Peptide nucleic acids (PNA). Oligonucleotide analogs with an achiral peptide backbone

Egholm, Michael; Buchardt, Ole; Nielsen, Peter E.; Berg, Rolf H.

doi:10.1021/ja00031a062

Cited by 761 publications

(503 citation statements)

References 4 publications

Supporting

Mentioning

492

Contrasting

Unclassified

Order By: Relevance

“…The sequences, linkers, and dyes used in the probes are shown in Table 1. The PNA is 5 to 15 bases in length, and in some probes one or two lysine residues are attached to the PNA C-terminus (NH 2 ) to improve PNA solubility (18). LUP1, LUP2, LUP6, LUP7, and LUP8 are mixed se-…”

Section: Absorption and Fluorescence Measurementsmentioning

confidence: 99%

Light-Up Probes: Thiazole Orange-Conjugated Peptide Nucleic Acid for Detection of Target Nucleic Acid in Homogeneous Solution

Svanvik

Westman

Wang³

et al. 2000

Analytical Biochemistry

237

147

View full text Add to dashboard Cite

We have constructed light-up probes for nucleic acid detection. The light-up probe is a peptide nucleic acid (PNA) oligonucleotide to which the asymmetric cyanine dye thiazole orange (TO) is tethered. It combines the excellent hybridization properties of PNA and the large fluorescence enhancement of TO upon binding to DNA. When the PNA hybridizes to target DNA, the dye binds and becomes fluorescent. Free probes have low fluorescence, which may increase almost 50-fold upon hybridization to complementary nucleic acid. This makes the light-up probes particularly suitable for homogeneous hybridization assays, where separation of the bound and free probe is not necessary. We find that the fluorescence enhancement upon hybridization varies among different probes, which is mainly due to variations in free probe fluorescence. For eight probes studied the fluorescence quantum yield at 25°C in the unbound state ranged from 0.0015 to 0.08 and seemed to depend mainly on the PNA sequence. The binding of the light-up probes to target DNA is highly sequence specific and a single mismatch in a 10-mer target sequence was readily identified.

show abstract

Section: Absorption and Fluorescence Measurementsmentioning

confidence: 99%

Light-Up Probes: Thiazole Orange-Conjugated Peptide Nucleic Acid for Detection of Target Nucleic Acid in Homogeneous Solution

Svanvik

Westman

Wang³

et al. 2000

Analytical Biochemistry

237

147

View full text Add to dashboard Cite

show abstract

“…These requirements have stimulated efforts to prepare backbone-modified derivatives which might be capable of penetrating membranes more readily whilst retaining their resistance to degradation. One widely used approach to improve cell penetration involves removal of the negative charges to produce neutral backbones such as, for example, methyl phosphonates [1], phosphoramidates [2] or peptide nucleic acids [3]. Methylphosphonates have been shown to be transported into cells by endocytosis [1] and were more resistant to degradation by nucleases [4].…”

Section: Introductionmentioning

confidence: 99%

“…The tetrachloro derivative was prepared using a similar procedure in which pyridinium (2-aminoethyl)phosphonate (ig, 3.53 mmol) was suspended in DMF (100 mL) and treated with and extracted with ethyl acetate (2 x 75 mL). The combined organic layers were washed with water (100 mL), dried over anhydrous sodium sulfate, filtered, and the filtrate was evaporated to dryness to give crude 1.…”

Section: Introductionmentioning

confidence: 99%

Oligonucleotides with novel, cationic backbone substituents: aminoethylphosphonates

et al. 1994

View full text Add to dashboard Cite

“…Peptide nucleic acids (PNAs) are structural homologues of DNA and RNA in which the entire phosphate-sugar backbone has been replaced by a flexible peptide backbone consisting of 2-aminoethyl glycine units linked to the purine and pyrimidine bases (1)(2)(3). The absence of phosphate groups in the PNA molecule facilitates its invasion of negatively charged DNA duplexes containing complementary base sequences (4)(5)(6).…”

mentioning

confidence: 99%

Isolation of active genes containing CAG repeats by DNA strand invasion by a peptide nucleic acid.

Boffa

Carpaneto

Allfrey

1995

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

An amplification of tandem CAG trinucleotide sequences in DNA due to errors in DNA replication is involved in at least four hereditary neurodegenerative diseases. The CAG triplet repeats when translated into protein give rise to tracts of glutamine residues, which are a prominent feature of many transcription factors, including the TATA-binding protein of transcription factor TFIID. We have used a biotin-labeled, complementary peptide nucleic acid (PNA) to invade the CAG repeats in intact chromatin and then employed a method for the selective isolation of transcriptionally active chromatin restriction fragments containing the PNA-DNA hybrids. The PNA-containing chromatin fragments were captured on streptavidin-agarose magnetic beads and shown to contain all the CAGPNA hybrids of the active chromatin fraction. DNA hybridization experiments using a DNA probe specific for unique sequences downstream of the CAG-tandem repeats confirmed that the PNA-DNA hybrids contained the transcribed gene for the TATA-binding protein.In contrast, no hybridization signal was detected with a DNA probe specific for the c-myc protooncogene, which is amplified and transcriptionally active in COLO 320DM cells but lacks CAG tandem repeats.Peptide nucleic acids (PNAs) are structural homologues of DNA and RNA in which the entire phosphate-sugar backbone has been replaced by a flexible peptide backbone consisting of 2-aminoethyl glycine units linked to the purine and pyrimidine bases (1-3). The absence of phosphate groups in the PNA molecule facilitates its invasion of negatively charged DNA duplexes containing complementary base sequences (4-6). When PNA hybridizes to a targeted DNA sequence, one strand of DNA may be rapidly displaced to form a D-loop (1, 5, 6), while the PNA binds to its complementary DNA sequence by WatsonCrick base pairing (7). PNAs show greater discrimination and form more stable associations with DNA than the corresponding DNADNA duplexes (7). PNA invasion of DNA strands to form stable PNADNA hybrids has profound implications for both positive and negative control of gene activity. For example, it has been shown that DNA loops displaced as a consequence of PNA binding act as artificial transcription promoters (8), but PNA binding to the transcribed strand of simian virus 40 DNA blocks transcript elongation beyond the site of PNA DNA duplex formation (9).Here, we explore the potential of a biotinylated PNA probe to invade DNA triplet repeat sequences in the chromatin of transcriptionally active genes. By using a PNA specific for multiple CAG repeats, together with a method for the separation of transcriptionally active chromatin restriction fragments from inactive chromatin restriction fragments (10), we show that the PNA probe can hybridize effectively to CAG triplet repeats in intact chromatin and that transcriptionally active chromatin fragments containing the PNA-DNA hybrids can be captured quantitatively on streptavidin-coated magnetic beads.An amplification of CAG triplet repeats occurs in at least four i...

show abstract

Peptide nucleic acids (PNA). Oligonucleotide analogs with an achiral peptide backbone

Cited by 761 publications

References 4 publications

Light-Up Probes: Thiazole Orange-Conjugated Peptide Nucleic Acid for Detection of Target Nucleic Acid in Homogeneous Solution

Light-Up Probes: Thiazole Orange-Conjugated Peptide Nucleic Acid for Detection of Target Nucleic Acid in Homogeneous Solution

Oligonucleotides with novel, cationic backbone substituents: aminoethylphosphonates

Isolation of active genes containing CAG repeats by DNA strand invasion by a peptide nucleic acid.

Contact Info

Product

Resources

About