Evidence for (PNA)2/DNA triplex structure upon binding of PNA to dsDNA by strand displacement

O Buchardt; Peter E. Nielsen

doi:10.1002/jmr.300070303

Evidence for (PNA)2/DNA triplex structure upon binding of PNA to dsDNA by strand displacement

O Buchardt, Peter E. Nielsen

Transcription, RNA, and Gene Medicine Program

131 Citationer (Scopus)

Abstract

The binding of PNA (peptide nucleic acid) T2CT2CT4-LysNH2 to the double-stranded DNA target 5'-A2GA2GA4 was studied by KMnO4 and dimethylsulfate (DMS) probing. It is found that upon sequence-specific strand displacement binding of the PNA to the dsDNA target concomitant protection of the N-7 of guanines within the target takes place. It is furthermore shown that the binding of this PNA is more efficient at pH 5.5 than at pH 6.5 and very inefficient at pH 7.5. These results clearly indicate that C+G Hoogsteen base pairing is present and important for binding and that the strand displacement complex therefore involves a PNA.DNA-PNA triplex.

Originalsprog	Engelsk
Tidsskrift	Journal of Molecular Recognition
Vol/bind	7
Udgave nummer	3
Sider (fra-til)	165-70
Antal sider	6
ISSN	0952-3499
DOI	https://doi.org/10.1002/jmr.300070303
Status	Udgivet - sep. 1994

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10.1002/jmr.300070303

Citationsformater

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title = "Evidence for (PNA)2/DNA triplex structure upon binding of PNA to dsDNA by strand displacement",

abstract = "The binding of PNA (peptide nucleic acid) T2CT2CT4-LysNH2 to the double-stranded DNA target 5'-A2GA2GA4 was studied by KMnO4 and dimethylsulfate (DMS) probing. It is found that upon sequence-specific strand displacement binding of the PNA to the dsDNA target concomitant protection of the N-7 of guanines within the target takes place. It is furthermore shown that the binding of this PNA is more efficient at pH 5.5 than at pH 6.5 and very inefficient at pH 7.5. These results clearly indicate that C+G Hoogsteen base pairing is present and important for binding and that the strand displacement complex therefore involves a PNA.DNA-PNA triplex.",

keywords = "Base Sequence, Cytosine/chemistry, DNA/chemistry, Guanine/chemistry, Hydrogen Bonding, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Conformation, Oligodeoxyribonucleotides/chemistry, Oligonucleotide Probes, Plasmids, Potassium Permanganate, Pyrimidine Nucleotides/chemistry, Sulfuric Acid Esters",

author = "O Buchardt and Nielsen, {Peter E.}",

year = "1994",

month = sep,

doi = "10.1002/jmr.300070303",

language = "English",

volume = "7",

pages = "165--70",

journal = "Journal of Molecular Recognition",

issn = "0952-3499",

publisher = "Wiley",

number = "3",

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TY - JOUR

T1 - Evidence for (PNA)2/DNA triplex structure upon binding of PNA to dsDNA by strand displacement

AU - Buchardt, O

AU - Nielsen, Peter E.

PY - 1994/9

Y1 - 1994/9

N2 - The binding of PNA (peptide nucleic acid) T2CT2CT4-LysNH2 to the double-stranded DNA target 5'-A2GA2GA4 was studied by KMnO4 and dimethylsulfate (DMS) probing. It is found that upon sequence-specific strand displacement binding of the PNA to the dsDNA target concomitant protection of the N-7 of guanines within the target takes place. It is furthermore shown that the binding of this PNA is more efficient at pH 5.5 than at pH 6.5 and very inefficient at pH 7.5. These results clearly indicate that C+G Hoogsteen base pairing is present and important for binding and that the strand displacement complex therefore involves a PNA.DNA-PNA triplex.

AB - The binding of PNA (peptide nucleic acid) T2CT2CT4-LysNH2 to the double-stranded DNA target 5'-A2GA2GA4 was studied by KMnO4 and dimethylsulfate (DMS) probing. It is found that upon sequence-specific strand displacement binding of the PNA to the dsDNA target concomitant protection of the N-7 of guanines within the target takes place. It is furthermore shown that the binding of this PNA is more efficient at pH 5.5 than at pH 6.5 and very inefficient at pH 7.5. These results clearly indicate that C+G Hoogsteen base pairing is present and important for binding and that the strand displacement complex therefore involves a PNA.DNA-PNA triplex.

KW - Base Sequence

KW - Cytosine/chemistry

KW - DNA/chemistry

KW - Guanine/chemistry

KW - Hydrogen Bonding

KW - Hydrogen-Ion Concentration

KW - Molecular Sequence Data

KW - Nucleic Acid Conformation

KW - Oligodeoxyribonucleotides/chemistry

KW - Oligonucleotide Probes

KW - Plasmids

KW - Potassium Permanganate

KW - Pyrimidine Nucleotides/chemistry

KW - Sulfuric Acid Esters

U2 - 10.1002/jmr.300070303

DO - 10.1002/jmr.300070303

M3 - Journal article

C2 - 7880540

SN - 0952-3499

VL - 7

SP - 165

EP - 170

JO - Journal of Molecular Recognition

JF - Journal of Molecular Recognition

IS - 3

ER -

Evidence for (PNA)2/DNA triplex structure upon binding of PNA to dsDNA by strand displacement

Abstract

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