantly more target DNA than either PNA or DNA oligomers. The efficacy of PNA clamps and oligomers was generally enhanced in the presence of excess nontarget DNA and in a low-salt extraction-hybridization buffer. Under high-salt conditions (200 mM NaPO(4), 100 mM disodium EDTA, and 0.5% SDS), however, capture efficiencies with the DNA oligomer were significantly greater than with the PNA clamp and PNA oligomer. Recovery and detection efficiencies for target DNA concentrations of > or =100 pg were generally >20% but depended upon the specific probe, solution background, and salt condition. The DNA probe had a lower absolute detection limit of 100 fg of target (830 zM [1 zM = 10(-21) M]) in high-salt buffer. In the absence of exogenous DNA (e.g., soil background), neither the bis-PNA nor the PNA oligomer achieved the same absolute detection limit even under a more favorable low-salt hybridization condition. In the presence of a soil background, however, both PNA probes provided more sensitive absolute purification and detection (830 zM) than the DNA oligomer. In varied environmental samples, the rank order for capture probe performance in high-salt buffer was DNA > PNA > clamp. Recovery of 16S rRNA from environmental samples mirrored quantitative results for DNA target recovery, with the DNA oligomer generating more positive results than either the bis-PNA or PNA oligomer, but PNA probes provided a greater incidence of detection from environmental samples that also contained a higher concentration of nontarget DNA and RNA. Significant interactions between probe type and environmental sample indicate that the most efficacious capture system depends upon the particular sample type (and background nucleic acid concentration), target (DNA or RNA), and detection objective.
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MESH Headings
- Chromatography, Affinity
- DNA Probes
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/isolation & purification
- DNA, Ribosomal/metabolism
- Deltaproteobacteria/genetics
- Deltaproteobacteria/isolation & purification
- Environmental Microbiology
- Nucleic Acid Conformation
- Nucleic Acid Hybridization
- Peptide Nucleic Acids/chemistry
- Peptide Nucleic Acids/metabolism
- Polymerase Chain Reaction
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/isolation & purification
- RNA, Ribosomal, 16S/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Sensitivity and Specificity
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Affiliation(s)
- D P Chandler
- Environmental Microbiology Group, Pacific Northwest National Laboratory, Richland, Washington 99352, USA.
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