Design and synthesis of RNA miniduplexes via a synthetic linker approach.
نویسندگان
چکیده
Double-stranded oligodeoxyribonucleotides or single-stranded oligoribonucleotides with specific secondary structure have been proposed as potential antagonists to target nucleic acid-binding proteins (the sense approach). A major limitation of this strategy is that these derivatives are generally considered to be too large for pharmaceutical applications. We have developed a synthetic linker approach whereby nucleic acid duplexes of a much smaller size (miniduplexes) can be generated directly from a standard oligonucleotide synthesis. In this approach, four synthetic linkers (derivatized respectively from 1,9-nonanediol, triethylene glycol, 1,3-propanediol, and hexaethylene glycol) of different length and hydrophobicity were designed and incorporated into a model RNA molecule based on the TAR stem-loop structure of HIV-1. Their thermal stabilities were evaluated by measuring denaturation profiles (Tm measurements). These linker-derivatized RNA molecules were then assessed for their ability to bind to either a full-length protein (HIV-1 Tat protein) or a short peptide (Tat-derived peptide) through RNA mobility shift assays. Results from this study indicate that such modified miniduplex structures retain full binding activity relative to that of the wild-type sequence (Kd values), while Tm values were increased by 24-31 degrees C compared to an open duplex of the same length. This system provides a new direction in the use of nucleic acid miniduplexes as a novel class of oligonucleotide analogues for both fundamental research and possible therapeutic applications.
منابع مشابه
Rapid SARS-CoV-2 RT-LAMP assay setup using gene construct design approach
Background and Objective: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still an ongoing challenge in health system worldwide. Molecular detection methods including reverse transcription loop-mediated isothermal amplification (RT-LAMP) can help cutting off the transmission chain of the virus. In this study, prompt setting up of the RT-LAMP assays were investigated using ge...
متن کاملGeneral approach for introduction of various chemical labels in specific RNA locations based on insertion of amino linkers.
Introduction of reporter groups at designed RNA sites is a widely accepted approach to gain information about the molecular environment of RNAs in their complexes with other biopolymers formed during various cellular processes. A general approach to obtain RNAs bearing diverse reporter groups at designed locations is based on site-specific insertion of groups containing primary aliphatic amine ...
متن کاملResponse surface strategy in the synthesis of Fe3O4 nanoparticles
In the present study, Fe3O4 super paramagnetic nanoparticles were synthesized via co-precipitation of Fe3+ and Fe2+ chloride salts in the presence of ammonia Solution. The product was characterized by Fourier Transform Infrared spectroscopy (FT-IR), Transmission Electron Microscopy (TEM), and zeta–potential particle size distributing methods. The synt...
متن کاملRNA synthesis using a universal, base-stable allyl linker.
The application of a universal allyl linker, 9-O-(4,4'-dimethoxytrityl)-10-undecenoic acid, to the solid phase synthesis of RNA molecules is described. Use of this linker simplifies significantly the isolation and purification steps in RNA synthesis. The linker is universal in that it does not contain a nucleoside. The 3'terminal nucleoside is instead attached to the support in the first coupli...
متن کاملResponse surface strategy in the synthesis of Fe3O4 nanoparticles
In the present study, Fe3O4 super paramagnetic nanoparticles were synthesized via co-precipitation of Fe3+ and Fe2+ chloride salts in the presence of ammonia Solution. The product was characterized by Fourier Transform Infrared spectroscopy (FT-IR), Transmission Electron Microscopy (TEM), and zeta–potential particle size distributing methods. The synt...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید
ثبت ناماگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید
ورودعنوان ژورنال:
- Nucleic acids research
دوره 21 11 شماره
صفحات -
تاریخ انتشار 1993