25 nt guanine rich vascular endothelial growth factor aptamer was studied with CD; UV and NMR spectroscopy. While unmodified aptamer folds into several G-quadruplex structures in the presence of potassium ions, modifications with locked and unlocked nucleotides lead to the stabilization of a single parallel structure with three G-quartets. Unusual features of the structure include five consecutive guanine residues that are all included in the G-quadruplex core, and a new type of D-shaped loop that brings isolated guanine residue in the G-quartet. The edgewise and propeller loops connect the remaining two G-rich tracts. 5' and 3' overhangs are well structured and were shown to importantly contribute to the formation of structurally pre-organized intermediates and stabilizations of the single G-quadruplex structure.
COBISS.SI-ID: 5373466
Infection with human papillomaviruses (HPVs) is one of the most common sexually transmitted infections and can lead to development of head and neck, skin, and anogenital cancer, including cervical cancer, which represents one of the world’s most significant health problems. In this study, we analyze G-rich regions in all known HPV genomes in order to evaluate their potential to fold into a G-quadruplex structure. G-rich regions with the capacity to form G-quadruplexes are located in the LCR, L2, E1, and E4 regions of the HPV genome. Some of the investigated G-rich oligonucleotides fold into G-quadruplex structures with a single topology in the presence of potassium ions, while in some cases aggregates have been observed. We have also shown that sequences consisting of at least four G-runs interrupted by three nucleotides may not fold into G-quadruplexes. If they contain a critical amount of cytosine residues, they prefer alternative Watson-Crick base-paired conformations.
COBISS.SI-ID: 5352218
G-wires consisting of stacked G-quartets are a promising element for use in nanotechnology, particularly in molecular electronics. Previous investigations showed that some guanine-rich oligonucleotides with GC-termini can form long G-quadruplexes (G-wires), that are linked via G:C:G:C-quartets. To assess the role of GC-ends in G-wire formation in solution, we designed four analogous G-quadruple forming oligonucleotides, which differed in the number and position of GC-termini in the sequence. The core of oligonucleotide sequences was in all four cases the same d(GGTG4TGG) To compare their properties four different techniques were used: UV-spectroscopy, circular dichroism, NMR and dynamic light scattering. We concluded that formation of G:C:G:C-quartets is only possible at the 5'-terminus, while 3'-GC-termini cannot participate in G:C:G:C-quartets and therefore hinder the formation of longer structures. In the case when one of the G-quartets at the end of the quadruplex was not obstructed by a GC-terminus, stacking of G-quadruplexes was enabled. The longest G-quadruplex stacks were observed in the solution of oligonucleotide without GC-termini. Their estimated length was nearly 20 nm.
COBISS.SI-ID: 2606436