DNA‐probes for the highly sensitive identification of single nucleotide polymorphism using single‐molecule spectroscopy

Friedrich, Achim; Hoheisel, Jörg D.; Marmé, Nicole; Knemeyer, Jens Peter

doi:10.1016/j.febslet.2007.03.031

Cited by 22 publications

(13 citation statements)

References 22 publications

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“…Furthermore, the probes are usually labeled with red-absorbing fluorophores that can be easily excited by inexpensive diode lasers. These features make Smart Probes ideal candidates for single-molecule experiments that enable very sensitive and specific detection of DNA sequences with and without amplification of the target DNA [15,68,69].…”

Section: N O T F O R D I S T R I B U T I O Nmentioning

confidence: 99%

Recent Patents on Self-Quenching DNA Probes

Knemeyer

Marmé

2007

DNAG

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In this review, we report on patents concerning self-quenching DNA probes for assaying DNA during or after amplification as well as for direct assaying DNA or RNA, for example in living cells. Usually the probes consist of fluorescently labeled oligonucleotides whose fluorescence is quenched in the absence of the matching target DNA. Thereby the fluorescence quenching is based on fluorescence resonance energy transfer (FRET), photoinduced electron transfer (PET), or electronically interactions between dye and quencher. However, upon hybridization to the target or after the degradation during a PCR, the fluorescence of the dye is restored. Although the presented probes were originally developed for use in homogeneous assay formats, most of them are also appropriate to improve surface-based assay methods. In particular we describe patents for self-quenching primers, self-quenching probes for TaqMan assays, probes based on G-quartets, Molecular Beacons, Smart Probes, and Pleiades Probes.

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Section: N O T F O R D I S T R I B U T I O Nmentioning

confidence: 99%

Recent Patents on Self-Quenching DNA Probes

Knemeyer

Marmé

2007

DNAG

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“…They prevent non-specific interactions between the probe and unintended nucleic acid (mismatch) sequences by specifically hybridizing with such mismatch sequences, thereby isolating the SP to hybridize exclusively with the target sequence of interest. Oligonucleotide blockers have been previously used in the detection of single nucleotide mutation [41,42], and our research group recently reported a simple protocol involving the use of hairpin-shaped NABs for mixed-base miRNA detection [40]. Thus, unlike other methods that have so far been used for miRNA detection, homogeneous methods based on the SP/NABs system can offer good sensitivity, while also presenting excellent discrimination between the miRNA target of interest and similar mismatch sequences, including single nucleotide polymorphism (SNP).…”

Section: Introductionmentioning

confidence: 99%

“…Furthermore, this universal detection system presents good sensitivity and sequence-specific discrimination in vitro that is better than previously-reported miRNA detection methods. We wish to state that this work involves the use of linear NABs (LNABs), whose performance and blocking characteristics may be quite different from hairpin-shaped NABs [40,41].…”

Section: Introductionmentioning

confidence: 99%

Detection of Several Homologous MicroRNAs by a Single Smart Probe System Consisting of Linear Nucleic Acid Blockers

Oladepo

Yusuf

2019

Molecules

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We report a universal smart probe (SP) that is capable of detecting several homologous let-7 microRNAs (miRNAs). While the SP is complementary to let-7a, and therefore, strongly binds to this target, due to sequence homology, the SP also has equal propensity to non-specifically hybridize with let-7b and let-7c, which are homologous to let-7a. The fluorescence signal of the SP was switched off in the absence of any homologous member target, but the signal was switched on when any of the three homologous members was present. With the assistance of nucleic acid blockers (NABs), this SP system can discriminate between homologous miRNAs. We show that the SP can discriminate between let-7a and the other two sequences by using linear NABs (LNABs) to block non-specific interactions between the SP and these sequences. We also found that LNABs used do not cross-react with the let-7a target due to the low LNABs:SP molar ratio of 6:1 used. Overall, this SP represents a universal probe for the recognition of a homologous miRNA family. The assay is sensitive, providing a detection limit of 6 fmol. The approach is simple, fast, usable at room temperature, and represents a general platform for the in vitro detection of homologous microRNAs by a single fluorescent hairpin probe.

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“…Also some long-established methods that have been applied at the radio-frequency regime are transformed into working concepts at optical frequencies [6,7]. The driving force behind the research is the desire to achieve ever more sensitive detection of molecules, with applications in, for example, in vivo imaging of cells [8] and early detection of malignant agents [9]. Among the properties of emitters that nowadays can be controlled on the nanoscale are the polarization [5,10], angular emission [11,12], lifetime [13,14] and emission wavelength [15,16].…”

Section: Introductionmentioning

confidence: 99%

Shaping single emitter emission with metallic hole arrays: strong focusing of dipolar radiation

2013

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Nanoscale plasmonic structures allow for control of the emission of single emitters, such as fluorescent molecules and quantum dots, enabling phenomena such as lifetime reduction, emission redirection and color sorting of photons. We present single emitter emission tailored with arrays of holes of heterogeneous size, perforated in a gold film. With spatial control of the local amplitude and phase of the electromagnetic field radiated by the emitter, a desired near- or far-field distribution of the electromagnetic waves can be obtained. This control is established by varying the aspect ratio of the individual holes and the periodicity of the array surrounding the emitter. As an example showing the versatility of the technique, we present the strong focusing of the radiation of a highly divergent dipole source, for both p- and s-polarized waves.

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DNA‐probes for the highly sensitive identification of single nucleotide polymorphism using single‐molecule spectroscopy

Cited by 22 publications

References 22 publications

Recent Patents on Self-Quenching DNA Probes

Recent Patents on Self-Quenching DNA Probes

Detection of Several Homologous MicroRNAs by a Single Smart Probe System Consisting of Linear Nucleic Acid Blockers

Shaping single emitter emission with metallic hole arrays: strong focusing of dipolar radiation

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