Abstract
The entropy and enthalpy changes which contribute to the thermodynamics of the B to Z transition were determined for three recombinant plasmids containing a (dC-dG)16 tract and for a plasmid containing a pair of (dT-dG)20 regions. For each base pair which adopts a left-handed conformation in the plasmids with (dC-dG)16 sequences, the delta HBZ and delta SBZ are -2.1 kcal/mol bp and -8.8 cal/K-mol bp, respectively. In the plasmid containing the (dT-dG)20 tracts, however, the delta HBZ and delta SBZ values are 0.58 kcal/mol bp and -0.76 cal/K-mol bp, respectively. Also, these determinations show that for each B-Z junction that forms in the plasmids containing the (dC-dG), the enthalpy and entropy changes are 24 kcal/mol junction and 65 cal/K-mol junction, whereas for the (dT-dG) plasmid, the enthalpy and entropy changes are -1.8 kcal/mol junction and -22 cal/K-mol junction, respectively. Those values for the enthalpy and entropy changes for the formation of a BZ junction in (dC-dG) and (dT-dG) plasmids suggest that the properties and possibly the structures of the junctions are different. Calculations using the enthalpy and entropy changes determined in this study reveal that the B to Z transition in plasmids containing (dC-dG) blocks are more temperature-dependent than the transitions in plasmids with (dT-dG) blocks. Surprisingly, at temperatures above 60 degrees C, calculations indicate that the B to Z transitions in (dT-dG) plasmids should be energetically favored over that transition in (dC-dG) plasmids.
Highlights
Born HIThe blue colonies were grown in 10 ml pRW155 cultures and screened for insert size by restriction enzyme digest
The entropy and enthalpy changes which contribuatesegment of right-handed primary helix to a left-handed to the therm ~ y n a moif~the B to 2 transition were confo ~ a t i o ncould be monitored by supercoil relaxation dedetermined for three recombinant plasmids containintegrminations because approximately two negative supercoil a ( d c - d C ~t)r~ac~t and for a plasmid containing a pair turns were removed whena single turn of left-handed Z-DNA ofzo regionsF. or each bast? pair which adopts was created [6, 13,14,15,16,17,18,19,20]
The dataobtained from twothat the B to Z transition in plasmids containing(dC- dimensional gels can be fitted to a statistical mechanical dG) blocks are more temperature-dependent than the model to obtain free energy values for ( a )each base pair in a transitions in plasmids with blocks
Summary
The blue colonies were grown in 10 ml pRW155 cultures and screened for insert size by restriction enzyme digest The sequences of these plasmids (Fig. 1) were verified by either M13. --2(a1;/1=0.5link+in1g/1d2if)f,ebre=ncceh, aatnge2ibn=twtoisttalfrhoemlicjaulntcwtiiosnt .diIfnfetrheniscet,raea=tment, the nonlinear least squares value fit is to three independent parameters: AGjxn,AGBz,and b This method is analogous to the "zipper model" for DNA thermal melting. Followingthe formation of the junction, it is relatively easy for each base pair to adopt a 2-DNA structure with a free energy of formation AGB. This model includes the possibility that the twist at thejunction region can change when Z-DNAis formed.
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