Cooperative Oligonucleotides Mediating Direct Capture of Hepatitis C Virus RNA from Serum

O’Meara, Deirdre; Yun, Zhibing; Sönnerborg, Anders; Lundeberg, Joakim

doi:10.1128/jcm.36.9.2454-2459.1998

Cited by 31 publications

(14 citation statements)

References 26 publications

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“…Here, the purification is performed with a capture probe covalently linked to paramagnetic beads and an adjacently annealing modular probe used to stabilize the complex. The improvement in capture efficiency using this modular probe has been documented in this report and in previous studies (12,13). Contributing factors to the improvement of capture include van der Waal's forces that appear between two adjacent positioned primers (i.e., capture and modular probes) and opening the secondary structure of the target sequence.…”

Section: Discussionsupporting

confidence: 68%

“…Improvements on probe design could involve varying the capture sequences or the use of nucleotide derivatives (such as PNA) or spacer sequences (10). For such purposes, it would be possible to take advantage of biosensor technology that has been used earlier for real-time, quantitative estimation of hybridization events (10)(11)(12)(13). We have previously shown that magnetic separation can successfully be automated using both commercial and in-house instrumentation for similar purposes (7,15,17).…”

Section: Discussionmentioning

confidence: 99%

“…This is probably because the modules interact in the opening of the secondary structure and contribute to a base stacking effect, even as a single-nucleotide gap between the probes decreases the stability significantly (12). This increase in affinity can be advantageous in array technology (1)(2)(3)6,14), antisense applications and nucleic acid sample preparation (4,8,13,16).…”

Section: Introductionmentioning

confidence: 99%

“…In this study, we investigated the use of a solid-phase capture method for the purification of cycle sequencing products. Capture probes complementary to the vectors were covalently coupled to the magnetic beads, and a second modular probe that anneals adjacent to the capture probe site was used to increase the efficiency of capturing sequencing products, as described earlier, for the direct capture of virus genomes (13).…”

Section: Introductionmentioning

confidence: 99%

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Cooperative Oligonucleotides in Purification of Cycle Sequencing Products

et al. 2000

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Nucleic acid hybridization is an essential component in many of today's standard molecular biology techniques. In a recent study, we investigated whether nucleic acid capture could be improved by taking advantage of stacking hybridization, which refers to the stabilizing effect that exists between oligonucleotides when they hybridize in a contiguous tandem fashion. Here, we describe a specific approach for purification of sequencing products using cooperative probes that hybridize to single-strand targets where one of the probes has been coupled to a magnetic bead. This approach has been developed for standard sequencing primers and has been applied to shotgun plasmid libraries. The cooperative probes have been designed to anneal within the common vector sequence and to avoid co-purification of nonextended sequencing primers and misprimed sequencing products. The reuse of magnetic beads, together with salt independent elution, makes the approach suitable for high-capacity capillary electrophoresis instruments.

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Section: Discussionsupporting

confidence: 68%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Cooperative Oligonucleotides in Purification of Cycle Sequencing Products

et al. 2000

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“…These are usually based on enzymatic lysis, binding of the nucleic acid to matrixcontaining spin columns using spin or vacuum technology for washing and buffer exchange. Alternatively, magnetic particles with coupled nucleic acid probes can be used for nucleic acid capture, utilizing a magnetic device for collection of the beads when buffer is changed (Albert, 1992;Deggerdal, 1997;O'Meara, 1998). A potential shortcut in sample preparation is to capture the whole target organism by for example immunomagnetic separation (Olsvik, 1994) or filtration (Bej, 1991), wash the isolated target and add it directly to the PCR vial, where it is lyzed prior to amplification.…”

Section: Sample Preparationmentioning

confidence: 99%

Molecular Diagnostics of Infectious Diseases

Valiathan

Asthana

2010

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In DNA-based diagnostics, the polymerase chain reaction (PCR) is the most widely used DNA amplification method. To enable both sensitive and specific detection of agents causing infectious diseases, the PCR needs to be combined with methods to prepare the clinical sample containing the genetic material of the pathogen. Furthermore, methods for detection and DNA sequence analysis of the PCR amplification products are needed. This thesis describes the development of integrated systems for detection, quantification and characterization of microorganisms.An immunomagnetic separation (IMS) technique has been used to isolate Bordetella pertussis from nasopharyngeal aspirate samples. The post-PCR detection and typing of Bordetella spp. was performed by a combination of restriction enzyme analysis of the amplified pertussis toxin (PT) promoter region and a solid-phase colorimetric detection system; detection of immobilized amplified nucleic acid (DIANA). To investigate whether this approach could be used for reliable discrimination between the three Bordetella spp. infecting humans, the PT promoter region used for diagnostics was sequenced in 33 strains. To determine the DNA sequence of this polymorphic and repetitive region, a new technique, bidirectional pyrosequencing, was utilized. This procedure was used to resolve the sequence of this DNA region, which is able to form stable secondary structures in conventional Sanger DNA sequencing. A quantitative assay using competitive PCR and the DIANA detection technique was also developed, for quantification of B. pertussis in clinical samples.By arbitrary PCR, a DNA sequence apparently specific for Vibrio cholerae O139 Bengal was isolated and characterized. A nested PCR assay was developed for sensitive and specific detection of V. cholerae O139 Bengal in clinical samples and in environmental water samples, where differentiation between V. cholerae O139 Bengal and V. cholera O1 is of epidemiological interest.The magnetic separation approach was also used to capture human immunodeficiency virus (HIV-1) RNA from patient plasma. A nested reverse transcription (RT)-PCR with four internal competitors was combined with electrophoretic separation and quantification of the PCR amplicons on an automated DNA sequencer. From the internal calibration curve, the amount of HIV-1 RNA in the sample could be determined. Furthermore, a primer extension assay was combined with detection and quantification of the competitive PCR products by the same biochemiluminescent detection technique that is used in pyrosequencing. Quantification of HIV-1 viral load has implications in monitoring of antiretroviral therapy and in assessment of disease progression into AIDS. LIST OF PUBLICATIONSThis thesis is based on the following papers, which in the text will be referred to by their Roman numerals:

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Survey of the 1998 optical biosensor literature

Myszka

1999

J. Mol. Recognit.

120

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The utilization of optical biosensors to study molecular interactions continues to expand. In 1998, 384 articles relating to the use of commercial biosensors were published in 130 different journals. While significant strides in new applications and methodology were made, a majority of the biosensor literature is of rather poor quality. Basic information about experimental conditions is often not presented and many publications fail to display the experimental data, bringing into question the credibility of the results. This review provides suggestions on how to collect, analyze and report biosensor data.

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Cooperative Oligonucleotides Mediating Direct Capture of Hepatitis C Virus RNA from Serum

Cited by 31 publications

References 26 publications

Cooperative Oligonucleotides in Purification of Cycle Sequencing Products

Cooperative Oligonucleotides in Purification of Cycle Sequencing Products

Molecular Diagnostics of Infectious Diseases

Survey of the 1998 optical biosensor literature

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