Recognition of mixed-sequence DNA using double-stranded probes with interstrand zipper arrangements of O2′-triphenylene- and coronene-functionalized RNA monomers,Organic & Biomolecular Chemistry

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Recognition of mixed-sequence DNA using double-stranded probes with interstrand zipper arrangements of O2′-triphenylene- and coronene-functionalized RNA monomers
Organic & Biomolecular Chemistry ( IF 2.9 ) Pub Date : 2017-10-14 00:00:00 , DOI: 10.1039/c7ob01920c
Saswata Karmakar _{1,

2,

3,

4} , Dale C. Guenther _{1,

2,

3,

4} , Bradley C. Gibbons _{1,

1,

2,

3,

4} , Patrick J. Hrdlicka _{1,

2,

3,

4}

Affiliation

Development of hybridization-based probes that enable recognition of specific mixed-sequence double-stranded DNA (dsDNA) regions is of considerable interest due to their potential applications in molecular biology, biotechnology, and medicine. We have recently demonstrated that nucleic acid duplexes with +1 interstrand zipper arrangements of intercalator-functionalized nucleotides such as 2′-O-(pyren-1-yl)methyl RNA monomers are inherently activated for recognition of mixed-sequence dsDNA targets, including chromosomal DNA. In the present work, we follow up on our previous structure–activity relationship studies and explore if the dsDNA-recognition efficiency of these so-called Invader probes can be improved by using larger intercalators than pyrene. Oligodeoxyribonucleotides modified with 2′-O-(triphenylen-2-yl)methyl-uridine monomer X and 2′-O-(coronen-1-yl)methyl-uridine monomer Z form extraordinarily stabilized duplexes with complementary DNA (ΔT_m's per modification of up to 13 °C and 20 °C, respectively). Invader probes based on X- and Z-monomers are shown to recognize model dsDNA targets with exceptional binding specificity, but are less efficient than reference probes modified with 2′-O-(pyren-1-yl)methyl-uridine monomer Y. The insight from this study will inform further optimization of Invader probes.

中文翻译：

使用带有O2'-三亚苯基和并苯功能化的RNA单体的链间拉链排列的双链探针识别混合序列DNA

能够识别特定的混合序列双链DNA（dsDNA）区域的基于杂交的探针的开发由于其在分子生物学，生物技术和医学中的潜在应用而备受关注。我们最近证明，具有嵌入剂官能化核苷酸（例如2' - O-（pyren-1-yl）甲基RNA单体）的+1链间拉链排列的核酸双链固有地被激活，以识别混合序列dsDNA靶标，包括染色体脱氧核糖核酸。在当前的工作中，我们将继续进行先前的结构-活性关系研究，并探讨通过使用比pyr更大的嵌入剂是否可以提高这些所谓的Invader探针的dsDNA识别效率。用2'- O修饰的寡脱氧核糖核苷酸-（三亚苯基-2-基）甲基-尿苷单体X和2' - O-（亚乙基-1-基）甲基-尿苷单体Z与互补DNA形成非常稳定的双链体（ΔT _m每次修饰最多13 °C和20°C）。显示基于X-和Z-单体的入侵探针可识别具有独特结合特异性的dsDNA靶标，但效率不及2' - O-（pyren-1-yl）甲基-尿苷单体Y修饰的参考探针。这项研究的见识将有助于进一步优化Invader探针。

更新日期：2017-11-15

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