Triple Hydrogen Bonds in DNA Modify the Transition from Right- to Left- Handed Forms

Abstract

Double-stranded DNA usually adopts a right-handed B-form in aqueous solution, but alternative DNA conformations can also exist and play important roles in a wide range of cellular processes. For example, DNA melting (strand separation) is required to initiate DNA replication as well as transcription. Moreover, the over-production of left-handed Z-form DNA in cells is thought to be the trigger for auto-immunity in lupus. Therefore, understanding the underlying mechanics of right- to left-handed DNA transitions is very important to begin to understand how cellular processes depend on alternative DNA conformations. Two of the most influential factors related to this transition are the tension on DNA and the degree of hydrogen bonding. Magnetic Tweezers enable us to unwind single DNA molecules to investigate the dynamics of right- to left-handed DNA transitions at different tensions. Moreover, by substituting diaminopurine (DAP) deoxyribonucleotides for dATP in PCR reactions, completely triply hydrogen-bonded DNA fragments have been produced. These and normal DNA fragments were used to observe the dynamics of right- to left-handed DNA transitions under tension. We found that this transition is highly hydrogen bond dependent. Although DAP and normal DNA exhibit similar patterns of conformational change, DAP DNA converted to left-handed DNA at lower tension. Also, we found pronounced hysteresis for normal DNA upon re-winding from a left- to right-handed form, which indicated the that heterogeneity of the number of hydrogen bonds between base pairs in normal DNA contributes to non-equilibrium conformational changes. The results suggest that hydrogen bonding can significantly affect cellular processes requiring certain under-wound DNA conformations, and DAP DNA provides a sequence-independent model for studying the effects of hydrogen bonding on conformational changes of DNA.