ABSTRACT
The properties of gapmer antisense oligonucleotide (ASO) flanked by deoxyribonucleic guanidine (DNG) were investigated for the potential application in antisense technology. DNG is a unique nucleotide analog which has a positively charged internucleotide guanidinium linkage instead of negatively charged phosphodiester backbone linkage. We prepared a gapmer ASO containing DNG units at both wings of the sequence and compared its properties with 2',4'-BNA/LNA gapmer ASOs with phosphorothioate (PS) backbone. Although DNG gapmer showed no stabilizing effect on the duplex formation with target RNA, the DNG modification was found to be tolerant to exonuclease digestion. Furthermore, DNG gapmer can induce RNase H-mediated cleavage of target RNA molecule, a requisite property for the antisense strategy. Therefore, the DNG gapmer developed in this study could be an interesting and useful candidate for the development of potent ASOs.
Subject(s)
Guanidines/chemistry , Oligonucleotides, Antisense/chemistry , Oligonucleotides, Antisense/genetics , Base Sequence , Chemistry Techniques, Synthetic , DNA/chemistry , DNA/genetics , Humans , Molecular Structure , Oligonucleotides, Antisense/chemical synthesis , RNA/chemistry , RNA/genetics , RNA Cleavage , Thermodynamics , Transition TemperatureABSTRACT
Oligonucleotide-based gene silencing, using molecules such as antisense oligonucleotides (ASOs), small interfering RNA, and aptamers, is widely studied. Another approach uses DNA/RNA heteroduplex oligonucleotides (HDOs). Here, we developed an antisense double-stranded DNA oligonucleotide (ADO) by modification of the complementary RNA in an HDO to generate DNA for increasing resistance to nucleases. Naked BCR-ABL-targeting ADO was significantly more potent than siRNA at reducing BCR-ABL chimeric mRNA expression in chronic myeloid leukemia (CML) cell lines. Further, naked BCR-ABL-targeting ADO suppressed BCR-ABL protein levels in a dose-dependent manner, inhibited CML cell proliferation, and augmented the inhibitory effects of imatinib mesylate. In conclusion, ADO technology is an attractive method for therapeutic application.
Subject(s)
DNA , Fusion Proteins, bcr-abl/genetics , Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy , Oligonucleotides, Antisense/pharmacology , Antineoplastic Agents/pharmacology , Cell Line, Tumor , Cell Proliferation/drug effects , Gene Silencing , Humans , Imatinib Mesylate/pharmacology , Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics , Protein Kinase Inhibitors/pharmacology , RNA, Messenger/geneticsABSTRACT
Peptide nucleic acids (PNAs) are structural mimics of nucleic acids that form stable hybrids with DNA and RNA. Due to these characteristics, PNAs are widely used as biochemical tools, for example, in antisense/antigene therapy. In this study, we have synthesized PNAs incorporating 2-amino-6-vinylpurine (AVP) for the covalent targeting of single-stranded DNA and RNA, and evaluated their reactivities for these targets. PNA containing AVP at the N-terminal position showed a high reactivity to uracil in RNA and thymine in DNA at the complementary site with AVP. In addition, the crosslinking reactions to pre-miR122 with PNA containing AVP increased the inhibition effect for the Dicer processing of pre-miR122 in vitro.
Subject(s)
Cross-Linking Reagents/pharmacology , DNA, Single-Stranded/antagonists & inhibitors , Peptide Nucleic Acids/pharmacology , RNA/antagonists & inhibitors , Cross-Linking Reagents/chemistry , Dose-Response Relationship, Drug , Molecular Structure , Peptide Nucleic Acids/chemical synthesis , Peptide Nucleic Acids/chemistry , Structure-Activity RelationshipABSTRACT
Peptide nucleic acids (PNAs) are structural mimics of nucleic acids that form stable hybrids with DNA and RNA. In addition, PNAs can invade double-stranded DNA. Due to these characteristics, PNAs are widely used as biochemical tools, for example, in antisense/antigene therapy. Interstrand crosslink formation in nucleic acids is one of the strategies for preparing a stable duplex by covalent bond formation. In this study, we have synthesized PNAs incorporating 4-amino-6-oxo-2-vinylpyrimidine (AOVP) as a crosslinking agent and evaluated their reactivities for targeting DNA and RNA.
Subject(s)
Cross-Linking Reagents/chemistry , Peptide Nucleic Acids/chemical synthesis , Pyrimidines/chemistry , DNA/chemistry , Peptide Nucleic Acids/chemistry , RNA/chemistryABSTRACT
A novel FRET couple of fluorescein is disclosed, and it was readily constructed by conjugating an amino-BODIPY dye, a new FRET donor, with fluorescein isocyanate. Its potential was demonstrated by a fluorescence sensing system for cysteine, which was prepared by introducing acryloyl groups to the fluorescein moiety. The FRET probe exhibited promising ratiometric response to cysteine with high selectivity and sensitivity in a buffer solution containing acetonitrile at a physiological pH of 7.4, but showed slow reactivity. This slow response was solved by addition of a surfactant, thus allowing ratiometric imaging and determination of the endogenous level of cysteine in cells in HEPES buffer, by confocal fluorescence microscopy. Imaging experiments toward various cells suggested that such aryl acrylate type probes are vulnerable to the ubiquitous esterase activity. For the selected C6 cell line, in which the esterase activity was minimal, the ratiometric quantification of cysteine level was demonstrated. The FRET probe was also applied to determine the level of cysteine in human blood plasma.
