Stabilization of triple helical structures is extremely important for carrying out their biological functions. Nucleic acid triple helices may be formed with DNA or RNA strands. In contrast to many studies in DNA, little has been reported concerning the recognition of the RNA triplex by transition-metal complexes. In this article, [Ru(phen)(2)(mdpz)](2+) (Ru1) is the first metal complex able to enhance the stability of the RNA triplex Poly(U)·Poly(A)*Poly(U) and serve as a prominent molecular "light switch" for the RNA triplex.
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http://dx.doi.org/10.1021/ic300093h | DOI Listing |
Anal Chem
January 2025
Synthetic Molecule Analytical Chemistry, Genentech Inc., South San Francisco, California 94080, United States.
Accurate characterization of therapeutic RNA, including purity and identity, is critical in drug discovery and development. Here, we utilize denaturing and non-denaturing chromatography for the analysis of ∼25 kDa divalent small interfering RNA (di-siRNA), which comprises a complex 2:1 triplex structure. Ion pair reversed-phase (IPRP) liquid chromatography (LC) experiments with UV absorbance and mass spectrometry (MS) showcase a single denaturing LC method for identity confirmation, impurity profiling, and sequencing with automated MS data interpretation.
View Article and Find Full Text PDFAnal Sci
January 2025
Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-Ku, Sendai, 980-8578, Japan.
The diverse functional roles of RNA within cells have led to a growing interest in developing RNA-binding fluorescent probes to investigate RNA functions. In particular, the probes for double-stranded RNA (dsRNA) structures are of significant value given the importance of the secondary and tertiary RNA structures on their biologic functions. This review highlights our recent efforts on the development of triplex-forming peptide nucleic acid (TFP)-based probes for fluorescence sensing of dsRNA structures.
View Article and Find Full Text PDFNAR Mol Med
October 2024
Department of Biology, Tufts University, 200 Boston Ave., Medford, MA 02155, USA.
H-DNA is an intramolecular DNA triplex formed by homopurine/homopyrimidine mirror repeats. Since its discovery, the field has advanced from characterizing the structure to discovering its existence and role . H-DNA interacts with cellular machinery in unique ways, stalling DNA and RNA polymerases and causing genome instability.
View Article and Find Full Text PDFACS Chem Biol
January 2025
Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States.
Noncanonical base pairs play an important role in enabling the structural and functional complexity of RNA. Molecular recognition of such motifs is challenging because of their diversity, significant deviation from the Watson-Crick structures, and dynamic behavior, resulting in alternative conformations of similar stability. Triplex-forming peptide nucleic acids (PNAs) have emerged as excellent ligands for the recognition of Watson-Crick base-paired double helical RNA.
View Article and Find Full Text PDFBiochemistry
January 2025
CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India.
There are surprisingly few RNA intramolecular triple helices known in the human transcriptome. The structure has been most well-studied as a stability-element at the 3' end of lncRNAs such as and , but the intrigue remains whether it is indeed as rare as it is understood to be or just waiting for a closer look from a new vantage point. TRIPinRNA, our Python-based in silico platform, allows for a comprehensive sequence-pattern search for potential triplex formation in the human transcriptome─noncoding as well as coding.
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