Kinetic sequence discrimination of cationic bis-PNAs upon targeting of double-stranded DNA

Heiko Kuhn; V.V. Demidov; M.D. Frank-Kamenetskii; P.E. Nielsen

doi:10.1093/nar/26.2.582

Kinetic sequence discrimination of cationic bis-PNAs upon targeting of double-stranded DNA

Heiko Kuhn, V.V. Demidov, M.D. Frank-Kamenetskii, P.E. Nielsen

Transcription, RNA, and Gene Medicine Program

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

86 Citationer (Scopus)

Abstract

Peptide nucleic acid, DNA targeting, sequence discrimination, anti-gene

Originalsprog	Engelsk
Tidsskrift	Nucleic Acids Research
Vol/bind	26
Udgave nummer	2
Sider (fra-til)	582-587
ISSN	0305-1048
DOI	https://doi.org/10.1093/nar/26.2.582
Status	Udgivet - 1998

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10.1093/nar/26.2.582Licens: Ikke-specificeret

Citationsformater

@article{33b2610074c111dbbee902004c4f4f50,

title = "Kinetic sequence discrimination of cationic bis-PNAs upon targeting of double-stranded DNA",

abstract = "Strand displacement binding kinetics of cationic pseudoisocytosine-containing linked homopyrimidine peptide nucleic acids (bis-PNAs) to fully matched and singly mismatched decapurine targets in double-stranded DNA (dsDNA) are reported. PNA-dsDNA complex formation was monitored by gel mobility shift assay and pseudo-first order kinetics of binding was obeyed in all cases studied. The kinetic specificity of PNA binding to dsDNA, defined as the ratio of the initial rates of binding to matched and mismatched targets, increases with increasing ionic strength, whereas the apparent rate constant for bis-PNA-dsDNA complex formation decreases exponentially. Surprisingly, at very low ionic strength two equally charged bis-PNAs which have the same sequence of nucleobases but different linkers and consequently different locations of three positive charges differ in their specificity of binding by one order of magnitude. Under appropriate experimental conditions the kinetic specificity for bis-PNA targeting of dsDNA is as high as 300. Thus multiply charged cationic bis-PNAs containing pseudoisocytosines (J bases) in the Hoogsteen strand combined with enhanced binding affinity also exhibit very high sequence specificity, thereby making such reagents extremely efficient for sequence-specific targeting of duplex DNA.",

author = "Heiko Kuhn and V.V. Demidov and M.D. Frank-Kamenetskii and P.E. Nielsen",

year = "1998",

doi = "10.1093/nar/26.2.582",

language = "English",

volume = "26",

pages = "582--587",

journal = "Nucleic Acids Research",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "2",

}

TY - JOUR

T1 - Kinetic sequence discrimination of cationic bis-PNAs upon targeting of double-stranded DNA

AU - Kuhn, Heiko

AU - Demidov, V.V.

AU - Frank-Kamenetskii, M.D.

AU - Nielsen, P.E.

PY - 1998

Y1 - 1998

N2 - Strand displacement binding kinetics of cationic pseudoisocytosine-containing linked homopyrimidine peptide nucleic acids (bis-PNAs) to fully matched and singly mismatched decapurine targets in double-stranded DNA (dsDNA) are reported. PNA-dsDNA complex formation was monitored by gel mobility shift assay and pseudo-first order kinetics of binding was obeyed in all cases studied. The kinetic specificity of PNA binding to dsDNA, defined as the ratio of the initial rates of binding to matched and mismatched targets, increases with increasing ionic strength, whereas the apparent rate constant for bis-PNA-dsDNA complex formation decreases exponentially. Surprisingly, at very low ionic strength two equally charged bis-PNAs which have the same sequence of nucleobases but different linkers and consequently different locations of three positive charges differ in their specificity of binding by one order of magnitude. Under appropriate experimental conditions the kinetic specificity for bis-PNA targeting of dsDNA is as high as 300. Thus multiply charged cationic bis-PNAs containing pseudoisocytosines (J bases) in the Hoogsteen strand combined with enhanced binding affinity also exhibit very high sequence specificity, thereby making such reagents extremely efficient for sequence-specific targeting of duplex DNA.

AB - Strand displacement binding kinetics of cationic pseudoisocytosine-containing linked homopyrimidine peptide nucleic acids (bis-PNAs) to fully matched and singly mismatched decapurine targets in double-stranded DNA (dsDNA) are reported. PNA-dsDNA complex formation was monitored by gel mobility shift assay and pseudo-first order kinetics of binding was obeyed in all cases studied. The kinetic specificity of PNA binding to dsDNA, defined as the ratio of the initial rates of binding to matched and mismatched targets, increases with increasing ionic strength, whereas the apparent rate constant for bis-PNA-dsDNA complex formation decreases exponentially. Surprisingly, at very low ionic strength two equally charged bis-PNAs which have the same sequence of nucleobases but different linkers and consequently different locations of three positive charges differ in their specificity of binding by one order of magnitude. Under appropriate experimental conditions the kinetic specificity for bis-PNA targeting of dsDNA is as high as 300. Thus multiply charged cationic bis-PNAs containing pseudoisocytosines (J bases) in the Hoogsteen strand combined with enhanced binding affinity also exhibit very high sequence specificity, thereby making such reagents extremely efficient for sequence-specific targeting of duplex DNA.

U2 - 10.1093/nar/26.2.582

DO - 10.1093/nar/26.2.582

M3 - Journal article

SN - 0305-1048

VL - 26

SP - 582

EP - 587

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - 2

ER -