Dolinnaya N G, Fresco J R
Department of Molecular Biology, Princeton University, NJ 08544.
Proc Natl Acad Sci U S A. 1992 Oct 1;89(19):9242-6. doi: 10.1073/pnas.89.19.9242.
We have identified a type of secondary structure for the homopurine oligomer d(A-G)10 below pH 6 in 0.01 M Na+ that is characterized by intense CD but only minor hypochromicity. The stability of this helix, designated d(A(+)-G)10, does not depend on oligomer concentration and increases sharply as ionic strength or pH drops, reaching a maximum at 4.0 (melting temperature, 37 degrees C). The pKa for the transition, 5.3 at 25 degrees C and even higher with decreasing temperature and [Na+], is much higher than the intrinsic pKa values for dA or dG residues. While the dA residues are protonated in the helix, further protonation of the dG residues disrupts it. When observed at 280 nm, melting of the helix first results in hypochromicity due to stacking of extrahelical dG residues with neighboring dA residues. The character and temperature dependence of the CD spectra of the constituent dinucleoside monophosphates indicate minimal chirality and base overlap for the A+pG sequences in d(A(+)-G)10 but left-handed twist with some base overlap for the GpA+ sequences. The observed properties are best satisfied by a model for an intramolecular helix with limited base overlap, stabilized by ionic bonds between dA residues protonated at N-1 and downstream negatively charged phosphates brought close due to the backbone helical twist, while Gsyn residues lie external to the helix. This structure could provide additional stabilizing energy for biologically relevant protonated non-B-DNA structures adopted by homopurine.homopyrimidine sequences due to topological stress or specific protein binding.
我们已经确定了在0.01 M Na⁺中pH值低于6时，同嘌呤寡聚物d(A-G)₁₀的一种二级结构，其特征是具有强烈的圆二色性（CD）但只有轻微的减色效应。这种螺旋结构，命名为d(A(⁺)-G)₁₀，其稳定性不依赖于寡聚物浓度，并且随着离子强度或pH值下降而急剧增加，在pH 4.0时达到最大值（解链温度，37摄氏度）。该转变的pKa值在25摄氏度时为5.3，并且随着温度和[Na⁺]的降低而更高，远高于dA或dG残基的固有pKa值。虽然dA残基在螺旋中被质子化，但dG残基的进一步质子化会破坏螺旋结构。当在280 nm处观察时，螺旋的解链首先由于螺旋外的dG残基与相邻dA残基的堆积而导致减色效应。组成二核苷酸单磷酸的CD光谱的特征和温度依赖性表明，d(A(⁺)-G)₁₀中A⁺pG序列的手性和碱基重叠最小，但GpA⁺序列具有一些碱基重叠的左手扭曲。所观察到的性质最符合一种分子内螺旋模型，该模型具有有限的碱基重叠，通过N-1位质子化的dA残基与由于主链螺旋扭曲而靠近的下游带负电荷的磷酸之间的离子键稳定，而Gsyn残基位于螺旋外部。由于拓扑应力或特定蛋白质结合，这种结构可以为同嘌呤-同嘧啶序列所采用的生物学相关质子化非B-DNA结构提供额外的稳定能量。
