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INTERFACIAL AND CONFINED WATER Part 7

Cấu tạo của nó là tương thích với bất kỳ chuỗi cặp cơ sở, và nó được tách ra từ hình thức-B chỉ là một rào cản năng lượng khiêm tốn [616]. Do tất cả các tính năng này, hồi phục địa phương B ↔ Một chuyển tiếp đại diện cho một trong các phương thức để quản lý các tương tác protein-DNA [617]. | 182 Interfacial and confined water Its conformation is compatible with any base pair sequence and it is separated from the B-form by only a modest energy barrier 616 . Due to all these features reversible local B A transitions represent one of the modes for governing protein-DNA interactions 617 . The B A transitions can be also induced in vitro by changing the DNA environment 488 618-620 . In condensed preparations that is in crystalline and amorphous fibers as well as in films DNA adopts the B-form under high relative humidity but it can be reversibly driven to the A-form by placing the samples under relative humidity below 80 488 618 620 . DNA molecules exhibit reversible B A transition in aqueous solutions upon addition of some organic solvents 613 619 . In all cases the transition occurs at about the same water activity suggesting that the B A conformational switch is driven by the hydration state of the double helix 492 . Hydration of nucleic acids has a number of distinctions due to their polyionic character and uneven nonspherical shapes 487 . In physiological conditions the double-helical DNA directly interacts with solvent ions in several water layers from its surface therefore the functional DNA hydration shell is very thick. Under limited hydration there is a strict relationship between the state of DNA and hydration number r measured as the number of water molecules per nucleotide or phosphate . When r is reduced below 30 the common B-form of DNA is already perturbed but it is maintained until r 20 487 488 . Below this hydration DNA undergoes different conformational transitions among which the transition from B- to A-form 489 with a midpoint at about r 15 is the most studied see Section 6 . Formation of a spanning network of hydration water at the DNA surface upon hydration was studied by computer simulations 200 621 using the water drop methods 622 623 . Simulations were carried out for a rigid dodecamer fragment of double-helical DNA. The structures