2024-03-28T13:09:36Zhttps://www.tdx.cat/oai/requestoai:www.tdx.cat:10803/3926532017-08-31T08:07:41Zcom_10803_183col_10803_208
nam a 5i 4500
Structural studies of AT-rich DNA
[Barcelona] :
Universitat Politècnica de Catalunya,
2016
Accés lliure
http://hdl.handle.net/10803/392653
cr |||||||||||
AAMMDDs2016 sp ||||fsm||||0|| 0 eng|c
Acosta Reyes, Francisco Javier,
autor
1 recurs en línia (227 pàgines)
Tesi
Doctorat
Universitat Politècnica de Catalunya. Departament d'Enginyeria Química
2016
Universitat Politècnica de Catalunya. Departament d'Enginyeria Química
Tesis i dissertacions electròniques
Campos López, Josefina de Lourdes,
supervisor acadèmic
Subirana Torrent, Juan Antonio,
supervisor acadèmic
TDX
Non-coding DNA is rich in adenines and thymines. Their unique properties, such as high polymorphism, flexibility, transitional states that lead to DNA hairpin formation and the possibility to adopt either Watson-Crick or Hoogsteen base pairing conformations, in conjunction with its distribution in genomes, suggest the possibility of a structural role. In spite of that, the available structural information for AT-rich oligonucleotides in databases such as Protein Data Bank (PDB) and Nucleic Acids Data Bank (NDB) is very limited in comparison to oligonucleotides of high CG content. These facts have motivated us to undertake the study of the structural characteristics specific for AT-rich oligonucleotides.
X-ray crystallography was used for the study of AT-rich oligonucleotides with particular sequences, such as a palindromic sequence suitable for the formation of a DNA hairpin, alternating-AT and A-tracts. Additionally, dynamic light scattering was used to identify the most suitable conditions for initial crystallization trials.
The unique properties of AT-rich sequences such a high polymorphism and flexibility constitute ideal features for their possible structural role, but also present difficulties for crystal organization, as required for X-ray crystallography. In several cases, only poor diffracting crystals were obtained.
The following structural features were identified in the AT-rich oligonucleotides studied by us:
Crystals of the oligonucleotide d((AT)3T3A(AT)3) in a DNA hairpin conformation have been obtained. The structure of the loop appears to be highly variable; as a result, the crystals have low resolution. A tentative model of the hairpin structure has been proposed.
The d(A4T4) octamer was crystallized as a complex with the CD27 drug. This drug has previously demonstrated a high antiprotozoal activity, in particular against Plasmodium falciparum and Trypanosoma brucei. The structure obtained shows how the CD27 drug fills completely the minor groove and interacts with molecules of stacked oligonucleotides and with the backbone of neighboring duplexes, stabilizing a complex organization. The elevated number of occurrences of the motif A4 in the genomes of Plasmodium falciparum and particularly in the kDNA of Trypanosoma brucei represents a suitable target for the CD27 drug.
The d(CG(AT)4CG)2 dodecamer in presence of Ni2+ crystallizes in the typical pseudo four-way helix-helix junction configuration, with extra-helical and terminal guanines coordinated to nickel. A bis-coordination of Ni2+ with two stacked helical guanines was identified in the structure of d(CG(AT)4CG)2 in the presence of Ni2+ and the CD27 drug.
The oligonucleotide d(A6T6)2 in the presence of Mn2+ and the S1010 drug in the crystallization conditions acquires a coiled-coil conformation.
The following structures were determined as part of a collaboration in several other projects:
The structure of the oligonucleotide d(AATAAATTTATT)2 in presence of different ions exhibits the typical high polymorphism of AT-rich DNA. The ions present in the crystallization conditions modulate the organization of duplexes, most likely through changes in the ionic atmosphere around the DNA duplexes.
The structure of the oligonucleotide d(ATTAAT)2 in Hoogsteen conformation demonstrates that any all-AT sequence may adopt the Hoogsteen conformation under appropriate conditions.
The structures of d(CGAATTAATTCG)2, d(ATATCGATAT)2 and d(ATATGCATAT)2 in the presence of ligands (ions, peptide or protein), were successfully determined. In the case of d(ATATGCATAT)2 a coiled-coil conformation was found in the presence of Mg2+.
p
ES-BaCBU
cat
rda
ES-BaCBU
text
txt
rdacontent
informàtic
c
rdamedia
recurs en línia
cr
rdacarrier