Deoxyribonucleic acids can form a wide variety of structural motifs which differ greatly from the typical antiparallel duplex stabilized by Watson–Crick base pairing. Many of these structures are thought to occur in vivo and may have essential roles in the biology of the cell. Among these is the parallel-stranded duplex—a structural motif in which DNA strands associate in a head-to-head fashion with the 5′ ends at the same end of the duplex—which is stabilized by reverse Watson–Crick base pairing. In this study, parallel- and antiparallel-stranded DNA duplexes formed from two different 12-mer oligonucleotides were studied using native electrospray ionization combined with trapped ion mobility spectrometry and mass spectrometry. The DNA duplex charge plays an important role in the gas-phase mobility profile, with a more compact form in negative mode than in positive mode (ΔΩ ≈ 100 Ų between −4 and +4). Despite sequence mismatches, homo- and hetero-DNA duplexes were formed in solution and transfer to the gas phase, where a more compact structure was observed for the parallel compared to the antiparallel duplexes (ΔΩ ≈ 50 Ų), in good agreement with theoretical calculations. Theoretical studies suggest that a reduction (or compaction) along the helical axis of the parallel and antiparallel DNA duplexes is observed upon transfer to the gas phase.

中文翻译：

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使用捕获离子迁移谱法区分气相中的平行和反平行 DNA 双链体

脱氧核糖核酸可以形成各种各样的结构基序，这些基序与由 Watson-Crick 碱基配对稳定的典型反平行双链体大不相同。许多这些结构被认为发生在体内，并且可能在细胞生物学中发挥重要作用。其中包括平行链双链体——一种结构基序，其中 DNA 链以头对头的方式与双链体同一末端的 5' 末端相关联——它通过反向 Watson-Crick 碱基配对稳定。在这项研究中，使用天然电喷雾电离结合捕获离子迁移谱和质谱法研究了由两种不同的 12 聚体寡核苷酸形成的平行和反平行链 DNA 双链体。DNA 双链电荷在气相迁移率曲线中起着重要作用，² -4 和 +4 之间）。尽管存在序列错配，但在溶液中形成了同源和异源 DNA 双链体并转移到气相，与反平行双链体相比，在气相中观察到平行结构更紧凑（ΔΩ ≈ 50 Å ²），与理论一致计算。理论研究表明，在转移到气相时观察到沿平行和反平行 DNA 双链体的螺旋轴的减少（或压缩）。