Han H, Dervan P B
Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena 91125.
Proc Natl Acad Sci U S A. 1993 May 1;90(9):3806-10. doi: 10.1073/pnas.90.9.3806.
The stabilities of eight triple helical pyrimidine.purine.pyrimidine structures comprised of identical sequence but different RNA (R) or DNA (D) strand combinations were measured by quantitative affinity cleavage titration. The differences in equilibrium binding affinities reveal the importance of strand composition. For the sequences studied here, the stabilities of complexes containing a pyrimidine third strand D or R and purine.pyrimidine double helical DD, DR, RD, and RR decrease in order: D + DD, R + DD, R + DR, D + DR > R + RD, R + RR >> D + RR, D + RD (pH 7.0, 25 degrees C, 100 mM NaCl/1 mM spermine). These findings suggest that RNA and DNA oligonucleotides will be useful for targeting (i) double helical DNA and (ii) RNA.DNA hybrids if the purine Watson-Crick strand is DNA. However, RNA, but not DNA, oligonucleotides will be useful for sequence-specific binding of (i) double helical RNA and (ii) RNA.DNA hybrids if the purine Watson-Crick strand is RNA. This has implications for the design of artificial ligands targeted to specific sequences of double helical RNA and RNA.DNA hybrids.
通过定量亲和切割滴定法测定了由相同序列但不同RNA（R）或DNA（D）链组合组成的8种三链嘧啶-嘌呤-嘧啶结构的稳定性。平衡结合亲和力的差异揭示了链组成的重要性。对于此处研究的序列，含有嘧啶第三链D或R以及嘌呤-嘧啶双链DD、DR、RD和RR的复合物的稳定性按以下顺序降低：D + DD、R + DD、R + DR、D + DR > R + RD、R + RR >> D + RR、D + RD（pH 7.0，25℃，100 mM NaCl/1 mM精胺）。这些发现表明，如果嘌呤沃森-克里克链是DNA，RNA和DNA寡核苷酸将可用于靶向（i）双链DNA和（ii）RNA-DNA杂交体。然而，如果嘌呤沃森-克里克链是RNA，RNA寡核苷酸而非DNA寡核苷酸将可用于（i）双链RNA和（ii）RNA-DNA杂交体的序列特异性结合。这对靶向双链RNA和RNA-DNA杂交体特定序列的人工配体的设计具有启示意义。
