Strand invasion by mixed base PNAs and a PNA-peptide chimera.
Peptide nucleic acid oligomers (PNAs) have a remarkable ability to invade duplex DNA at polypurine-polypyrimidine target sequences. Applications for PNAs in medicine and biotechnology would increase if the rules governing their hybridization to mixed base sequences were also clear. Here we describe hybridization of PNAs to mixed base sequences and demonstrate that simple chemical modifications can enhance recognition. Easily synthesized and readily soluble eight and 10 base PNAs bind to plasmid DNA at an inverted repeat that is likely to form a cruciform structure, providing convenient tags for creating PNA-plasmid complexes. PNAs also bind to mixed base sequences that cannot form cruciforms, suggesting that recognition is a general phenomenon. Rates of strand invasion are temperature dependent and can be enhanced by attaching PNAs to positively charged peptides. Our results support use of PNAs to access the information within duplex DNA and demonstrate that simple chemical modifications can make PNAs even more powerful agents for strand invasion. Simple strategies for enhancing strand invasion should facilitate the use of PNAs: (i) as biophysical probes of double-stranded DNA; (ii) to target promoters to control gene expression; and (iii) to direct sequence-specific mutagenesis.
Zhang
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Department of Pharmacology and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390-9041, USA.
Ishihara
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Corey
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D020137:Base Pair Mismatch / Q000235:genetics; D001483:Base Sequence; D001665:Binding Sites; D001709:Biotechnology / Q000379:methods; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D004278:DNA, Superhelical / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D007700:Kinetics; D015335:Molecular Probes / Q000737:chemistry / Q000378:metabolism; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization / Q000235:genetics; D020135:Peptide Nucleic Acids / Q000737:chemistry / Q000378:metabolism*; D010455:Peptides / Q000737:chemistry / Q000378:metabolism*; D010957:Plasmids / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011993:Recombinant Fusion Proteins / Q000737:chemistry / Q000378:metabolism*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D012995:Solubility; D055672:Static Electricity; D013379:Substrate Specificity; D013696:Temperature; D013698:Templates, Genetic
D004278:DNA, Superhelical; D015335:Molecular Probes; D020135:Peptide Nucleic Acids; D010455:Peptides; D011993:Recombinant Fusion Proteins; D004247:DNA