The Influence of the Thymine C5 Methyl Group on Spontaneous Base Pair Breathing in DNA

Abstract

Sequences of four or more AT base pairs without a 5-TA-3 step, so-called A-tracts, influence the global properties of DNA by causing curvature of the helix axis if phased with the helical repeat and also influence nucleosome packaging. Hence it is interesting to understand this phenomenon on the molecular level, and numerous studies have been devoted to investigations of dynamical and structural features of A-tract DNA. It was early observed that anomalously slow base pair-opening kinetics were a striking physical property unique to DNA A-tracts (Leroy, J. L., Charretier, E., Kochoyan, M., and Gueron, M. (1988) Biochemistry 27, 8894 -8898). Furthermore, a strong correlation between DNA curvature and anomalously slow base pair-opening dynamics was found. In the present work it is shown, using imino proton exchange measurements by NMR spectroscopy that the main contribution to the dampening of the base pair-opening fluctuations in A-tracts comes from the C5 methylation of the thymine base. Because the methyl group has been shown to have a very limited effect on the DNA curvature as well as the structure of the DNA helix, the thymine C5 methyl group stabilizes the helix directly. Empirical potential energy calculations show that methylation of the tract improves the stacking energy of a base pair with its neighbors in the tract by 3-4 kcal/mol.

Balance of Attraction and Repulsion in Nucleic-Acid Base Stacking: CCSD(T)/Complete-Basis-Set-Limit Calculations on Uracil Dimer and a Comparison with the Force-Field Description

“…However, the reduction of the hydrogen radius, which markedly improved the quality of the empirical force-field stacking energy scans, had no visible effect in test simulations. 135 An exaggerated short-range repulsion in the force field description was also reported for cation-solute interactions and affects for example simulations of quadruplex DNA where the cations residing in the channel of the quadruplex stem look oversized. This effect was originally attributed to the lack of polarization in the force field, 136,137 but it is more likely caused by the short-range repulsion imbalance discussed in the present paper.…”

Theoretical and Experimental Investigations of DNA Open States

“…Методами молекулярной динамики подтверждено, что она сохраняется и в растворе, хотя точные значения параметров сильно зависели от выбора протокола [324]. Помимо трёхцентровых Н-связей, А-тракты стабилизированы за счёт повышенной энергии стэкинг-взаимодействий [325,326].…”

“…Заменой тиминовых оснований на дезоксиуридиновые в олигомерах, содержащих А-тракты, установлено, что основной вклад в стабилизацию этих структур вносят CH 3 -группы тимина [325]. Повышенной стабильностью в B'-ДНК обладает не только дуплекс, но и сами открытые состояния.…”

“…При τ cl ≤ 2 нс и α ⋅ K d превышающем α′ ⋅ K d ′ не менее, чем на порядок, Τ ex (0)/τ op ≥ 0,8, что является вполне допустимой погрешностью. Однако, по данным многих экспериментов, τ cl отдельных оснований могут достигать 100 нс и более [28,282,299,305,318,319,325,330,331,357]. Для сохранения неравенства…”

“…Объектом иследования в работе [299] были олигомеры, включающие А-тракты -элементы структуры, обладающие наибольшим τ cl оснований, вплоть до сотен наносекунд [299,305,318,319,325,330,331] [299]. Была также проведена аппроксимация данных по парам GC 3 и GC 4 того же олигомера [299] (только для NH 3 в качестве катализатора).…”