title: Competition between stacked and hydrogen bonded structures of cytosine aggregates.
abstract: The four bases of DNA constitute what is known as the "alphabet of life". Their combination of proton-donor and acceptor groups and aromatic rings allows them to form stacking structures and at the same time establish hydrogen bonds with their counterparts, resulting in the formation of the well-known double-helix structure of DNA. Here we explore the aggregation preferences of cytosine in supersonic expansions, using a combination of laser spectroscopic techniques and computations. The data obtained from the experiments carried out in the cold and isolated environment of the expansion allowed us to establish which are the leading interactions behind aggregation of cytosine molecules. The results obtained demonstrated that ribbon-like structures held together by hydrogen bonds are the preferred conformations in the small clusters, but once the tetramer was reached, the stacking structures became enthalpically more stable. Stacking is further favoured when cytosine is replaced by its 1'-methylated version, as demonstrated by quantum-mechanical calculations performed using the same level that reproduced the experimental results obtained for cytosine aggregates. A discussion on the biological implications that such observations may have is also offered.
authors.affiliation: Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain. josea.fernandez@ehu.es.
authors.forename: Jorge
authors.initials: J
authors.lastname: González
authors.affiliation: Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain. josea.fernandez@ehu.es.
authors.forename: Imanol
authors.initials: I
authors.lastname: Usabiaga
authors.affiliation: Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain. josea.fernandez@ehu.es.
authors.forename: Pedro F
authors.initials: PF
authors.lastname: Arnaiz
authors.affiliation: Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain. josea.fernandez@ehu.es.
authors.forename: Iker
authors.initials: I
authors.lastname: León
authors.affiliation: Department of Chemistry, Faculty of Science and Technology, University of La Rioja, Madre de Dios, 53, Logroño, 26006, Spain.
authors.forename: Rodrigo
authors.identifier: http://orcid.org/0000-0002-5850-8494
authors.initials: R
authors.lastname: Martínez
authors.affiliation: Department of Chemistry, Faculty of Science and Technology, University of La Rioja, Madre de Dios, 53, Logroño, 26006, Spain.
authors.forename: Judith
authors.identifier: http://orcid.org/0000-0001-5755-9567
authors.initials: J
authors.lastname: Millán
authors.affiliation: Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain. josea.fernandez@ehu.es.
authors.forename: José A
authors.identifier: http://orcid.org/0000-0002-7315-2326
authors.initials: JA
authors.lastname: Fernández
mesh_terms: D003596:Cytosine / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D006859:Hydrogen; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D013816:Thermodynamics
chemical_list: D006859:Hydrogen; D003596:Cytosine; D004247:DNA