Cooperative monomer binding by polynucleotides. Effect of multiple-loop configurations on formation of triple-stranded complexes
✍ Scribed by Kenneth S. Schmitz
- Publisher
- Wiley (John Wiley & Sons)
- Year
- 1974
- Tongue
- English
- Weight
- 660 KB
- Volume
- 13
- Category
- Article
- ISSN
- 0006-3525
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✦ Synopsis
Abstract
Simulated binding curves for the reaction 2 polymer + monomer = triple‐stranded complex are presented, in which loop formation and sliding degeneracy of the polymer adsorption surface are considered. Exact calculations for a polymer chain length N of 11 units suggest that configurations of two or more loops have negligible effect on the isotherm when SW > 1, where S and W are exponential weighting factors for monomer–monomer S and polymer–polymer W nearest neighbor interactions. There is a pronounced effect, however, when SW ≪ 1. Limiting expressions (N ≫ 1, but finite) for the single‐loop configurations suggest these configurations are negligible at any degree of saturation θ if θ (1 − θ)^2–k^ N^3–k^ ≪ SW, where k is defined by the weighting factor (j + 1)^−k^ for a ring of j units. This expression suggests that single monomer‐stack configurations are the only significant contributors to the grand partition function at the midpoint of the isotherm if N^3–k^ ≪ SW. Furthermore, single‐loop configurations are negligible below θ = 0.5 but become dominant above the isotherm midpoint when SW ∼ 1 (random binding) if 2 < k < 3. For k > 3 and N → ∞, loop configurations have no effect in any region of the random binding isotherm usually analyzed experimentally (θ < 0.95). Equivalence of matrix and sequence generating methods is also demonstrated.