Surface density dependence of PCR amplicon hybridization on PNA/DNA probe layers (2005)
Yao,D. F., Kim,J., Yu,F., Nielsen,P. E., Sinner,E. K., Knoll,W.
Surface density dependence of PCR amplicon hybridization on PNA/DNA probe layers (2005)
Yao,D. F., Kim,J., Yu,F., Nielsen,P. E., Sinner,E. K., Knoll,Wolfgang
In situ hybridization of PNA/DNA studied label-free by electrochemical impedance spectroscopy (2005)
Transcription arrest caused by long nascent RNA chains (2005)
Bentin, T., Cherny, D. I., Larsen, H. J., Nielsen, P. E.
The transcription process is highly processive. However, specific sequence elements encoded in the nascent RNA may signal transcription pausing and/or termination. We find that under certain...
Surface density dependence of PCR amplicon hybridization on PNA/DNA probe layers (2005)
Yao, D. F., Kim, J., Yu, F., Nielsen, P. E., Sinner, E. K., Knoll, Wolfgang
In situ hybridization of PNA/DNA studied label-free by electrochemical impedance spectroscopy (2005)
Surface density dependence of PCR amplicon hybridization on PNA/DNA probe layers (2005)
Yao, D. F., Kim, J., Yu, F., Nielsen, P. E., Sinner, E. K., Knoll, W.
Yao,D. F., Yu,F., Kim,J. Y., Scholz,J., Nielsen,P. E., Sinner,E. K., ...
Yao,D. F., Yu,F., Kim,J. Y., Scholz,J., Nielsen,P. E., Sinner,E. K., ...
Dheur, S, Nielsen, P E, Gryaznov, S, ...
We have previously described the rational design of mutation-selective antisense oligonucleotides targeted to codon 12 of oncogenic Ha-ras mRNA. In order to further improve the biological efficacy of...
MOMENTUM TRANSFER TO SOLID TARGETS IN THE PRESENCE OF LASER-SUPPORTED DETONATION WAVES. (1998)
#L023390 (U) Laser induced spallation has been demonstrated experimentally by irradiating 1mm thick 6061-T6 aluminum under vacuum conditions by a 1.5 nsec laser pulse of 1.06 microns wavelength. It...
MADSEN, J. KYST, GARBARSCH, C., NIELSEN, P. E.
The effect of catheterisation on the rabbit aortic wall is investigated employing a technique identical to that used for continuous monitoring of blood pressure in humans. The catheters were...
NIELSEN, P. E., BELL, G., AUGUSTENBORG, G., PAASKE-HANSEN, O., LASSEN, N. A
AUTHORS' SYNOPSISSystolic blood pressure in the big toe decreased from 59 mm Hg to 42 mm Hg after lumbar sympathetic block by xylocaine in 16 patients with occlusive arterial disease. The decrease in...
BELL, G., NIELSEN, P. E., LASSEN, N. A., WOLFSON, B.
AUTHORS' SYNOPSISThe systolic blood pressure in the thigh, calf, and first toe was measured in 30 normal subjects between the ages of 13 and 55, using a mercury in rubber strain gauge on the toe as...
Kinetics and mechanism of polyamide ("peptide") nucleic acid binding to duplex DNA.
Demidov, V V, Yavnilovich, M V, Belotserkovskii, B P, Frank-Kamenetskii, M D, Nielsen, P E
To elucidate the mechanism of recognition of double-stranded DNA (dsDNA) by homopyrimidine polyamide ("peptide") nucleic acid (PNA) leading to the strand-displacement, the kinetics of the...
Peptide nucleic acid.DNA strand displacement loops as artificial transcription promoters.
Møllegaard, N E, Buchardt, O, Egholm, M, Nielsen, P E
Homopyrimidine peptide nucleic acids (PNAs) form loop structures when binding to complementary double-stranded DNA by strand displacement, and we now show that RNA polymerase recognizes these and...
Cherny, D Y, Belotserkovskii, B P, Frank-Kamenetskii, M D, Egholm, M, Buchardt, O, Berg, R H, ...
It was recently found that polyamide nucleic acid (PNA) analogues consisting of thymines attached to an aminoethylglycine backbone bind strongly and sequence-selectively to adenine sequences of...
Peptide nucleic acid (PNA) forms sequence-specific (PNA)2/DNA triplexes with one strand of double-stranded DNA by strand invasion. When formed with the template strand of DNA such a (PNA)2/DNA...
Antisense properties of duplex- and triplex-forming PNAs.
The potential of peptide nucleic acids (PNAs) as specific inhibitors of translation has been studied. PNAs with a mixed purine/pyrimidine sequence form duplexes, while homopyrimidine PNAs form...
Koppelhus, U, Zachar, V, Nielsen, P E, Liu, X, Eugen-Olsen, J, Ebbesen, P
We have tested the inhibitory potential of peptide nucleic acid (PNA) on in vitro reverse transcription of the HIV-1 gag gene. PNA was designed to target different regions of the HIV-1 gag gene and...
Mollegaard, N E, Bailly, C, Waring, M J, Nielsen, P E
Gel migration and uranyl photoprobing have been used to study the effects of inosine and 2,6-diaminopurine (2,6-DAP) substitution on adenine-tract (A-tract) induced DNA curvature. Using a 10mer...
Increased DNA binding and sequence discrimination of PNA oligomers containing 2,6-diaminopurine.
Haaima, G, Hansen, H F, Christensen, L, Dahl, O, Nielsen, P E
The synthesis of a diaminopurine PNA monomer, N-[N6-(benzyloxycarbonyl)-2,6-diaminopurine-9-yl] acetyl-N-(2-t-butyloxycarbonylaminoethyl)glycine, and the incorporation of this monomer into PNA...
Information transfer from DNA to peptide nucleic acids by template-directed syntheses.
Schmidt, J G, Christensen, L, Nielsen, P E, Orgel, L E
Peptide nucleic acids (PNAs) are analogs of nucleic acids in which the ribose-phosphate backbone is replaced by a backbone held together by amide bonds. PNAs are interesting as models of alternative...
Information transfer from peptide nucleic acids to RNA by template-directed syntheses.
Schmidt, J G, Nielsen, P E, Orgel, L E
Peptide nucleic acids (PNAs) are uncharged analogs of DNA and RNA in which the ribose-phosphate backbone is substituted by a backbone held together by amide bonds. PNAs are interesting as models of...
Kinetic sequence discrimination of cationic bis-PNAs upon targeting of double-stranded DNA.
Kuhn, H, Demidov, V V, Frank-Kamenetskii, M D, Nielsen, P E
Strand displacement binding kinetics of cationic pseudoisocytosine-containing linked homopyrimidine peptide nucleic acids (bis-PNAs) to fully matched and singly mismatched decapurine targets in...
Additive antisense effects of different PNAs on the in vitro translation of the PML/RARalpha gene.
Mologni, L, LeCoutre, P, Nielsen, P E, Gambacorti-Passerini, C
The potential use of peptide nucleic acid (PNA) as a sequence-specific inhibitor of RNA translation is investigated in this report. Three different regions of the PML/RARalpha oncogene, including two...
Inhibition of PNA triplex formation by N4-benzoylated cytosine.
Christensen, L, Hansen, H F, Koch, T, Nielsen, P E
The synthesis of N-((N4-(benzoyl)cytosine-1-yl)acetyl)- N -(2-Boc-aminoethyl)glycine (CBz) and the incorporation of this monomer into PNA oligomers are described. A single CBzresidue within a 10mer...
A formula for thermal stability (Tm) prediction of PNA/DNA duplexes.
Giesen, U, Kleider, W, Berding, C, Geiger, A, Orum, H, Nielsen, P E
An empirical formula for thermal stability (T m) prediction of PNA/DNA duplexes has been derived. The model is based on the T m as calculated for the corresponding DNA/DNA duplex employing a nearest...
Boulmé, F, Freund, F, Moreau, S, Nielsen, P E, Gryaznov, S, Toulmé, J J, ...
Natural beta-phosphodiester 16mer and 15mer antisense oligonucleotides targeted against the HIV-1 and HIV-2 TAR RNAs respectively were previously described as sequence-specific inhibitors of in vitro...
Helical periodicity of (PNA)2.(DNA) triplexes in strand displacement complexes.
Kim, J H, Kim, K H, Møllegaard, N E, Nielsen, P E, Koo, H S
To study the helical structure in a P-loop formed by an invasion of oligopyrimidine peptide nucleic acid (PNA) into DNA duplex, bent DNA fragments containing a homopurine.homopyrimidine sequence...
Zhang, G H, Baek, L, Nielsen, P E, Buchardt, O, Koch, C
Limulus peptide C, a 28-amino-acid fragment of coagulogen formed by the reaction of endotoxin with Limulus amebocyte lysate, was synthesized, and a monoclonal antibody against it was raised. A new...
Efficient pH-independent sequence-specific DNA binding by pseudoisocytosine-containing bis-PNA.
Egholm, M, Christensen, L, Dueholm, K L, Buchardt, O, Coull, J, Nielsen, P E
The synthesis and DNA binding properties of bis-PNA (peptide nucleic acid) are reported. Two PNA segments each of seven nucleobases in length were connected in a continuous synthesis via a flexible...
Sequence specific inhibition of DNA restriction enzyme cleavage by PNA.
Nielsen, P E, Egholm, M, Berg, R H, Buchardt, O
Plasmids containing double-stranded 10-mer PNA (peptide nucleic acid chimera) targets proximally flanked by two restriction enzyme sites were challenged with the complementary PNA or PNAs having one...
Demidov, V, Frank-Kamenetskii, M D, Egholm, M, Buchardt, O, Nielsen, P E
A novel method for sequence specific double strand DNA cleavage using PNA (peptide nucleic acid) targeting is described. Nuclease S1 digestion of double stranded DNA gives rise to double strand...
Single base pair mutation analysis by PNA directed PCR clamping.
Orum, H, Nielsen, P E, Egholm, M, Berg, R H, Buchardt, O, Stanley, C
A novel method that allows direct analysis of single base mutation by the polymerase chain reaction (PCR) is described. The method utilizes the finding that PNAs (peptide nucleic acids) recognize and...
Employing a newly developed uranyl photofootprinting technique (Nielsen et al. (1988) FEBS Lett. 235, 122), we have analyzed the structure of the E. coli RNA polymerase deoP1 promoter open complex....
DNA conformational analysis in solution by uranyl mediated photocleavage.
Nielsen, P E, Møllegaard, N E, Jeppesen, C
Uranyl mediated photocleavage of double stranded DNA is proposed as a general probing for DNA helix conformation in terms of minor groove width/electronegative potential. Specifically, it is found...
Electron microscopy mapping of oligopurine tracts in duplex DNA by peptide nucleic acid targeting.
Demidov, V V, Cherny, D I, Kurakin, A V, Yavnilovich, M V, Malkov, V A, Frank-Kamenetskii, M D, ...
Biotinylated homopyrimidine decamer peptide nucleic acids (PNAs) are shown to form sequence-specific and stable complexes with complementary oligopurine targets in linear double-stranded DNA. The...
Nielsen, P E, Jeppesen, C, Egholm, M, Buchardt, O
The photoreactions of 9-[6-(4-azidobenzamido)hexylamino]acridine (AHA) and 9-[6-(2-diazocyclopentadienylcarbonyloxy)hexylamino]acridine (DHA) with double stranded DNA result in formation of single...
Jeppesen, C, Buchardt, O, Henriksen, U, Nielsen, P E
The long-wavelength ultraviolet (lambda approximately 420 nm) radiation induced reaction between 6-azido-2-methoxy-9-acridinylamines and supercoiled plasmid DNA results in single strand scissions and...
Uranyl photofootprinting of triple helical DNA.
Two triple helix structures (15-mers containing only T.A-T triplets or containing mixed T.A-T and C.G-C triplets) have been studied by uranyl mediated DNA photocleavage to probe the accessibility of...
Jeppesen, C, Jensen, K F, Nielsen, P E
Upon irradiation of the RNA polymerase-lacUV5 or deoP1 promoter complex with short wavelength ultraviolet light (lambda less than or equal to 300 nm) the polymerase is covalently crosslinked at an...
Treatment of the ciliated protozoan Tetrahymena thermophila with 8-methoxypsoralen combined with long wavelength ultraviolet irradiation (UVA, lambda approximately 360 nm) resulted in a dose...
Uranyl photoprobing of a four-way DNA junction: evidence for specific metal ion binding.
Møllegaard, N E, Murchie, A I, Lilley, D M, Nielsen, P E
Metal ions are very important in mediating the folding of nucleic acids, as exemplified by the folding of the four-way DNA junction into the stacked X-conformation. Uranyl ion-mediated photocleavage...
Bailly, C, Møllegaard, N E, Nielsen, P E, Waring, M J
The conformation of the DNA helix is supposed to be a critical element in site-specific recognition by ligands both large and small. Groove width is one important measure of the conformation which...
Nielsen, P E, Hansen, J B, Buchardt, O
A novel cleavable photo-cross-linking reagent, N-(2-methoxy-6-azidoacridin-9-yl)-N'-(4-azidobenzoyl)cystamine, for analysis of protein-nucleic acid interactions, has been synthesized. The reagent...
Analysis of various sequence-specific triplexes by electron and atomic force microscopies.
Cherny, D I, Fourcade, A, Svinarchuk, F, Nielsen, P E, Malvy, C, Delain, E
Sequence-specific interactions of 20-mer G,A-containing triple helix-forming oligonucleotides (TFOs) and bis-PNAs (peptide nucleic acids) with double-stranded DNA was visualized by electron (EM) and...
Kinetics and mechanism of polyamide ("peptide") nucleic acid binding to duplex DNA.
Demidov, V V, Yavnilovich, M V, Belotserkovskii, B P, Frank-Kamenetskii, M D, Nielsen, P E
To elucidate the mechanism of recognition of double-stranded DNA (dsDNA) by homopyrimidine polyamide ("peptide") nucleic acid (PNA) leading to the strand-displacement, the kinetics of the...
Peptide nucleic acid.DNA strand displacement loops as artificial transcription promoters.
Møllegaard, N E, Buchardt, O, Egholm, M, Nielsen, P E
Homopyrimidine peptide nucleic acids (PNAs) form loop structures when binding to complementary double-stranded DNA by strand displacement, and we now show that RNA polymerase recognizes these and...
Cherny, D Y, Belotserkovskii, B P, Frank-Kamenetskii, M D, Egholm, M, Buchardt, O, Berg, R H, ...
It was recently found that polyamide nucleic acid (PNA) analogues consisting of thymines attached to an aminoethylglycine backbone bind strongly and sequence-selectively to adenine sequences of...
Peptide nucleic acid (PNA) forms sequence-specific (PNA)2/DNA triplexes with one strand of double-stranded DNA by strand invasion. When formed with the template strand of DNA such a (PNA)2/DNA...
Antisense properties of duplex- and triplex-forming PNAs.
The potential of peptide nucleic acids (PNAs) as specific inhibitors of translation has been studied. PNAs with a mixed purine/pyrimidine sequence form duplexes, while homopyrimidine PNAs form...
Koppelhus, U, Zachar, V, Nielsen, P E, Liu, X, Eugen-Olsen, J, Ebbesen, P
We have tested the inhibitory potential of peptide nucleic acid (PNA) on in vitro reverse transcription of the HIV-1 gag gene. PNA was designed to target different regions of the HIV-1 gag gene and...
Mollegaard, N E, Bailly, C, Waring, M J, Nielsen, P E
Gel migration and uranyl photoprobing have been used to study the effects of inosine and 2,6-diaminopurine (2,6-DAP) substitution on adenine-tract (A-tract) induced DNA curvature. Using a 10mer...
Increased DNA binding and sequence discrimination of PNA oligomers containing 2,6-diaminopurine.
Haaima, G, Hansen, H F, Christensen, L, Dahl, O, Nielsen, P E
The synthesis of a diaminopurine PNA monomer, N-[N6-(benzyloxycarbonyl)-2,6-diaminopurine-9-yl] acetyl-N-(2-t-butyloxycarbonylaminoethyl)glycine, and the incorporation of this monomer into PNA...
Information transfer from DNA to peptide nucleic acids by template-directed syntheses.
Schmidt, J G, Christensen, L, Nielsen, P E, Orgel, L E
Peptide nucleic acids (PNAs) are analogs of nucleic acids in which the ribose-phosphate backbone is replaced by a backbone held together by amide bonds. PNAs are interesting as models of alternative...
Information transfer from peptide nucleic acids to RNA by template-directed syntheses.
Schmidt, J G, Nielsen, P E, Orgel, L E
Peptide nucleic acids (PNAs) are uncharged analogs of DNA and RNA in which the ribose-phosphate backbone is substituted by a backbone held together by amide bonds. PNAs are interesting as models of...
Kinetic sequence discrimination of cationic bis-PNAs upon targeting of double-stranded DNA.
Kuhn, H, Demidov, V V, Frank-Kamenetskii, M D, Nielsen, P E
Strand displacement binding kinetics of cationic pseudoisocytosine-containing linked homopyrimidine peptide nucleic acids (bis-PNAs) to fully matched and singly mismatched decapurine targets in...
Additive antisense effects of different PNAs on the in vitro translation of the PML/RARalpha gene.
Mologni, L, LeCoutre, P, Nielsen, P E, Gambacorti-Passerini, C
The potential use of peptide nucleic acid (PNA) as a sequence-specific inhibitor of RNA translation is investigated in this report. Three different regions of the PML/RARalpha oncogene, including two...
Inhibition of PNA triplex formation by N4-benzoylated cytosine.
Christensen, L, Hansen, H F, Koch, T, Nielsen, P E
The synthesis of N-((N4-(benzoyl)cytosine-1-yl)acetyl)- N -(2-Boc-aminoethyl)glycine (CBz) and the incorporation of this monomer into PNA oligomers are described. A single CBzresidue within a 10mer...
A formula for thermal stability (Tm) prediction of PNA/DNA duplexes.
Giesen, U, Kleider, W, Berding, C, Geiger, A, Orum, H, Nielsen, P E
An empirical formula for thermal stability (T m) prediction of PNA/DNA duplexes has been derived. The model is based on the T m as calculated for the corresponding DNA/DNA duplex employing a nearest...
Boulmé, F, Freund, F, Moreau, S, Nielsen, P E, Gryaznov, S, Toulmé, J J, ...
Natural beta-phosphodiester 16mer and 15mer antisense oligonucleotides targeted against the HIV-1 and HIV-2 TAR RNAs respectively were previously described as sequence-specific inhibitors of in vitro...
Helical periodicity of (PNA)2.(DNA) triplexes in strand displacement complexes.
Kim, J H, Kim, K H, Møllegaard, N E, Nielsen, P E, Koo, H S
To study the helical structure in a P-loop formed by an invasion of oligopyrimidine peptide nucleic acid (PNA) into DNA duplex, bent DNA fragments containing a homopurine.homopyrimidine sequence...
Zhang, G H, Baek, L, Nielsen, P E, Buchardt, O, Koch, C
Limulus peptide C, a 28-amino-acid fragment of coagulogen formed by the reaction of endotoxin with Limulus amebocyte lysate, was synthesized, and a monoclonal antibody against it was raised. A new...
Efficient pH-independent sequence-specific DNA binding by pseudoisocytosine-containing bis-PNA.
Egholm, M, Christensen, L, Dueholm, K L, Buchardt, O, Coull, J, Nielsen, P E
The synthesis and DNA binding properties of bis-PNA (peptide nucleic acid) are reported. Two PNA segments each of seven nucleobases in length were connected in a continuous synthesis via a flexible...
Sequence specific inhibition of DNA restriction enzyme cleavage by PNA.
Nielsen, P E, Egholm, M, Berg, R H, Buchardt, O
Plasmids containing double-stranded 10-mer PNA (peptide nucleic acid chimera) targets proximally flanked by two restriction enzyme sites were challenged with the complementary PNA or PNAs having one...
Demidov, V, Frank-Kamenetskii, M D, Egholm, M, Buchardt, O, Nielsen, P E
A novel method for sequence specific double strand DNA cleavage using PNA (peptide nucleic acid) targeting is described. Nuclease S1 digestion of double stranded DNA gives rise to double strand...
Single base pair mutation analysis by PNA directed PCR clamping.
Orum, H, Nielsen, P E, Egholm, M, Berg, R H, Buchardt, O, Stanley, C
A novel method that allows direct analysis of single base mutation by the polymerase chain reaction (PCR) is described. The method utilizes the finding that PNAs (peptide nucleic acids) recognize and...
Employing a newly developed uranyl photofootprinting technique (Nielsen et al. (1988) FEBS Lett. 235, 122), we have analyzed the structure of the E. coli RNA polymerase deoP1 promoter open complex....
DNA conformational analysis in solution by uranyl mediated photocleavage.
Nielsen, P E, Møllegaard, N E, Jeppesen, C
Uranyl mediated photocleavage of double stranded DNA is proposed as a general probing for DNA helix conformation in terms of minor groove width/electronegative potential. Specifically, it is found...
Electron microscopy mapping of oligopurine tracts in duplex DNA by peptide nucleic acid targeting.
Demidov, V V, Cherny, D I, Kurakin, A V, Yavnilovich, M V, Malkov, V A, Frank-Kamenetskii, M D, ...
Biotinylated homopyrimidine decamer peptide nucleic acids (PNAs) are shown to form sequence-specific and stable complexes with complementary oligopurine targets in linear double-stranded DNA. The...
Nielsen, P E, Jeppesen, C, Egholm, M, Buchardt, O
The photoreactions of 9-[6-(4-azidobenzamido)hexylamino]acridine (AHA) and 9-[6-(2-diazocyclopentadienylcarbonyloxy)hexylamino]acridine (DHA) with double stranded DNA result in formation of single...
Jeppesen, C, Buchardt, O, Henriksen, U, Nielsen, P E
The long-wavelength ultraviolet (lambda approximately 420 nm) radiation induced reaction between 6-azido-2-methoxy-9-acridinylamines and supercoiled plasmid DNA results in single strand scissions and...
Uranyl photofootprinting of triple helical DNA.
Two triple helix structures (15-mers containing only T.A-T triplets or containing mixed T.A-T and C.G-C triplets) have been studied by uranyl mediated DNA photocleavage to probe the accessibility of...
Jeppesen, C, Jensen, K F, Nielsen, P E
Upon irradiation of the RNA polymerase-lacUV5 or deoP1 promoter complex with short wavelength ultraviolet light (lambda less than or equal to 300 nm) the polymerase is covalently crosslinked at an...
Treatment of the ciliated protozoan Tetrahymena thermophila with 8-methoxypsoralen combined with long wavelength ultraviolet irradiation (UVA, lambda approximately 360 nm) resulted in a dose...
Uranyl photoprobing of a four-way DNA junction: evidence for specific metal ion binding.
Møllegaard, N E, Murchie, A I, Lilley, D M, Nielsen, P E
Metal ions are very important in mediating the folding of nucleic acids, as exemplified by the folding of the four-way DNA junction into the stacked X-conformation. Uranyl ion-mediated photocleavage...
Bailly, C, Møllegaard, N E, Nielsen, P E, Waring, M J
The conformation of the DNA helix is supposed to be a critical element in site-specific recognition by ligands both large and small. Groove width is one important measure of the conformation which...
Nielsen, P E, Hansen, J B, Buchardt, O
A novel cleavable photo-cross-linking reagent, N-(2-methoxy-6-azidoacridin-9-yl)-N'-(4-azidobenzoyl)cystamine, for analysis of protein-nucleic acid interactions, has been synthesized. The reagent...
Analysis of various sequence-specific triplexes by electron and atomic force microscopies.
Cherny, D I, Fourcade, A, Svinarchuk, F, Nielsen, P E, Malvy, C, Delain, E
Sequence-specific interactions of 20-mer G,A-containing triple helix-forming oligonucleotides (TFOs) and bis-PNAs (peptide nucleic acids) with double-stranded DNA was visualized by electron (EM) and...
1 In a single blind study seventeen patients with mild or moderate essential hypertension and normal renal function were treated with labetalol alone in increasing doses from 300 via 600 to 1200 mg...
A comparative study of atenolol and metoprolol in the treatment of hypertension.
Rasmussen, S, Arnung, K, Eskildsen, P C, Nielsen, P E
1 In an open, randomized cross-over investigation of thirteen patients (nine and four women, aged 37-67 years) with mild or moderate essential hypertension a comparison between atenolol and...