@article{Cubero2003,
	title = {Theoretical study of a new {DNA} structure: the antiparallel {Hoogsteen} duplex.},
	volume = {125},
	issn = {0002-7863},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/14624611},
	doi = {10.1021/ja035918f},
	abstract = {The structure of a new form of duplex DNA, the antiparallel Hoogsteen duplex, is studied in polyd(AT) sequences by means of state-of-the-art molecular dynamics simulations in aqueous solution. The structure, which was found to be stable in all of the simulations, has many similarities with the standard Watson-Crick duplex in terms of general structure, flexibility, and molecular recognition patterns. Accurate MM-PB/SA (and MM-GB/SA) analysis shows that the new structure has an effective energy similar to that of the B-type duplex, while it is slightly disfavored by intramolecular entropic considerations. Overall, MD simulations strongly suggest that the antiparallel Hoogsteen duplex is an accessible structure for a polyd(AT) sequence, which might compete under proper experimental conditions with normal B-DNA. MD simulations also suggest that chimeras containing Watson-Crick duplex and Hoogsteen antiparallel helices might coexist in a common structure, but with the differential characteristics of both type of structures preserved.},
	number = {47},
	journal = {Journal of the American Chemical Society},
	author = {Cubero, Elena and Abrescia, Nicola G a and Subirana, Juan a. and Luque, F. Javier and Orozco, Modesto},
	month = nov,
	year = {2003},
	pmid = {14624611},
	keywords = {\#nosource, DNA, DNA: chemistry, Models, Molecular, Nucleic Acid Conformation, Poly dA-dT, Poly dA-dT: chemistry, Solutions, Thermodynamics, Water, Water: chemistry},
	pages = {14603--12},
}

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Accurate MM-PB/SA (and MM-GB/SA) analysis shows that the new structure has an effective energy similar to that of the B-type duplex, while it is slightly disfavored by intramolecular entropic considerations. Overall, MD simulations strongly suggest that the antiparallel Hoogsteen duplex is an accessible structure for a polyd(AT) sequence, which might compete under proper experimental conditions with normal B-DNA. MD simulations also suggest that chimeras containing Watson-Crick duplex and Hoogsteen antiparallel helices might coexist in a common structure, but with the differential characteristics of both type of structures preserved.","number":"47","journal":"Journal of the American Chemical Society","author":[{"propositions":[],"lastnames":["Cubero"],"firstnames":["Elena"],"suffixes":[]},{"propositions":[],"lastnames":["Abrescia"],"firstnames":["Nicola","G","a"],"suffixes":[]},{"propositions":[],"lastnames":["Subirana"],"firstnames":["Juan","a."],"suffixes":[]},{"propositions":[],"lastnames":["Luque"],"firstnames":["F.","Javier"],"suffixes":[]},{"propositions":[],"lastnames":["Orozco"],"firstnames":["Modesto"],"suffixes":[]}],"month":"November","year":"2003","pmid":"14624611","keywords":"#nosource, DNA, DNA: chemistry, Models, Molecular, Nucleic Acid Conformation, Poly dA-dT, Poly dA-dT: chemistry, Solutions, Thermodynamics, Water, Water: chemistry","pages":"14603–12","bibtex":"@article{Cubero2003,\n\ttitle = {Theoretical study of a new {DNA} structure: the antiparallel {Hoogsteen} duplex.},\n\tvolume = {125},\n\tissn = {0002-7863},\n\turl = {http://www.ncbi.nlm.nih.gov/pubmed/14624611},\n\tdoi = {10.1021/ja035918f},\n\tabstract = {The structure of a new form of duplex DNA, the antiparallel Hoogsteen duplex, is studied in polyd(AT) sequences by means of state-of-the-art molecular dynamics simulations in aqueous solution. 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MD simulations also suggest that chimeras containing Watson-Crick duplex and Hoogsteen antiparallel helices might coexist in a common structure, but with the differential characteristics of both type of structures preserved.},\n\tnumber = {47},\n\tjournal = {Journal of the American Chemical Society},\n\tauthor = {Cubero, Elena and Abrescia, Nicola G a and Subirana, Juan a. and Luque, F. Javier and Orozco, Modesto},\n\tmonth = nov,\n\tyear = {2003},\n\tpmid = {14624611},\n\tkeywords = {\\#nosource, DNA, DNA: chemistry, Models, Molecular, Nucleic Acid Conformation, Poly dA-dT, Poly dA-dT: chemistry, Solutions, Thermodynamics, Water, Water: chemistry},\n\tpages = {14603--12},\n}\n\n","author_short":["Cubero, E.","Abrescia, N. G a","Subirana, J. a.","Luque, F. 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