Extended Thermodynamic Database for Modified Oligonucleotides

修饰寡核苷酸的扩展热力学数据库

• 批准号: 7901462
• 负责人: William J. Kennelly
• 金额: $ 21.81万
• 依托单位: DNA SOFTWARE, INC.
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-02-01 至 2011-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7901462
• 关键词: 2,6-Diaminopurine; 2-Aminopurine; 2-thiothymine; 7-deazaguanine; Address; Algorithms; Alternative Splicing; Arts; Behavior; Betaine; Binding; Biochemical; Biological Assay; Buffers; Complement; Computer Simulation; Computer software; Data; Databases; Dimethyl Sulfoxide; Experimental Designs; Flucytosine; Fluorouracil; Forensic Medicine; Foundations; Funding; Genome; Genomics; Genotype; Glycols; Government; Grant; Guidelines; Human Genome; Inosine; Investigation; Kinetics; Knowledge; Laboratories; Length; Link; Literature; Measurement; Measures; Mission; Modeling; Modification; Molecular Profiling; Nucleic Acid Folding; Nucleic Acids; Nucleotides; Oligonucleotides; Pathogen detection; Performance; Phase; Pyrimidine; Pyrimidines; RNA; RNA Interference; Research; Research Personnel; Sampling; Series; Small Business Innovation Research Grant; Sodium Chloride; Software Design; Software Tools; Structure; Surveys; System; Technology; Testing; Therapeutic; Thermodynamics; Time; Update; Vertebral column; Visual; Work; base; cost; design; fluorophore; fluoropyrimidine; genome sequencing; graphical user interface; heuristics; improved; in vivo; inorganic phosphate; mRNA Expression; meetings; melting; models and simulation; phosphorothioate; programs; research study; simulation; simulation software; success; triethylene glycol; wasting

DESCRIPTION (provided by applicant): A greatly expanded thermodynamic database for modified oligonucleotides will be developed in this project and incorporated into existing design software. This Fast Track SBIR proposal focuses on determining thermodynamic parameters for modifications that are currently finding widespread applications. The new thermodynamic database and software will enable a large number of researchers throughout the world to more easily develop advanced applications with modified oligonucleotides and will add substantial commercial value to the software products. In this new proposal, the range of modified oligonucleotides will be greatly increased to include a variety of non-nucleotide linkers and 13 additional modified nucleotides that have found the widest applications. These modifications include modified nucleotides that improve thermodynamic stability (2,6- diaminopurine, 2'-O-methyl RNA, 5-propynylpyrimidines), universal bases (5-nitroindole and 3-nitropyrole), modified oligonucleotides used in therapeutics (phosphorothioates, 2'-O-methyl RNA, 2'-fluoropyrimidines) and modified oligonucleotides with other applications (2-aminopurine, 2-thiothymine, 5-methylcytosine, 7- deazaguanine). This work complements the work done on other modified nucleotides whose thermodynamic parameters were measured during a previous project (under R44GM076745). The study involves a systematic series of measurements on over 500 modified duplexes along with unmodified controls. The newly determined parameters will be incorporated into a software database to enable simulation and in silico optimization of hybridization experiments in the presence of a wider coverage of modified oligonucleotides than previously possible. This will aid researchers in designing more robust assays and therapeutics. Modified oligonucleotides can be categorized either by the structure of the modified nucleotide or by its intended application. In this proposed research, a representative sample of the most commonly used modifications, both by structure and by function, is examined. Although many modifications are used in combination with one another, it is not proposed to study combinations of different modifications within the same oligonucleotide in this project as the number of possible combinations would make this task untenable. Some examples of modifications used in combination include: 2'-O-methyl-RNA containing terminal phosphorothioate, LNA-2'-O-methyl-RNA combinations, and phosphorothioate-LNA combinations. In addition to the measurements of thermodynamic parameters for oligonucleotides not previously measured, it will be necessary to restructure the software modeling and simulation program to allow for the inclusion of these nucleotides in both calculation and display modules of the program.

描述（由申请人提供）：本项目将开发一个大大扩展的修饰寡核苷酸热力学数据库，并将其纳入现有设计软件。这一快速SBIR提案的重点是确定热力学参数的修改，目前正在寻找广泛的应用。新的热力学数据库和软件将使世界各地的大量研究人员能够更容易地利用修饰的寡核苷酸开发高级应用，并将为软件产品增加大量的商业价值。在这个新的提议中，修饰的寡核苷酸的范围将大大增加，包括各种非核苷酸接头和13个额外的修饰核苷酸，这些核苷酸已经发现了最广泛的应用。这些修饰包括改进热力学稳定性的修饰核苷酸（2，6-二氨基嘌呤，2 '-O-甲基RNA，5-丙炔基嘧啶），通用碱基（5-硝基吲哚和3-硝基吡咯），用于治疗的修饰寡核苷酸（硫代磷酸酯、2 ′-O-甲基RNA、2 ′-氟嘧啶）和具有其它应用的修饰的寡核苷酸（2-氨基嘌呤、2-硫代胸腺嘧啶、5-甲基胞嘧啶、7-脱氮鸟嘌呤）。这项工作补充了对其他修饰核苷酸所做的工作，这些核苷酸的热力学参数是在以前的项目（根据R44 GM 076745）中测量的。该研究包括对500多个修饰的双链体沿着未修饰的对照进行系统的一系列测量。新确定的参数将被纳入软件数据库，以便在修饰寡核苷酸覆盖范围比以前更广的情况下对杂交实验进行模拟和计算机优化。这将有助于研究人员设计更强大的检测和治疗方法。修饰的寡核苷酸可以通过修饰的核苷酸的结构或通过其预期的应用来分类。在这项拟议的研究中，最常用的修改，无论是结构和功能的代表性样本，检查。尽管许多修饰彼此组合使用，但不建议在本项目中研究同一寡核苷酸内不同修饰的组合，因为可能的组合数量会使该任务难以完成。组合使用的修饰的一些实例包括：含有末端硫代磷酸酯的2 '-0-甲基-RNA、LNA-2'-0-甲基-RNA组合和硫代磷酸酯-LNA组合。除了先前未测量的寡核苷酸的热力学参数的测量之外，将有必要重构软件建模和模拟程序，以允许在程序的计算和显示模块中包含这些核苷酸。