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Literature DB >> 9016597

Evaluation of pyrimidine PNA binding to ssDNA targets from nonequilibrium melting experiments.

E A Lesnik¹, L M Risen, D A Driver, M C Griffith, K Sprankle, S M Freier.

Abstract

Slow kinetics of homopyrimidine PNA binding to single stranded DNA and RNA targets is manifested in significant hysteresis in thermal UV absorption experiments. We have compared temperatures of dissociation (Tdis) and reassociation (Tass) for triplexes formed by DNA and single or bis PNAs with K50 derived from gel mobility experiments. Results indicated there was no correlation between Tdis and K50 while reasonable correlation between Tass and K50 was found. This correlation enabled use of easy thermal UV absorption experiments for evaluation of PNA binding to DNA/RNA targets.

Entities: Chemical

Mesh：

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Year: 1997 PMID： 9016597 PMCID： PMC146474 DOI： 10.1093/nar/25.3.568

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

19 in total

1. PNA hybridizes to complementary oligonucleotides obeying the Watson-Crick hydrogen-bonding rules.

Authors: M Egholm; O Buchardt; L Christensen; C Behrens; S M Freier; D A Driver; R H Berg; S K Kim; B Norden; P E Nielsen
Journal: Nature Date: 1993-10-07 Impact factor: 49.962

2. Uniformly modified 2'-deoxy-2'-fluoro phosphorothioate oligonucleotides as nuclease-resistant antisense compounds with high affinity and specificity for RNA targets.

Authors: A M Kawasaki; M D Casper; S M Freier; E A Lesnik; M C Zounes; L L Cummins; C Gonzalez; P D Cook
Journal: J Med Chem Date: 1993-04-02 Impact factor: 7.446

3. Kinetics and mechanism of polyamide ("peptide") nucleic acid binding to duplex DNA.

Authors: V V Demidov; M V Yavnilovich; B P Belotserkovskii; M D Frank-Kamenetskii; P E Nielsen
Journal: Proc Natl Acad Sci U S A Date: 1995-03-28 Impact factor: 11.205

4. Thermodynamic and kinetic studies of DNA triplex formation of an oligohomopyrimidine and a matched duplex by filter binding assay.

Authors: H Shindo; H Torigoe; A Sarai
Journal: Biochemistry Date: 1993-08-31 Impact factor: 3.162

Evaluation of pyrimidine PNA binding to ssDNA targets from nonequilibrium melting experiments.

1. PNA hybridizes to complementary oligonucleotides obeying the Watson-Crick hydrogen-bonding rules.

2. Uniformly modified 2'-deoxy-2'-fluoro phosphorothioate oligonucleotides as nuclease-resistant antisense compounds with high affinity and specificity for RNA targets.

3. Kinetics and mechanism of polyamide ("peptide") nucleic acid binding to duplex DNA.

4. Thermodynamic and kinetic studies of DNA triplex formation of an oligohomopyrimidine and a matched duplex by filter binding assay.

5. Implication of RNA structure on antisense oligonucleotide hybridization kinetics.

6. Characterization of antisense binding properties of peptide nucleic acids by capillary gel electrophoresis.

7. Peptide nucleic acid (PNA) conformation and polymorphism in PNA-DNA and PNA-RNA hybrids.

8. Pseudo--half-knot formation with RNA.

9. Efficient pH-independent sequence-specific DNA binding by pseudoisocytosine-containing bis-PNA.

10. Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide.

Review 1. Peptide nucleic acids: versatile tools for gene therapy strategies.

2. Hybridization of complementary and homologous peptide nucleic acid oligomers to a guanine quadruplex-forming RNA.

3. Inhibition of PNA triplex formation by N4-benzoylated cytosine.

4. Synthesis and evaluation of some properties of chimeric oligomers containing PNA and phosphono-PNA residues.

5. Cellular antisense activity of peptide nucleic acid (PNAs) targeted to HIV-1 polypurine tract (PPT) containing RNA.