Abstract: Methods are provided for reducing the number of aldehyde adducts and/or crosslinks from fixed biomolecules. In some cases, subject methods include contacting a sample having aldehyde fixed biomolecules (e.g., a biological sample such as a formalin fixed paraffin embedded (FFPE) tissue sample) with an adduct reversal agent in an amount and for a period of time sufficient to reduce the number of aldehyde fixation related adducts and/or crosslinks in the sample. In some cases, the adduct reversal agent is a compound that includes an aromatic ring and at least one of: an amine group and a proton-donating group. In some cases, the adduct reversal agent is a compound selected from the compounds of Table 1. Compositions and kits for practicing the subject methods are also provided.

Abstract: Methods for obtaining structural data from RNA in a sample, and RNA probes for performing the same, are provided. Methods of reversibly modifying RNA is a sample, in vitro or in vivo, and reversible probes for performing the same, are provided. The RNA probes may be SHAPE probes that include aryl or heteroaryl acyl imidazoles. The RNA probes may be reversible probes that include an aryl or heteroaryl ring substituted with a hydroxyl-reactive group and an azido-containing group. Also provided are methods of comparing in vitro and in vivo RNA structural data. Also provided are methods of diagnosing a cellular proliferative disease condition, e.g., by probing HOTAIR RNA. Aspects of the invention further include compositions, e.g., probes and kits, etc., that find use in methods of the invention.

Abstract: Probes comprising one or more selectively cleavable ?-azidoether moieties are provided; and linkers comprising the one or more selectively cleavable ?-azidoether moieties. The ?-azidoether moiety will undergo a Staudinger reaction with a suitable reducing agent, resulting in cleavage. The probes find use in a variety of detection assays, e.g. specific polynucleotide binding assays, polypeptide binding assays, etc. The cleavable linkers are suitable for synthetic reactions, e.g. to prepare probes of the invention; in the synthesis of cleavable peptide conjugates; and the like.

Abstract: Nucleoside analogs are provided; and fluorescent sensors comprising the nucleoside analogs. The sensors comprise multiple chromophores built on a DNA backbone, in which all the natural DNA bases are replaced by excimeric or exciplex-forming fluorophores, ligands, quenchers and spacers in thousands of combinations. The sensors find use in the detection and identification of target analytes by fluorescence, e.g., detection of metal ions, neutral organic compounds and anions. The sensors find use in the detection and identification of molecular species in the vapor or gaseous phase, or the liquid phase. The sensors find use in qualitative and quantitative screening and detection methods.

Abstract: Methods for obtaining structural data from RNA in a sample, and RNA probes for performing the same, are provided. Methods of reversibly modifying RNA is a sample, in vitro or in vivo, and reversible probes for performing the same, are provided. The RNA probes may be SHAPE probes that include aryl or heteroaryl acyl imidazoles. The RNA probes may be reversible probes that include an aryl or heteroaryl ring substituted with a hydroxyl-reactive group and an azido-containing group. Also provided are methods of comparing in vitro and in vivo RNA structural data. Also provided are methods of diagnosing a cellular proliferative disease condition, e.g., by probing HOTAIR RNA. Aspects of the invention further include compositions, e.g., probes and kits, etc., that find use in methods of the invention.

Abstract: Nucleoside analogs are provided; and fluorescent sensors comprising the nucleoside analogs. The sensors comprise multiple chromophores built on a DNA backbone, in which all the natural DNA bases are replaced by excimeric or exciplex-forming fluorophores, ligands, quenchers and spacers in thousands of combinations. The sensors find use in the detection and identification of target analytes by fluorescence, e.g., detection of metal ions, neutral organic compounds and anions. The sensors find use in the detection and identification of molecular species in the vapor or gaseous phase, or the liquid phase. The sensors find use in qualitative and quantitative screening and detection methods.

Abstract: Compositions and systems are provided for the high efficiency quenching small water-soluble oligomers, or oligofluors, of from about 1-10 kd in size, where the oligofluors comprise multiple excimeric or exciplex forming fluorophores arranged on a scaffold, which are efficiently quenched by a quencher entity linked to the oligomer through a cleavable moiety. Fluorophores of interest include, without limitation, aromatic fluorophores such as pyrenes, e.g. benzopyrene, perylene, pyrene, etc. In some embodiments the oligofluor/quencher combination provides for a Stern-Vollmer constant (KSV) of greater than about 106 M?1, and may be greater than about 107 M?1, greater than about 108 M?1, or more. In some embodiments of the invention, the scaffold is a phosphodiester/glycoside backbone, e.g. an analog of a polynucleotide.

Abstract: Probes comprising one or more selectively cleavable ?-azidoether moieties are provided; and linkers comprising the one or more selectively cleavable ?-azidoether moieties. The ?-azidoether moiety will undergo a Staudinger reaction with a suitable reducing agent, resulting in cleavage. The probes find use in a variety of detection assays, e.g. specific polynucleotide binding assays, polypeptide binding assays, etc. The cleavable linkers are suitable for synthetic reactions, e.g. to prepare probes of the invention; in the synthesis of cleavable peptide conjugates; and the like.

Abstract: A universal linker structure is provided, in which a functional group and activating leaving group are placed on a tether, allowing the placement of an electrophile at the end of any nucleic acid sequence. The electrophile on the tether can react with a second nucleic acid carrying a nucleophile when the two nucleic acids are hybridized near one another, resulting in release of the leaving group, and creation of a functional change. The linker can be designed to destabilize the ligation product without slowing the rate of reaction. This lowers product inhibition, and the target DNA or RNA can become a catalyst for isothermally generating multiple signals for detection. This enhanced signal is demonstrated in solution experiments and in solid supported assays. The universal linkers of the present invention are simple and inexpensive to prepare, and can be appended to any polynucleotide in automated steps on a standard DNA synthesizer.

Abstract: Compositions and systems are provided for the high efficiency quenching small water-soluble oligomers, or oligofluors, of from about 1-10 kd in size, where the oligofluors comprise multiple excimeric or exciplex forming fluorophores arranged on a scaffold, which are efficiently quenched by a quencher entity linked to the oligomer through a cleavable moiety. Fluorophores of interest include, without limitation, aromatic fluorophores such as pyrenes, e.g. benzopyrene, perylene, pyrene, etc. In some embodiments the oligofluor/quencher combination provides for a Stern-Vollmer constant (KSV) of greater than about 106 M?1, and may be greater than about 107 M?1, greater than about 108 M?1, or more. In some embodiments of the invention, the scaffold is a phosphodiester/glycoside backbone, e.g. an analog of a polynucleotide.

Abstract: Nonpolar thymidine analogs are provided comprising a dihalogenated or trihalogenated base of the structure: where R1 is a sugar moiety; R2 is H or CH3; an imaging moiety or a cytotoxic moiety and X1 and X2 are independently selected from I, Cl, Br, and F, with the proviso that not more than one F will be present at these positions.