PNA: Synthetic Polyamide Nucleic Acids with Unusual Binding Properties

Uhlmann, Eugen; Peyman, Anusch; Breipohl, Gerhard; Will, David W.

doi:10.1002/(sici)1521-3773(19981102)37:20<2796::aid-anie2796>3.0.co;2-k

Cited by 397 publications

(220 citation statements)

References 124 publications

Supporting

Mentioning

217

Contrasting

Unclassified

Order By: Relevance

“…Indeed, as it can be seen in Figure 4, the pcPNA-dsDNA complex formation is very sensitive to ionic conditions in case of linear dsDNA targets, thus additionally verifying the PNA-to-DNA strand invasion mechanism. 3 Under physiological pH and temperature, the invasion of pcPNAs into linear dsDNA is absent at 80 mM Na + during 0.5-1 h (and even during more prolonged incubations; data not shown). (lanes 1 and 4), 0.63 µM (lanes 2 and 5), and 1.3 µM (lanes 3 and 6) PNAs (total PNA concentration).…”

Section: Double-duplexmentioning

confidence: 91%

Sequence-Specific Protection of Duplex DNA against Restriction and Methylation Enzymes by Pseudocomplementary PNAs

et al. 2000

View full text Add to dashboard Cite

A new generation of PNAs, so-called pseudocomplementary PNAs (pcPNAs), which are able to target the designated sites on duplex DNA with mixed sequence of purines and pyrimidines via doubleduplex invasion mode, has recently been introduced. It has been demonstrated that appropriate pairs of decameric pcPNAs block an access of RNA polymerase to the corresponding promoter. Here, we show that this type of PNAs protects selected DNA sites containing all four nucleobases from the action of restriction enzymes and DNA methyltransferases. We have found that pcPNAs as short as octamers form stable and sequence-specific complexes with duplex DNA in a very salt-dependent manner. In accord with a strand-invasion mode of complex formation, the pcPNA binding proceeds much faster with supercoiled than with linear plasmids. The double-duplex invasion complexes selectively shield specific DNA sites from BclI restriction endonuclease and dam methylase. The pcPNA-assisted protection against enzymatic methylation is more efficient when the PNA-binding site embodies the methylase-recognition site rather than overlaps it. We conclude that pcPNAs may provide the robust tools allowing to sequencespecifically manipulate DNA duplexes in a virtually sequence-unrestricted manner.

show abstract

Section: Double-duplexmentioning

confidence: 91%

Sequence-Specific Protection of Duplex DNA against Restriction and Methylation Enzymes by Pseudocomplementary PNAs

et al. 2000

View full text Add to dashboard Cite

show abstract

“…Additionally, PNA is resistant to nucleases and proteases [5]. For further reading about the affinity and specificity, as well as the chemical and biophysical properties of PNA molecules, we recommend two reviews [6,7].…”

mentioning

confidence: 99%

Peptide nucleic acids on microarrays and other biosensors

Brandt¹,

Hoheisel²

2004

Trends in Biotechnology

102

View full text Add to dashboard Cite

“…At pH values below the pKa of piperidine, the excess of protonated piperidine acts as a cation and electrostatically binds to the phosphate backbone neutralizing the repulsive negative charges and thus creating an effect similar to peptide nucleic acid (PNA) duplex stability where Coulombic repulsions have been eliminated [47]. This effect is analogous to the Na ϩ cation binding to the negatively charged phosphate backbone stabilizing the duplex by reducing the electrostatic repulsion [48,49].…”

Section: Resultsmentioning

confidence: 99%

“…Temperatures reaching 100°C were necessary to achieve dissociation of the duplex structure. Analogous to PNA-PNA duplex stability [47], the oligonucleotide electrosprayed from a solution of lower pH (i.e., more protonated piperidine) stabilizes the anionic phosphate backbone of the double helix and melts at a temperature that is roughly twice that of the duplex electrosprayed from a higher pH solution. The decrease in the pH from 10.9 to 10.7 is also reflected in the charge-states of the duplex structures at ambient temperature; when the concentration of protonated piperidine increases by 9%, the average charge-state decreases.…”

Section: Methodsmentioning

confidence: 99%

Solution composition and thermal denaturation for the production of single-stranded PCR amplicons: Piperidine-induced destabilization of the DNA duplex?

Mangrum

Flora

Muddiman

2002

J. Am. Soc. Mass Spectrom.

View full text Add to dashboard Cite

Strategies to produce single-stranded PCR amplicons for detection by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) were investigated using modified electrospray solutions and by thermally denaturing the duplex structures with a resistively heated electrospray ionization source. A synthetic 20-mer oligonucleotide annealed to its complementary strand was used as a model system for initial experiments. Electrospray solutions were altered by varying the relative proportion of aqueous phase in efforts to induce destabilization of the double helix. When the electrospray solution contains a 25% aqueous content, the 20-mer oligonucleotide is detected in its double-stranded form. Increasing the proportion of aqueous phase in the electrospray solution to 60% destabilized the double helix, resulting in the detection of only single-stranded species. This strategy was extended to an 82-bp polymerase chain reaction (PCR) product derived from the human tyrosine hydroxylase gene (HUMTH01). In efforts to destabilize the 82-bp PCR product, electrospray solutions reaching 70% aqueous content were necessary to promote the detection of only single-stranded amplicons. Implementation of the resistively heated transfer line and an electrospray solution in which the oligonucleotide is on the threshold of duplex stability allowed for double-stranded and single-stranded species to be generated from the same ESI solutions at both ambient and elevated transfer line temperatures, respectively, without disruption of the electrospray process. The volatile base piperidine, present at 20 mM concentrations in the electrospray solution, was found to play a critical role in the formation of single-stranded species at the higher aqueous percentages and a duplex destabilization mechanism has been proposed. (J Am Soc Mass Spectrom 2002, 13, 232-240)

show abstract

PNA: Synthetic Polyamide Nucleic Acids with Unusual Binding Properties

Cited by 397 publications

References 124 publications

Sequence-Specific Protection of Duplex DNA against Restriction and Methylation Enzymes by Pseudocomplementary PNAs

Sequence-Specific Protection of Duplex DNA against Restriction and Methylation Enzymes by Pseudocomplementary PNAs

Peptide nucleic acids on microarrays and other biosensors

Solution composition and thermal denaturation for the production of single-stranded PCR amplicons: Piperidine-induced destabilization of the DNA duplex?

Contact Info

Product

Resources

About