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- W2098843335 abstract "A new formalism for calculation of the partition function of sin- gle stranded nucleic acids is presented. Secondary structures and the to pol- ogy of structure elements are the level of resolution that is used. The fold - ing model deals with matches, mismatches, symmetric and asymmetric interior loops, stacked pairs in loop and dangling end regions, multi-branched loops, bulges and single base stacking that might exist at duplex ends or at the ends of helices. Calculations on short and long sequences show that for short oligonu- cleotides, a duplex formation often displays a two-state transition. However, for longer oligonucleotides, the thermodynamic properties of the single self-f olding transition affects the transition nature of the duplex formation, resulting in a p op- ulation of intermediate hairpin species in the solution. The role of intermediate hairpin species is analyzed in the case when a short oligonucleotides (molecular beacons) have to reliably identify and hybridize to accessible nucleotides w ithin their targeted mRNA sequences. It is shown that the enhanced specificity of the molecular beacons is a result of their constrained conformational flexib ility and the all-or-none mechanism of their hybridization to the target sequence." @default.
- W2098843335 created "2016-06-24" @default.
- W2098843335 creator A5064582772 @default.
- W2098843335 date "2005-10-05" @default.
- W2098843335 modified "2023-09-27" @default.
- W2098843335 title "A new formalism for calculation of the partition function of single stranded nucleic acids" @default.
- W2098843335 hasPublicationYear "2005" @default.
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