The Influence of Nearest Neighbors on the Efficiency of Coaxial Stacking at Contiguous Stacking Hybridization of Oligodeoxyribonucleotides

Abstract

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Stacked–Unstacked Equilibrium at the Nick Site of DNA

“…This range is generally consistent with parameter values for coaxial stacking reported before. [5][6][7][8] In fact, similarly to results obtained in melting studies, 8 we find that GC is the most stable contact, TA is the least stable contact and a tendency towards more efficient stacking for mixed dinucleotides in order TG!AG!GA!GT is observed.…”

“…Note that unlike our DG ST KL values, which are close for pKL/F and pKL/R series supporting the validity of our basic model, parameters of coaxial stacking of Pyshniy et al obtained in melting experiments 7,8 fail this test. These authors made complexes between DNA hairpins carrying a single-stranded overhang and a short oligonucleotide fully complementary to the overhang.…”

“…Coaxial stacking at the interface of two adjacent DNA helices contributes to stabilization of duplexes formed by in tandem binding of oligonucleotides to complementary single-stranded DNA probe. [6][7][8] Thus achieved stabilization of short duplexes has been exercised to improve the efficiency of short primer hybridization for standard sequencing protocols 47 and within the format of sequencing by hybridization approach. 48 Another biotechnology approach relying on the efficient stacking interaction at the helical interface at the nick site is associated with the formation of padlock and earring probes via ligation of a nick formed by two termini of artificial oligonucleotide hybridized to single-stranded or locally opened duplex DNA.…”

“…Free energy values of coaxial stacking obtained from the data of this kind range from K0.85 kcal/mol for TA dinucleotide stack to K2.76 kcal/mol for GC stack. 7 Although stacking free energies determined in different studies agree in the range, there are major discrepancies in the values for individual stacks. For example, the study on coaxial stacking contribution to stabilization of gel-immobilized duplexes by intandem hybridization of pentamers revealed the adenine stacking with other bases to be significantly stronger than stacking of other bases.…”

“…[13][14][15] The other approach is based on the fact that stacking entails pronounced mutual stabilization of DNA duplexes formed due to tandem binding of short oligonucleotides to DNA template. [5][6][7][8] Direct stacking interactions of the terminal bases of the oligonucleotides have been implicated in differential stabilizing effects observed for dinucleotide stacks forming the nick interface. Free energy values of coaxial stacking obtained from the data of this kind range from K0.85 kcal/mol for TA dinucleotide stack to K2.76 kcal/mol for GC stack.…”