THERMODYNAMICS OF DNA DUPLEXES WITH ADJACENT G.A MISMATCHES
THERMODYNAMICS OF DNA DUPLEXES WITH ADJACENT G.A MISMATCHES
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DOI：
10.1021/bi00244a028
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发表时间：
1991-07-30
期刊：
影响因子：
2.9
通讯作者：
WILSON, WD
中科院分区：
文献类型：
--
作者：
LI, Y;ZON, G;WILSON, WD
序列5 '-d（ATGAGCGAAT）与总共10个碱基对中的4个G. A错配碱基对（下划线）形成非常稳定的自身互补双链体[Li等人（1991）Proc.Natl. Acad. Sci. U.S.A. 88，26-30]。构象是在一般的B-家庭和稳定的碱基对氢键的一种不寻常的类型，有利的基地偶极子方向，并通过广泛的嘌呤-嘌呤堆积在错配位点。我们已经合成了13个在上述序列中具有系统性变异的十聚体，以确定侧翼序列、GA错配的数量和错配序列顺序（5 '-GA-3'或5 '-AG-3'）如何影响双链体稳定性。将错配侧翼序列中的A.T碱基对改变为G. C碱基对可以稳定双链体，但仅在B型DNA中观察到的程度。然而，序列5 '-嘧啶-GA-嘌呤-3'比5 '-嘌呤-GA-嘧啶-3'稳定得多。具有两对相邻G. A错配的最稳定序列具有与完全沃森-克里克碱基配对的双链体相当的双链体形成的热力学参数。具有单个G. A对的相似序列比具有相邻G. A错配的序列稳定性差得多。将错配顺序从5 '-GA-3'逆转为5 '-AG-3'导致不形成双链体的寡聚体。这些结果与来自NMR和分子力学的模型的预测一致，并且表明序列5 '-嘧啶-GA-嘌呤-3'形成了非常适合于B型双螺旋的稳定构象单元。为了使二级核酸靶位点处的结合最小化，当设计DNA探针或反义药物分子时，考虑这种稳定构象单元的可能形成显然是非常重要的。
The sequence 5'-d(ATGAGCGAAT) forms a very stable self-complementary duplex with four G.A mismatch base pairs (underlined) out of ten total base pairs [Li et al. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 26-30]. The conformation is in the general B-family and is stabilized by base-pair hydrogen bonding of an unusual type, by favorable base dipole orientations, and by extensive purine-purine stacking at the mismatched sites. We have synthesized 13 decamers with systematic variations in the sequence above to determine how the flanking sequences, the number of G.A mismatches, and the mismatch sequence order (5'-GA-3' or 5'-AG-3') affect the duplex stability. Changing A.T to G.C base pairs in sequences flanking the mismatches stabilizes the duplexes, but only to the extent observed with B-form DNA. The sequence 5'-pyrimidine-GA-purine-3', however, is considerably more stable than 5'-purine-GA-pyrimidine-3'. The most stable sequences with two pairs of adjacent G.A mismatches have thermodynamic parameters for duplex formation that are comparable to those for fully Watson-Crick base-paired duplexes. Similar sequences with single G.A pairs are much less stable than sequences with adjacent G.A mismatches. Reversing the mismatch order from 5'-GA-3' to 5'-AG-3' results in an oligomer that does not form a duplex. These results agree with predictions from the model derived from NMR and molecular mechanics and indicate that the sequence 5'-pyrimidine-GA-purine-3' forms a stable conformational unit that fits quite well into a B-form double helix. In order to minimize binding at secondary nucleic acid target sites, it is obviously of great importance to consider the possible formation of such stable conformational units when designing DNA probes or antisense drug molecules.