Abstract:
:G-rich oligonucleotides tend to fall into kinetically trapped unstable structures because of their conformational polymorphism. Nucleic acid chaperones accelerate association of nucleic acids assemblies into the thermodynamically most stable conformations by decreasing the energy barrier for breakage or re-assembly of base pairings. Here, we report that an artificial nucleic acid chaperone, a cationic comb-type copolymer, promotes tetramolecular quadruplex assembly from mixtures of two different G-rich sequences, 5'-TGGGGT-3' (TG(4)T) and 5'-TGGGGGT-3' (TG(5)T). A 1:1 mixture of TG(4)T and TG(5)T mainly gave [TG(4)T▪(TG(5)T)(3)], [(TG(4)T)(2)▪(TG(5)T)(2)] and [(TG(4)T)(3)▪TG(5)T] heteroquadruplexes when the mixture was annealed by cooling from 90 °C to 4 °C at 1.0 °C/min. At a cooling rate of 0.01 °C/min the mixture mostly assembled into [TG(4)T](4) and [TG(5)T](4) homoquadruplexes, indicating that homoquadruplexes were thermodynamically more stable than heteroquadruplexes. In the presence of the copolymer, mainly homoquadruplexes were obtained at cooling rate of 1 °C/min, suggesting that the copolymer promoted formation of the thermodynamically most stable structures. We also showed that the copolymer facilitated the recombination of heteroquadruplexes to homoquadruplexes even at 20-30 °C, implying that the copolymer can promote thermodynamically preferred quadruplex assembly from oligonucleotides trapped in metastable structures. These results show that the copolymer works as a DNA annealer that induces proper assembly of stable DNA structures from heterogeneous kinetically trapped mixtures of structures.
journal_name
Biomaterialsjournal_title
Biomaterialsauthors
Moriyama R,Shimada N,Kano A,Maruyama Adoi
10.1016/j.biomaterials.2011.06.056subject
Has Abstractpub_date
2011-10-01 00:00:00pages
7671-6issue
30eissn
0142-9612issn
1878-5905pii
S0142-9612(11)00736-8journal_volume
32pub_type
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