Helical periodicity of (PNA)2·(DNA) triplexes in strand displacement complexes

Ji Hoon Kim, Ki Hyun Kim, Niels Erik Møllegaard, Peter E. Nielsen, Hyeon Sook Koo

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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 between two bent DNA loci were prepared. As the spacer DNA length between the two bent loci varied by 1 bp over one helical turn, the electrophoretic mobility, reflecting the overall extent of DNA bending, was modulated sinusoidally in non-denaturing 5% polyacrylamide gel. When the bent DNA fragments differing in the spacer DNA length were preincubated with an oligopyrimidine PNA, the gel mobilities were changed due to a P-loop formation. By analyzing the gel mobility data with variations of the P-loop size, average helical parameters at the P-loop structure were determined. (PNA)2·(DNA) triplex within a P-loop had the helical periodicities of 15.6 (±0.2) bp per turn at 20°C and 17.4 (±0.7) bp per turn at 10°C. In addition, the results indicate that a helical unwinding by 57 (±7) degrees at 20°C and 37 (±13) degrees at 10°C is present at the two junctions between a P-loop and its adjacent DNA duplex.

Original languageEnglish
Pages (from-to)2842-2847
Number of pages6
JournalNucleic acids research
Issue number14
Publication statusPublished - 1999 Jul 15

Bibliographical note

Funding Information:
We thank Prof. Donald M. Crothers at Yale University for the LB series plasmids. This work was supported by Grant 981-0304-0202 from the Korea Science Foundation to H.-S.K. and by a grant from the Danish National Research Foundation to P.E.N.

All Science Journal Classification (ASJC) codes

  • Genetics


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