Biopolymer -- DNA.pptVIP

Base Pairs Chargaff’s Law: A—T, C—G by H-bonds Spatial Geometry and Secondary Structure Two polynucleotide chains are wound around a common axis to produce a double helix Diameter = 20? Distance of adjacent bases = 3.4? Rotation of adjacent bases = 36° Forces Stabilizing DNA Secondary Structure: H-Bonds H-Bond strength of the base pairs: A—T ~ 7 kcal/mole C—G ~ 17 kcal/mole Comparison: Covalent bond EC—C =83.1 kcal/mole Rigidity of bonds: to lengthen the bonds by 0.1?, we need the energy 0.1 kcal/mole for H-bonds 3.25 kcal/mole for C—C covalent bond Forces Stabilizing DNA Secondary Structure: Stacking Interactions Polymorphism of DNA B-DNA: 正常條件下的結構 A-DNA: 低濕度下可能由B-DNA變為A-DNA Z-DNA: 某些特殊序列在特殊條件下，如GCGCGC在高濃度的食鹽水中可能變成這種結構 Tertiary Structure: Supercoil This is a famous electron micrograph of an E. coli cell that has been carefully lysed, then all the proteins were removed, and it was spread on an EM grid to? reveal all of its DNA. Relaxed － inactive Supercoiled － active Energetics of DNA Spercoil L (Link): number of times that one ribbon edge winds around the other (integer for closed loop) T (Twist): number of times either edge winds around the helix axis W (Writhe): number of turns that the helix makes around the supercoil axis (can be positive or negative) L=T+W Energis for the three parts: EL=aL(L-L0)2 ET=aT(T-T0)2 EW is complicated Chen, J. and Seeman, N.C. (1991), Nature (London) 350, 631-633. Zhang, Y. and Seeman, N.C. (1994), J. Am. Chem. Soc. 116, 1661-1669. Approximate Models for DNA Structure – Coarse Graining DNA 是很複雜的生物大分子，要直接以原子尺度研究非常困難，因此必須做許多層次的近似 首先掌握主要的結構特性與交互作用 Backbone 上的糖以及磷酸原子團是週期性的 DNA 分子結構具有某種程度的規則性 – 其「骨架」可能可以用固態物理的方法近似 但又不似晶體完美，較具彈性，需引入聚合體物理方法研究 鹼基的排列沒有規則性（？） First Level of Hierarchy Linear Rod-Like Model H=Hs+Ht+Hb+Hs-t+Hs-b+Ht-b Stretch: 拉長或壓縮；Twist: 扭轉；Bend: 彎曲，後三項為交叉作用項 各能量大小比較：Hs, Ht較大，Hb小1~2 orders，Hs-b與Ht-b可以忽略 用discrete model 更簡單： Linear Rod-Like Model (Conti.) Hs-t comes from the interaction between longitudinal and torsional motio