Garcia A E, Gupta G, Soumpasis D M, Tung C S
Theoretical Division, Los Alamos National Laboratory, NM 87545.
J Biomol Struct Dyn. 1990 Aug;8(1):173-86. doi: 10.1080/07391102.1990.10507796.
We report Potential of Mean Force studies to describe the relative thermodynamic stabilities of d(GCCGCAGC) in a mismatched duplex and a hairpin monomer conformation in NaCl solution. The PMF calculations are combined with previous molecular mechanics and normal mode analysis in order to estimate the role of different components of the free energy in determining the relative stability of the duplex and hairpin structures. The high entropy associated with the loop region and the lack of minor groove phosphate-phosphate interactions in the hairpin compete against the gain in enthalpic contribution to the free energy due to base pairing in the mismatched duplex. The combined free energy calculations show that the hairpin is the most stable conformation at low salt and that a hairpin to duplex transition takes place at approximately 0.47 M NaCl. In addition, we studied the hairpin to partially stacked single helical conformation equilibrium at low salt. We found a small variation in transition temperature in salt concentration, delta Tm/delta log10(cs) approximately 2-3 degrees K/decade, in contrast to the duplex to hairpin or duplex to partially stacked single helix transition where the transition temperature exhibited marked dependence on salt concentration. This is in qualitative agreement with experimental data. Based on the Potential of Mean Force free energy calculation, the order of relative stability of the three-conformations studied varies with salt concentration. We observed the following orders of stability: stacked single helix greater than hairpin greater than duplex for cs less than 0.77 M NaCl; single helix greater than duplex greater than hairpin for 0.77 less than Cs less than 2.1 M; and duplex greater than hairpin greater than single strand for cs greater than 2.1 M. From the calculated PMF free energy curves in the NaCl concentration range, 0.012 less than cs less than 5.0 M, we can assign upper and lower bounds for the non-ionic differences in free energy between the duplex, hairpin, and stacked single helical states (at standard conditions: cs = 1.0 M, T = 25 degrees C, and 1 M oligomer concentration). We found that for delta G duplex single helix = G duplex - 2 x G single helix less than -7.38 Kcal/mol, the single helix is the least stable state. For the duplex-to-hairpin free energy difference in the range, -1.87 less than delta G duplex-hairpin less than 0.03 Kcal/mol, there will always be a salt-induced hairpin-to-duplex transition for 0.01 less than cs less than 1.6 M NaCl. If delta G duplex-hairpin less than -1.87, the duplex is always more stable than the hairpin; and for delta G duplex-hairpin greater than Kcal/mol, the hairpin state is always more stable than the duplex, for all salt concentrations.
我们报告了平均力势研究，以描述在NaCl溶液中错配双链体和发夹单体构象中d(GCCGCAGC)的相对热力学稳定性。将平均力势计算与先前的分子力学和正常模式分析相结合，以估计自由能不同组分在确定双链体和发夹结构相对稳定性中的作用。与环区域相关的高熵以及发夹中缺少小沟磷酸 - 磷酸相互作用，与错配双链体中碱基配对导致的自由能焓贡献增加相互竞争。综合自由能计算表明，发夹在低盐浓度下是最稳定的构象，并且在约0.47 M NaCl时发生发夹向双链体的转变。此外，我们研究了低盐浓度下发夹向部分堆叠单螺旋构象的平衡。我们发现盐浓度变化时转变温度的变化很小，ΔTm/Δlog10(cs)约为2 - 3 K/十倍浓度，这与双链体向发夹或双链体向部分堆叠单螺旋转变不同，后者转变温度对盐浓度有明显依赖性。这与实验数据在定性上一致。基于平均力势自由能计算，所研究的三种构象的相对稳定性顺序随盐浓度而变化。我们观察到以下稳定性顺序：对于cs小于0.77 M NaCl，堆叠单螺旋大于发夹大于双链体；对于0.77小于Cs小于2.1 M，单螺旋大于双链体大于发夹；对于cs大于2.1 M，双链体大于发夹大于单链。从NaCl浓度范围0.012小于cs小于5.0 M内计算的平均力势自由能曲线，我们可以确定双链体、发夹和堆叠单螺旋状态之间自由能非离子差异的上下限（在标准条件下：cs = 1.0 M，T = 25℃，以及1 M寡聚物浓度）。我们发现，对于ΔG双链体 - 单螺旋 = G双链体 - 2×G单螺旋小于 - 7.38 Kcal/mol，单螺旋是最不稳定的状态。对于双链体 - 发夹自由能差异在 - 1.87小于ΔG双链体 - 发夹小于0.03 Kcal/mol范围内，对于0.01小于cs小于1.6 M NaCl，总会有盐诱导的发夹向双链体转变。如果ΔG双链体 - 发夹小于 - 1.87，双链体总是比发夹更稳定；对于ΔG双链体 - 发夹大于Kcal/mol，对于所有盐浓度，发夹状态总是比双链体更稳定。
