Pasternak Anna, Kierzek Elzbieta, Pasternak Karol, Turner Douglas H, Kierzek Ryszard
Institute of Bioorganic Chemistry, Polish Academy of Sciences, 60-714 Poznan, Noskowskiego 12/14, Poland.
Nucleic Acids Res. 2007;35(12):4055-63. doi: 10.1093/nar/gkm421. Epub 2007 Jun 12.
Modified nucleotides are useful tools to study the structures, biological functions and chemical and thermodynamic stabilities of nucleic acids. Derivatives of 2,6-diaminopurine riboside (D) are one type of modified nucleotide. The presence of an additional amino group at position 2 relative to adenine results in formation of a third hydrogen bond when interacting with uridine. New method for chemical synthesis of protected 3'-O-phosphoramidite of LNA-2,6-diaminopurine riboside is described. The derivatives of 2'-O-methyl-2,6-diaminopurine and LNA-2,6-diaminopurine ribosides were used to prepare complete 2'-O-methyl RNA and LNA-2'-O-methyl RNA chimeric oligonucleotides to pair with RNA oligonucleotides. Thermodynamic stabilities of these duplexes demonstrated that replacement of a single internal 2'-O-methyladenosine with 2'-O-methyl-2,6-diaminopurine riboside (D(M)) or LNA-2,6-diaminopurine riboside (D(L)) increases the thermodynamic stability (DeltaDeltaG degrees 37) on average by 0.9 and 2.3 kcal/mol, respectively. Moreover, the results fit a nearest neighbor model for predicting duplex stability at 37 degrees C. D-A and D-G but not D-C mismatches formed by D(M) or D(L) generally destabilize 2'-O-methyl RNA/RNA and LNA-2'-O-methyl RNA/RNA duplexes relative to the same type of mismatches formed by 2'-O-methyladenosine and LNA-adenosine, respectively. The enhanced thermodynamic stability of fully complementary duplexes and decreased thermodynamic stability of some mismatched duplexes are useful for many RNA studies, including those involving microarrays.
修饰核苷酸是研究核酸结构、生物学功能以及化学和热力学稳定性的有用工具。2,6-二氨基嘌呤核糖核苷（D）的衍生物是一类修饰核苷酸。相对于腺嘌呤，在2位存在一个额外的氨基会导致与尿苷相互作用时形成第三个氢键。本文描述了LNA-2,6-二氨基嘌呤核糖核苷的3'-O-亚磷酰胺保护基团的化学合成新方法。2'-O-甲基-2,6-二氨基嘌呤和LNA-2,6-二氨基嘌呤核糖核苷的衍生物被用于制备完整的2'-O-甲基RNA和LNA-2'-O-甲基RNA嵌合寡核苷酸，以与RNA寡核苷酸配对。这些双链体的热力学稳定性表明，用2'-O-甲基-2,6-二氨基嘌呤核糖核苷（D(M)）或LNA-2,6-二氨基嘌呤核糖核苷（D(L)）取代单个内部2'-O-甲基腺苷，平均分别使热力学稳定性（ΔΔG°37）提高0.9和2.3千卡/摩尔。此外，结果符合预测37℃时双链体稳定性的最近邻模型。由D(M)或D(L)形成的D-A和D-G错配而非D-C错配，相对于分别由2'-O-甲基腺苷和LNA-腺苷形成的相同类型错配，通常会使2'-O-甲基RNA/RNA和LNA-2'-O-甲基RNA/RNA双链体不稳定。完全互补双链体增强的热力学稳定性和一些错配双链体降低的热力学稳定性对许多RNA研究有用，包括那些涉及微阵列的研究。
