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Paranemic crossover DNA: a generalized Holliday structure with applications in nanotechnology

Paranemic crossover (PX) DNA is a four-stranded coaxial DNA complex containing a central dyad axis that relates two flanking parallel double helices. The strands are held together exclusively by Watson-Crick base pairing. The key feature of the structure is that the two adjacent parallel DNA double... Full description

Journal Title: Journal of the American Chemical Society 18 February 2004, Vol.126(6), pp.1666-74
Main Author: Shen, Zhiyong
Other Authors: Yan, Hao , Wang, Tong , Seeman, Nadrian C
Format: Electronic Article Electronic Article
Language: English
Subjects:
ID: ISSN: 0002-7863 ; PMID: 14871096 Version:1
Link: http://pubmed.gov/14871096
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recordid: medline14871096
title: Paranemic crossover DNA: a generalized Holliday structure with applications in nanotechnology
format: Article
creator:
  • Shen, Zhiyong
  • Yan, Hao
  • Wang, Tong
  • Seeman, Nadrian C
subjects:
  • DNA -- Chemistry
  • Nanotechnology -- Methods
ispartof: Journal of the American Chemical Society, 18 February 2004, Vol.126(6), pp.1666-74
description: Paranemic crossover (PX) DNA is a four-stranded coaxial DNA complex containing a central dyad axis that relates two flanking parallel double helices. The strands are held together exclusively by Watson-Crick base pairing. The key feature of the structure is that the two adjacent parallel DNA double helices form crossovers at every point possible. Hence, reciprocal crossover points flank the central dyad axis at every major or minor groove separation. This motif has been modeled and characterized in an oligonucleotide system; a minor groove separation of five nucleotide pairs and major groove separations of six, seven, or eight nucleotide pairs produce stable PX DNA molecules; a major groove separation of 9 nucleotide pairs is possible at low concentrations. Every strand undergoes a crossover every helical repeat (11, 12, 13, or 14 nucleotides), but the structural period of each strand corresponds to two helical repeats (22, 24, 26, or 28 nucleotides). Nondenaturing gel electrophoresis shows that the molecules are stable, forming well-behaved complexes. PX DNA can be produced from closed dumbbells, demonstrating that the molecule is paranemic. Ferguson analysis indicates that the molecules are similar in shape to DNA double crossover molecules. Circular dichroism spectra are consistent with B-form DNA. Thermal transition profiles suggest a premelting transition in each of the molecules. Hydroxyl radical autofootprinting analysis confirms that there is a crossover point at each of the positions expected in the secondary structure. These molecules are generalized Holliday junctions.
language: eng
source:
identifier: ISSN: 0002-7863 ; PMID: 14871096 Version:1
fulltext: no_fulltext
issn:
  • 00027863
  • 0002-7863
url: Link


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titleParanemic crossover DNA: a generalized Holliday structure with applications in nanotechnology
creatorShen, Zhiyong ; Yan, Hao ; Wang, Tong ; Seeman, Nadrian C
ispartofJournal of the American Chemical Society, 18 February 2004, Vol.126(6), pp.1666-74
identifierISSN: 0002-7863 ; PMID: 14871096 Version:1
subjectDNA -- Chemistry ; Nanotechnology -- Methods
descriptionParanemic crossover (PX) DNA is a four-stranded coaxial DNA complex containing a central dyad axis that relates two flanking parallel double helices. The strands are held together exclusively by Watson-Crick base pairing. The key feature of the structure is that the two adjacent parallel DNA double helices form crossovers at every point possible. Hence, reciprocal crossover points flank the central dyad axis at every major or minor groove separation. This motif has been modeled and characterized in an oligonucleotide system; a minor groove separation of five nucleotide pairs and major groove separations of six, seven, or eight nucleotide pairs produce stable PX DNA molecules; a major groove separation of 9 nucleotide pairs is possible at low concentrations. Every strand undergoes a crossover every helical repeat (11, 12, 13, or 14 nucleotides), but the structural period of each strand corresponds to two helical repeats (22, 24, 26, or 28 nucleotides). Nondenaturing gel electrophoresis shows that the molecules are stable, forming well-behaved complexes. PX DNA can be produced from closed dumbbells, demonstrating that the molecule is paranemic. Ferguson analysis indicates that the molecules are similar in shape to DNA double crossover molecules. Circular dichroism spectra are consistent with B-form DNA. Thermal transition profiles suggest a premelting transition in each of the molecules. Hydroxyl radical autofootprinting analysis confirms that there is a crossover point at each of the positions expected in the secondary structure. These molecules are generalized Holliday junctions.
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descriptionParanemic crossover (PX) DNA is a four-stranded coaxial DNA complex containing a central dyad axis that relates two flanking parallel double helices. The strands are held together exclusively by Watson-Crick base pairing. The key feature of the structure is that the two adjacent parallel DNA double helices form crossovers at every point possible. Hence, reciprocal crossover points flank the central dyad axis at every major or minor groove separation. This motif has been modeled and characterized in an oligonucleotide system; a minor groove separation of five nucleotide pairs and major groove separations of six, seven, or eight nucleotide pairs produce stable PX DNA molecules; a major groove separation of 9 nucleotide pairs is possible at low concentrations. Every strand undergoes a crossover every helical repeat (11, 12, 13, or 14 nucleotides), but the structural period of each strand corresponds to two helical repeats (22, 24, 26, or 28 nucleotides). Nondenaturing gel electrophoresis shows that the molecules are stable, forming well-behaved complexes. PX DNA can be produced from closed dumbbells, demonstrating that the molecule is paranemic. Ferguson analysis indicates that the molecules are similar in shape to DNA double crossover molecules. Circular dichroism spectra are consistent with B-form DNA. Thermal transition profiles suggest a premelting transition in each of the molecules. Hydroxyl radical autofootprinting analysis confirms that there is a crossover point at each of the positions expected in the secondary structure. These molecules are generalized Holliday junctions.
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abstractParanemic crossover (PX) DNA is a four-stranded coaxial DNA complex containing a central dyad axis that relates two flanking parallel double helices. The strands are held together exclusively by Watson-Crick base pairing. The key feature of the structure is that the two adjacent parallel DNA double helices form crossovers at every point possible. Hence, reciprocal crossover points flank the central dyad axis at every major or minor groove separation. This motif has been modeled and characterized in an oligonucleotide system; a minor groove separation of five nucleotide pairs and major groove separations of six, seven, or eight nucleotide pairs produce stable PX DNA molecules; a major groove separation of 9 nucleotide pairs is possible at low concentrations. Every strand undergoes a crossover every helical repeat (11, 12, 13, or 14 nucleotides), but the structural period of each strand corresponds to two helical repeats (22, 24, 26, or 28 nucleotides). Nondenaturing gel electrophoresis shows that the molecules are stable, forming well-behaved complexes. PX DNA can be produced from closed dumbbells, demonstrating that the molecule is paranemic. Ferguson analysis indicates that the molecules are similar in shape to DNA double crossover molecules. Circular dichroism spectra are consistent with B-form DNA. Thermal transition profiles suggest a premelting transition in each of the molecules. Hydroxyl radical autofootprinting analysis confirms that there is a crossover point at each of the positions expected in the secondary structure. These molecules are generalized Holliday junctions.
pmid14871096
doi10.1021/ja038381e
eissn15205126
oafree_for_read
date2004-02-18