Synthesis, Thermodynamic Properties, and Crystal Structure of RNA Oligonucleotides Containing 5-Hydroxymethylcytosine

被引:10
作者
Riml, Christian [1 ,2 ]
Lusser, Alexandra [3 ]
Ennifar, Eric [4 ]
Micura, Ronald [1 ,2 ]
机构
[1] Univ Innsbruck, Inst Organ Chem, A-6020 Innsbruck, Austria
[2] Univ Innsbruck, Ctr Mol Biosci, A-6020 Innsbruck, Austria
[3] Med Univ Innsbruck, Div Mol Biol, Bioctr, A-6020 Innsbruck, Austria
[4] Univ Strasbourg, CNRS, Architecture & React ARN, UPR 9002, F-67000 Strasbourg, France
基金
奥地利科学基金会;
关键词
SOLID-PHASE SYNTHESIS; DNA; 5-METHYLCYTOSINE; 5-FORMYLCYTOSINE; STABILITY; TARGETS; SYSTEM; REPAIR; NSUN3;
D O I
10.1021/acs.joc.7b01171
中图分类号
O62 [有机化学];
学科分类号
070303 ; 081704 ;
摘要
5-Hydroxymethylcytosine (hm(5)C) is an RNA modification that has attracted significant interest because of the finding that RNA hydroxyrnethylation can favor mRNA translation. For insight into the mechanistic details of hm(5)C function to be obtained, the availability of RNAs containing this modification at defined positions that can be used for in vitro studies is highly desirable. In this Work, we present an eight-step route to 5-hydroxymethylcytidine (hm(5)rC) phosphoramidite for solid-phase synthesis of modified RNA oligonucleotides. Furthermore, we examined the effects of hm(5)rC on RNA duplex stability and its impact on structure formation using the sarcin-ricin loop (SRL) motif. Thermal denaturation experiments revealed that hm(5)rC increases RNA duplex stability. By contrast, when cytosine within an UNCG tetraloop motif was replaced by hm(5)rC, the thermodynamic stability of the corresponding hairpin fold was attenuated. Importantly, incorporation of hm(5)rC into the SRL motif resulted in an RNA crystal structure at 0.85 angstrom resolution. Besides changes in the hydration pattern at the site of modification, a slight opening of the hm(5)rC-G pair compared to the unmodified C-G in the native structure was revealed.
引用
收藏
页码:7939 / 7945
页数:7
相关论文
共 50 条
  • [41] Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA
    Squires, Jeffrey E.
    Patel, Hardip R.
    Nousch, Marco
    Sibbritt, Tennille
    Humphreys, David T.
    Parker, Brian J.
    Suter, Catherine M.
    Preiss, Thomas
    [J]. NUCLEIC ACIDS RESEARCH, 2012, 40 (11) : 5023 - 5033
  • [42] Squires JE, 2010, EPIGENOMICS-UK, V2, P709, DOI [10.2217/epi.10.47, 10.2217/EPI.10.47]
  • [43] Differential Stabilities and Sequence-Dependent Base Pair Opening Dynamics of Watson-Crick Base Pairs with 5-Hydroxymethylcytosine, 5-Formylcytosine, or 5-Carboxylcytosine (vol 54, pg 1294, 2015)
    Szulik, Marta W.
    Pallan, Pradeep S.
    Nocek, Boguslaw
    Voehler, Markus
    Banerjee, Surajit
    Brooks, Sonja
    Joachimiak, Andrzej
    Egli, Martin
    Eichman, Brandt F.
    Stone, Michael P.
    [J]. BIOCHEMISTRY, 2015, 54 (15) : 2550 - 2550
  • [44] Differential Stabilities and Sequence-Dependent Base Pair Opening Dynamics of Watson-Crick Base Pairs with 5-Hydroxymethylcytosine, 5-Formylcytosine, or 5-Carboxylcytosine
    Szulik, Marta W.
    Pallan, Pradeep S.
    Nocek, Boguslaw
    Voehler, Markus
    Banerjee, Surajit
    Brooks, Sonja
    Joachimiak, Andrzej
    Egli, Martin
    Eichman, Brandt F.
    Stone, Michael P.
    [J]. BIOCHEMISTRY, 2015, 54 (05) : 1294 - 1305
  • [45] Solid phase synthesis and restriction endonuclease cleavage of oligodeoxynucleotides containing 5-(hydroxymethyl)-cytosine
    TardyPlanechaud, S
    Fujimoto, J
    Lin, SS
    Sowers, LC
    [J]. NUCLEIC ACIDS RESEARCH, 1997, 25 (03) : 553 - 558
  • [46] THALHAMMER A, 2011, J CHEM SOC CHEM COMM, V47, P5325, DOI DOI 10.1039/C0CC05671E
  • [47] Molecular replacement with MOLREP
    Vagin, Alexei
    Teplyakov, Alexei
    [J]. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2010, 66 : 22 - 25
  • [48] Regulation of telomeric i-motif stability by 5-methylcytosine and 5-hydroxymethylcytosine modification
    Xu, Baochang
    Devi, Gitali
    Shao, Fangwei
    [J]. ORGANIC & BIOMOLECULAR CHEMISTRY, 2015, 13 (20) : 5646 - 5651
  • [49] The existence of 5-hydroxymethylcytosine and 5-formylcytosine in both DNA and RNA in mammals
    Zhang, Hao-Ying
    Xiong, Jun
    Qi, Bao-Ling
    Feng, Yu-Qi
    Yuan, Bi-Feng
    [J]. CHEMICAL COMMUNICATIONS, 2016, 52 (04) : 737 - 740
  • [50] Nucleic Acid Oxidation in DNA Damage Repair and Epigenetics
    Zheng, Guanqun
    Fu, Ye
    He, Chuan
    [J]. CHEMICAL REVIEWS, 2014, 114 (08) : 4602 - 4620