DNA microarrays for hybridization detection by surface plasmon resonance spectroscopy

Kick, Alfred; Bönsch, Martin; Katzschner, Beate; Voigt, J.; Herr, Alexander; Brabetz, Werner; Jung, Martin; Sonntag, Frank; Klotzbach, Udo; Danz, Norbert; Howitz, S.; Mertig, Michael

doi:10.1016/j.bios.2010.07.108

Cited by 26 publications

(22 citation statements)

References 19 publications

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“…This is especially intended for designing strands where a molecular spacer is located between the neighboring sequence and the TAG. For example, such a spacer could be a hexaethylene glycol moiety [9]. Actually, overlapping subsequences, which would evolve through directly attaching one neighboring sequence to either the 3’ or 5’ end of a TAG, are not considered.…”

Section: Resultsmentioning

confidence: 99%

“…Such structure formation competes against the hybridization with target DNA strands. Hence, a fast and sensitive detection on microarrays is hindered by secondary structures [9]. Accordingly, we generated sequences not only with minimum criton length L c for a global criton rule but we also prevented self-complementarity and the risk of hairpin formation.…”

Section: Resultsmentioning

confidence: 99%

“…Additionally, specific care has to be taken with regard to secondary structures that can occur by folding due to intrastrand interactions. Hairpin structures reduce the hybridization efficiency, the binding rates, and thus, the detection limits on DNA microarrays [9]. …”

Section: Introductionmentioning

confidence: 99%

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EGNAS: an exhaustive DNA sequence design algorithm

2012

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BackgroundThe molecular recognition based on the complementary base pairing of deoxyribonucleic acid (DNA) is the fundamental principle in the fields of genetics, DNA nanotechnology and DNA computing. We present an exhaustive DNA sequence design algorithm that allows to generate sets containing a maximum number of sequences with defined properties. EGNAS (Exhaustive Generation of Nucleic Acid Sequences) offers the possibility of controlling both interstrand and intrastrand properties. The guanine-cytosine content can be adjusted. Sequences can be forced to start and end with guanine or cytosine. This option reduces the risk of “fraying” of DNA strands. It is possible to limit cross hybridizations of a defined length, and to adjust the uniqueness of sequences. Self-complementarity and hairpin structures of certain length can be avoided. Sequences and subsequences can optionally be forbidden. Furthermore, sequences can be designed to have minimum interactions with predefined strands and neighboring sequences.ResultsThe algorithm is realized in a C++ program. TAG sequences can be generated and combined with primers for single-base extension reactions, which were described for multiplexed genotyping of single nucleotide polymorphisms. Thereby, possible foldback through intrastrand interaction of TAG-primer pairs can be limited. The design of sequences for specific attachment of molecular constructs to DNA origami is presented.ConclusionsWe developed a new software tool called EGNAS for the design of unique nucleic acid sequences. The presented exhaustive algorithm allows to generate greater sets of sequences than with previous software and equal constraints. EGNAS is freely available for noncommercial use at http://www.chm.tu-dresden.de/pc6/EGNAS.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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EGNAS: an exhaustive DNA sequence design algorithm

2012

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“…It has been applied to different applications such as DNA hybridization [7] as well as protein sensing recently [8]. The optical system relies on disposable, injection moulded polymer chips and quasi monochromatic illumination.…”

Section: Spr Platformmentioning

confidence: 99%

Improving the sensitivity of optical biosensors by means of Bloch surface waves

Danz

Sinibaldi

Michelotti

et al. 2012

Biomedical Engineering / Biomedizinische Technik

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One factor limiting the performance of Surface Plasmon Resonance (SPR) biosensors is the width of the resonance that basically originates from metal absorption. In contrast, comparable sensing schemes based upon the concept of Bloch surface waves (BSW) have been proposed. As such sensors are prepared from dielectric materials only, losses as well as the resonance width decrease significantly in comparison to SPR. By preparing BSW stacks that feature a similar resonance position as Gold based SPR sensors, both approaches are compared directly using one detection system only. We obtain an increased performance of BSW although utilizing an optical system optimized for SPR analysis.

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“…So far, various simpler and faster techniques have been developed for DNA hybridization detection, including electrochemistry [13–15], fluorescence [16,17], surface plasmon resonance spectroscopy and quartz crystal microbalance [18–21]. Among these methods, the electrochemical technique has attracted great attention in recent years due to its low cost, simple instrumentation, and fast response time.…”

Section: Introductionmentioning

confidence: 99%

Impedimetric DNA Biosensor Based on a Nanoporous Alumina Membrane for the Detection of the Specific Oligonucleotide Sequence of Dengue Virus

Deng

Toh

2013

Sensors

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A novel and integrated membrane sensing platform for DNA detection is developed based on an anodic aluminum oxide (AAO) membrane. Platinum electrodes (∼50–100 nm thick) are coated directly on both sides of the alumina membrane to eliminate the solution resistance outside the nanopores. The electrochemical impedance technique is employed to monitor the impedance changes within the nanopores upon DNA binding. Pore resistance (Rp) linearly increases in response towards the increasing concentration of the target DNA in the range of 1 × 10−12 to 1 × 10−6 M. Moreover, the biosensor selectively differentiates the complementary sequence from single base mismatched (MM-1) strands and non-complementary strands. This study reveals a simple, selective and sensitive method to fabricate a label-free DNA biosensor.

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DNA microarrays for hybridization detection by surface plasmon resonance spectroscopy

Cited by 26 publications

References 19 publications

EGNAS: an exhaustive DNA sequence design algorithm

EGNAS: an exhaustive DNA sequence design algorithm

Improving the sensitivity of optical biosensors by means of Bloch surface waves

Impedimetric DNA Biosensor Based on a Nanoporous Alumina Membrane for the Detection of the Specific Oligonucleotide Sequence of Dengue Virus

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