title: Recombination R-triplex: H-bonds contribution to stability as revealed with minor base substitutions for adenine.
abstract: Several cellular processes involve alignment of three nucleic acids strands, in which the third strand (DNA or RNA) is identical and in a parallel orientation to one of the DNA duplex strands. Earlier, using 2-aminopurine as a fluorescent reporter base, we demonstrated that a self-folding oligonucleotide forms a recombination-like structure consistent with the R-triplex. Here, we extended this approach, placing the reporter 2-aminopurine either in the 5'- or 3'-strand. We obtained direct evidence that the 3'-strand forms a stable duplex with the complementary central strand, while the 5'-strand participates in non-Watson-Crick interactions. Substituting 2,6-diaminopurine or 7-deazaadenine for adenine, we tested and confirmed the proposed hydrogen bonding scheme of the A*(T.A) R-type triplet. The adenine substitutions expected to provide additional H-bonds led to triplex structures with increased stability, whereas the substitutions consistent with a decrease in the number of H-bonds destabilized the triplex. The triplex formation enthalpies and free energies exhibited linear dependences on the number of H-bonds predicted from the A*(T.A) triplet scheme. The enthalpy of the 10 nt long intramolecular triplex of -100 kJ x mol(-1) demonstrates that the R-triplex is relatively unstable and thus an ideal candidate for a transient intermediate in homologous recombination, t-loop formation at the mammalian telomere ends, and short RNA invasion into a duplex. On the other hand, the impact of a single H-bond, 18 kJ x mol(-1), is high compared with the overall triplex formation enthalpy. The observed energy advantage of a 'correct' base in the third strand opposite the Watson-Crick base pair may be a powerful mechanism for securing selectivity of recognition between the single strand and the duplex.
authors.affiliation: Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
authors.forename: Anna K
authors.initials: AK
authors.lastname: Shchyolkina
authors.forename: Dmitry N
authors.initials: DN
authors.lastname: Kaluzhny
authors.forename: Donna J
authors.initials: DJ
authors.lastname: Arndt-Jovin
authors.forename: Thomas M
authors.initials: TM
authors.lastname: Jovin
authors.forename: Victor B
authors.initials: VB
authors.lastname: Zhurkin
mesh_terms: D015075:2-Aminopurine / Q000031:analogs & derivatives / Q000737:chemistry; D000225:Adenine / Q000031:analogs & derivatives* / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D006860:Hydrogen Bonding; D009690:Nucleic Acid Conformation; D011995:Recombination, Genetic; D013816:Thermodynamics; D014372:Tubercidin / Q000737:chemistry
chemical_list: C051802:triplex DNA; D015075:2-Aminopurine; C007300:2,6-diaminopurine; D004247:DNA; D000225:Adenine; D014372:Tubercidin