Fiber optic biosensor for fluorimetric detection of DNA hybridization

Piunno, Paul A. E.; Krull, Ulrich J.; Hudson, Robert H. E.; Damha, Masad J.; Cohen, Huguette

doi:10.1016/0003-2670(93)e0611-a

Cited by 148 publications

(79 citation statements)

References 23 publications

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“…The development of oligonucleotides with selective hybridization properties may prove useful in the design of more selective antisense systems and novel hybridization probes for nucleic acids biosensors (42,43).…”

Section: Resultsmentioning

confidence: 99%

Structural basis for the RNA binding selectivity of oligonucleotide analogues containing alkylsulfide internucleoside linkages and 2′-substituted 3′-deoxyribonucleosides

et al. 1995

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INTRODUCTIONIn this report we describe the synthesis of oligonucleotides containing sulfide-linked dinucleoside units, namely rT(2'OH)dT, rT(2'0Me)5dT, dT8rU(2'OMe) and dT(2o0Me)5rU(2oMe). We also describe the interactions of such oligomers with complementary DNA and RNA targets, and provide the structural basis for their remarkable RNA binding selectivity. In all cases, the Tm values of the SIP-chimera duplexes were lower than those of the corresponding unmodified duplexes. We attribute this to steric interactions between the 5' sulfur and the atoms of the nearby base/sugar residues. The 2'-substituents (i.e., 2'OH or 2'OMe) vicinal to the alkylsulfide internucleoside linkage significantly perturb the structure and stability of the duplexes formed with DNA, and more so than with RNA. The introduction of three rT(2'OH)sdTp ( ' (5,6).Our research in the antisense field has focused on oligonucleotide analogues in which some of the phosphodiester groups are replaced by the dialkyl sulfide linkage 3'-CH2-CH2-S-CH2-5' (7-11). This linkage is non-hydrolyzable, non-ionic, and its length approximates that of a phosphodiester linkage reasonably well. More recently, we focused attention on the preparation of rT(20OH)SdT, rT(2 OMe)SdT, dTsrU(2'OMe) and rT(2'OMe)SrU(2'OMe) dimer units as well as their 3'-O-phosphoramidite derivatives for incorporation into oligonucleotides (11,12 (55°C, 16 h). The ammonia solution was collected by centrifuging the Eppendorf tube and then run through a Sephadex NAP-10 column which was pre-washed with 15 ml deionized water. The first eluting fractions (1.5 ml) were lyophilized to dryness and the resulting oligomer was redissolved in 1 ml of water. Purity of each oligomer was confmed by PAGE (26% polyacrylamide-7 M urea) run at 4°C, at a current of 10 mA, for 6-8 h (9). Melting experimentsMelting curves were measured in 10 mM NaH2PO4/Na2HPO4, 1 M NaCl buffer (pH 7.0) and analyzed the same way as described in reference 9. Circular dichroismThe CD spectrum ofeach sample was measured on a Jasco 500-C spectropolarimeter with a Jasco DP-J800/300 data processor. The cell temperature was kept at 50C. The concentration of the oligonucleotides were -2.5 jM (each strand).

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Section: Resultsmentioning

confidence: 99%

Structural basis for the RNA binding selectivity of oligonucleotide analogues containing alkylsulfide internucleoside linkages and 2′-substituted 3′-deoxyribonucleosides

et al. 1995

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“…DNA biosensors probe and/or detect the hybridization event, which is then transduced, for example, into an electrochemical [17][18][19][20][21][22] or optical [23][24][25][26] signal (Figure 3). In principle, an analytical sample, which contains, amongst others, the DNA sequence-of-interest (the target), is deposited onto the recognition layer of a transducer.…”

Section: Metal-containing Pnas For Biosensing Purposesmentioning

confidence: 99%

Metal-containing peptide nucleic acid conjugates

2011

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Peptide Nucleic Acids (PNAs) are non-natural DNA/RNA analogues with favourable physicochemical properties and promising applications. Discovered nearly 20 years ago, PNAs have recently re-gained quite a lot of attention. In this Perspective article, we discuss the latest advances on the preparation and utilisation of PNA monomers and oligomers containing metal complexes. These metalconjugates have found applications in various research fields such as in the sequence-specific detection of nucleic acids, in the hydrolysis of nucleic acids and peptides, as radioactive probes or as modulators of PNA˙DNA hybrid stability, and last but not least as probes for molecular and cell biology.

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“…Furthermore, the readout of those arrays involves highly precise and expensive instrumentation and requires sophisticated numerical algorithms to interpret the data, which makes the analysis time consuming. 3 In contrast, the method for direct DNA sequence detection reported here requires no labels as indicators. On the surface of silica optical fiber tip with a 125 m diameter, single stranded capture DNA is immobilized by layer-bylayer electrostatic self-assembly ͑L-b-L ESA͒.…”

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confidence: 95%