Many RNAs cause disease, however RNA is rarely exploited as a small molecule drug target. Disclosed herein are methods for identifying privileged RNA motif-small molecule interactions to enable the rational design of compounds that modulate RNA biology starting from only sequence. A massive, library-versus-library screen was completed that probed over 50 million binding events between RNA motifs and small molecules. The resulting data provide a rich encyclopedia of small molecule-RNA recognition patterns, defining chemotypes and RNA motifs that confer selective, avid binding. The resulting interaction maps were mined against the entire viral genome of hepatitis C virus (HCV). A small molecule was identified that avidly bound RNA motifs present in the HCV3′ untranslated region and inhibited viral replication while having no effect on host cells. Collectively, this investigation represents the first whole genome pattern recognition between small molecules and RNA folds.

Many RNAs cause disease, however RNA is rarely exploited as a small molecule drug target. Disclosed herein are methods for identifying privileged RNA motif-small molecule interactions to enable the rational design of compounds that modulate RNA biology starting from only sequence. A massive, library-versus-library screen was completed that probed over 50 million binding events between RNA motifs and small molecules. The resulting data provide a rich encyclopedia of small molecule-RNA recognition patterns, defining chemotypes and RNA motifs that confer selective, avid binding. The resulting interaction maps were mined against the entire viral genome of hepatitis C virus (HCV). A small molecule was identified that avidly bound RNA motifs present in the HCV3′ untranslated region and inhibited viral replication while having no effect on host cells. Collectively, this investigation represents the first whole genome pattern recognition between small molecules and RNA folds.

Disclosed is a single-stranded nucleic acid for real-time detection of the genetic variation of a single target gene and a detection method using the same, and more particularly a real-time detection method for the genetic variation of a single target gene and a kit for the same, where the real-time detection method uses a single-stranded nucleic acid having a structure of X-Y-Z and comprising a nucleotide sequence that can form a complementary bond to all or part of the nucleotide sequence of a single target gene containing a genetic variation such as single nucleotide polymorphism (SNP), point mutation, or miRNA isoform. The novel real-time detection method for detecting the genetic variation of a single target gene using a single-stranded nucleic acid that can be cleaved only by a cleavage reagent is advantageous in the precise measurement over the conventional method for detecting a genetic variation using a probe.

Disclosed is a single-stranded nucleic acid for real-time detection of the genetic variation of a single target gene and a detection method using the same, and more particularly a real-time detection method for the genetic variation of a single target gene and a kit for the same, where the real-time detection method uses a single-stranded nucleic acid having a structure of X-Y-Z and comprising a nucleotide sequence that can form a complementary bond to all or part of the nucleotide sequence of a single target gene containing a genetic variation such as single nucleotide polymorphism (SNP), point mutation, or miRNA isoform. The novel real-time detection method for detecting the genetic variation of a single target gene using a single-stranded nucleic acid that can be cleaved only by a cleavage reagent is advantageous in the precise measurement over the conventional method for detecting a genetic variation using a probe.

The present invention relates to an inner primer which includes, in the 3′-end direction, a blocker for inhibiting gene amplification and an RNA sequence that is complementary to a template target nucleic acid sequence and is cleaved by a ribonuclease; a primer composition and a kit including the same; and a method for detecting a target nucleic acid sequence by using the same. The present invention can increase amplification efficiency and detection specificity by inhibiting non-specific binding during an amplification process.

The present invention relates to an inner primer which includes, in the 3′-end direction, a blocker for inhibiting gene amplification and an RNA sequence that is complementary to a template target nucleic acid sequence and is cleaved by a ribonuclease; a primer composition and a kit including the same; and a method for detecting a target nucleic acid sequence by using the same. The present invention can increase amplification efficiency and detection specificity by inhibiting non-specific binding during an amplification process.

The present disclosure is directed to a polynucleotide capable of signaling under preselected conditions. For example, the present disclosure relates to a method of reconfiguring a nucleic acid or polynucleotide, including: contacting a deoxyribonucleic acid (DNA) nanoswitch and nucleic acid to form a DNA nanoswitch-nucleic acid complex having a first conformation, wherein the first conformation is characterized as locked; contacting the DNA nanoswitch-nucleic acid complex with a biological specimen to form a mixture, wherein when the nucleic acid is ribonucleic acid (RNA) and the biological specimen includes one or more ribonucleases, the first conformation changes to a second conformation characterized as open; processing the mixture under conditions sufficient to separate the first conformation, and when present, the second conformation; and reacting the first conformation, and when present, the second conformation with an indicator under conditions sufficient to form a signal.

The present disclosure is directed to a polynucleotide capable of signaling under preselected conditions. For example, the present disclosure relates to a method of reconfiguring a nucleic acid or polynucleotide, including: contacting a deoxyribonucleic acid (DNA) nanoswitch and nucleic acid to form a DNA nanoswitch-nucleic acid complex having a first conformation, wherein the first conformation is characterized as locked; contacting the DNA nanoswitch-nucleic acid complex with a biological specimen to form a mixture, wherein when the nucleic acid is ribonucleic acid (RNA) and the biological specimen includes one or more ribonucleases, the first conformation changes to a second conformation characterized as open; processing the mixture under conditions sufficient to separate the first conformation, and when present, the second conformation; and reacting the first conformation, and when present, the second conformation with an indicator under conditions sufficient to form a signal.

The present disclosure relates to methods for detecting unique genetic signatures derived from markers such as, for example, mutations, somatic or germ-line, in nucleic acids obtained from biological samples. The sensitivity of the methods provides for detection of mutations associated with a disease, e.g., cancer mutations, or with inherited disease, e.g., an autosomal recessive disease, in a noninvasive manner at ultra-low proportions of sequences carrying mutations to sequences carrying normal, e.g., non-cancer sequences, or a reference sequence, e.g., a human reference genome.

The present disclosure relates to methods for detecting unique genetic signatures derived from markers such as, for example, mutations, somatic or germ-line, in nucleic acids obtained from biological samples. The sensitivity of the methods provides for detection of mutations associated with a disease, e.g., cancer mutations, or with inherited disease, e.g., an autosomal recessive disease, in a noninvasive manner at ultra-low proportions of sequences carrying mutations to sequences carrying normal, e.g., non-cancer sequences, or a reference sequence, e.g., a human reference genome.