RNA-targeted

Lee NS, Dohjima T, Bauer G, Li H, Li MJ, Ehsani A, Salvaterra P, Rossi J (2002) Expression of small interfering RNAs targeted against HIV-1 rev transcripts in human cells, Nat Biotechnol 20 500-505... 

Nishitsuji H, Kohara M, Kannagi M, Masuda T (2006) Effective suppression of human immunodeficiency virus type 1 through a combination of short- or long-hairpin RNAs targeting essential sequences for retroviral integration, J Virol 80 7658-7666 Novina CD, Murray ME, Dykxhoorn DM, Beresford PJ, Riess J, Lee SK, Collman RG, Lieberman J, Shankar P, Sharp PA (2002) siRNA-directed inhibition of HlV-1 infection, Nat Med 8 681-686... 

Zhou N, Fang J, Mukhtar M, Acheampong E, Pomerantz RJ (2004) Inhibition of HIV-1 fusion with small interfering RNAs targeting the chemokine coreceptor CXCR4. Gene Ther 11 1703-1712... 

Filikov AV, Mohan V, Vickers TA, Griffey RH, Cook PD, Abagyan RA, James TL. Identification of ligands for RNA targets via structure-based virtual screening HIV-1 TAR. / Comput Aided Mol Design 2000 14 593-610. 

Berkhout B, Silverman RH, Jeang KT (1989) Tat trans-activates the human immunodeficiency virus through a nascent RNA target. CeU 59(2) 273-282... 

Darnell, J. C., Mostovetsky, O., and Darnell, R. B. (2005). FMRP RNA targets Identification and validation. Genes Brain Behav. 4, 341-349. 

An amplification reaction that is used to amplify target RNA or denatured DNA is called the transcription-based amplification system (TAS). This technique involves using an enzyme called reverse transcriptase and a primer with sequence complementary to the sample target RNA molecule in order to synthesize a complementary DNA (cDNA) copy of the sample target RNA. After denaturation to separate the strands, another primer and additional reverse transcriptase are added to synthesize a double-stranded cDNA molecule. Since the first primer has also an RNA polymerase binding site, it can, in the presence of T7 RNA polymerase, amplify the double-stranded cDNA to produce 10 to 100 copies of RNA. The cycle of denaturation, synthesis of cDNA, and amplification to produce multiple RNA copies is repeated. With as few as four cycles, a 2- to 5-millionfold amplification of the original sample RNA target is possible. However, the time required to achieve a millionfold amplification is approximately 4 hours, which is the same amount of time required by PCR. The TAS requires, however, the addition of two enzymes at each cycle and, as such, can be cumbersome. 

Genes, env DNA sequences that form the coding region for the viral envelope (env) proteins in retroviruses. The env genes contain a cis-acting RNA target sequence for the rev protein (= gene products, rev), termed the rev-responsive element (RRE). [NIH]... 

Allain FFI, Gilbert DE, Bouvet P, Feigon J (2000b) Solution structure of the two N-terminal RNA-binding domains of nucleolin and NMR study of the interaction with its RNA target [In Process Citation], J Mol Biol 303 227-241... 

In situ hybridization (ISH) permits the detection and iocaiization of DNA and RNA in a cytoiogicai preparation affixed to a microscope siide. Such detection and iocaiization is made possibie by hybridization of cellular DNA and/or RNA targets with nucleic acid probes tagged with a signal generating system such as a fluorochrome or enzyme. 

The DNA or RNA target is localized within a cellular compartment (i.e., the DNA of chromosomes or mRNA in the cytoplasm) in a cytological preparation. 

Inadvertent digestion of RNA targets by cellular or contaminating RNase must be avoided. 

VOURLOUMIS, D., Takahashi, M., SiMONSEN, K., Ayida, B., Barluenga, S., WiNTERSA, G., and Hermann, T. Solid-phase synthesis of benzimidazole libraries biased for RNA targets. Tetrahedron Lett. 2003, 44, 2807-2811. 

J. A. Loo, V. Thanabal, H.-Y. Mei Studying noncovalent small molecule interactions with protein and RNA targets by mass spectrometry. Mass Spectrom. Biol. Med. 2000, 2000,... 

Fig. 10.7 ESI-FTICR mass spectra of three RNA targets at 2.5 pM each screened against 11 compounds at 25 pM each. The percent complexes and one-point values are shown for each ligand complex, (a) An example of a ligand that specifically binds target 2. (b) An example of a ligand that nonspecifically binds to all targets.

Fig. 10.8 SAR by MS applied to the A1061 construct (see text), (a) Structures of key motifs screened against the RNA target. Compound A is a D-amino acid. Compounds B1 and B2 are quinoxalin-2,3-diones. Compound AB is the rigid biaryl linked compound, (b) Binding affinity for the motifs when screened individually as well as binding affinity for motifs when screened in competition experiments are shown. Binding...

SAR by MS a ligand based technique for drug lead discovery against structured RNA targets. J Med Chem 2002, 45, 3816-3819. 

Similarly, the authors also examined the stabilization effect of dynamic modification of a U-NH -appended RNA aptamer that forms a kissing complex with the HIVl transactivation-responsive RNA element TAR. In this dynamic library, 2-chloro-6-methoxy-3-quinofinecarboxaldehyde (Rd) was incorporated in place of benzaldehyde (Ra). After equilibration of the U-NHj-substituted aptamer and aldehydes Rb-Rd in the presence of the TAR RNA target, it was found that the nalidixic aldehyde Rc-appended RNA was amplified 20%, and accompanied by an increased (Fig. 3.17). Interestingly, the nalidixic aldehyde Rc was selected in both DNA and RNA complexation experiments. 

In the DCC SELEX screen, aldehydes, the TAR RNA target, and a random library of 2 -amino RNAs were allowed to equilibrate. Next, the TAR RNA target and bound ligands were separated from the aptamer library. The selected 2 -amino RNAs that bound the TAR RNA target were then reverse transcribed into DNA and PCR amplified. These double-stranded... 

The TAR RNA target sequence, the 2 -amino RNA library and the appended aldehydes were subjected to the DCC SELEX system. The screen selected a 19-nt sequence with U-NH appended at position 9 and unmodified at positions 6 and 7 (Eig. 3.20). Importantly, it was shown that different sequences were identified when control selections were carried out in the absence of aldehydes, proving that the imino-conjugated nucleic acids are being selected. 

Figure 10.4. Schematic representation of the Tat protein and its functional regions, highlighting the basic RNA binding domain. The secondary structure of its RNA target, TAR, is shown. Critical residues for Tat binding within the recognition domain (highlighted) are shown in bold.

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