Homopurine-homopyrimidine sequences that flank certain actively transcribed genes are hypersensitive to single strand-specific nucleases such as S1. This has raised the possibility an unusual structure exists in these regions might be involved recognition or regulation. Several of sequences, including d(C-T) n ⋅d(A-G) , known undergo a transition plasmids underwound state is nucleases; this occurs under conditions moderately acid p H and negative supercoiling. Chemical probes were used...

RNA interference offers enormous potential to develop therapeutic agents for a variety of diseases. To assess the stability siRNAs under conditions relevant clinical use with particular emphasis on topical delivery considerations, study three different unmodified was performed. The results indicate that neither repeated freeze/thaw cycles, extended incubations (over 1 year at 21 degrees C), nor shorter high temperatures (up 95 C) have any effect siRNA integrity as measured by nondenaturing...

A robust screening assay employing solid phase extraction (SPE) followed by a novel aptamer-based procedure is presented for the rapid detection and semiquantitation of triphenylmethane dye, Malachite Green (MG) its primary metabolite Leucomalachite (LMG) in fish tissue. To authors' knowledge, this first reported use an RNA aptamer development diagnostic chemical residues food. The based found to be highly specific MG; but has negligible affinity LMG metabolite. However, because lipophilic...

Samples of DNA which contain adducts a new psoralen derivative, but no cross-links, have been prepared by irradiating mixtures and the derivative with single, 15-nanosecond pulses laser light. Succeeding introduce cross-links. The ability to rapidly selectively create monoadducts corss-links may allow use psoralens as probes dynamic processes in living cells.

Small hairpin RNAs (shRNAs) are widely used in RNAi studies and typically consist of a stem 19–29 base pairs (bp), loop at least 4 nucleotides (nt), dinucleotide overhang the 3′ end. Compared with shRNAs 21–29 bp stems, we have found that 19-bp or shorter stems (sshRNAs) possess some unique structure–activity features depend on whether antisense strand is positioned 5′ to (L- R-type sshRNAs, respectively). L sshRNAs can IC 50 s very low picomolar range, nominal sizes 1 nt were as active...

The ability to accurately quantify all the microRNAs (miRNAs) in a sample is important for understanding miRNA biology and development of new biomarkers therapeutic targets. We develop method preparing sequencing libraries, RealSeq®-AC, that involves ligating miRNAs with single adapter circularizing ligation products. When compared other methods, RealSeq®-AC provides greatly reduced bias allows identification largest variety biological samples. This also robust quantification present samples...

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe chemistry of cyclic vinyl ethers. 6. Total synthesis polyether ionophore antibiotics the calcimycin (A-23187) classRobert K. Boeckman Jr., Andre B. Charette, Theodros Asberom, and Brian H. JohnstonCite this: J. Am. Chem. Soc. 1991, 113, 14, 5337–5353Publication Date (Print):July 1, 1991Publication History Published online1 May 2002Published inissue 1 July...

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA convergent general synthetic protocol for construction of spirocyclic ketal ionophores: an application to the total synthesis (-)-A-23187 (calcimycin)Robert K. Boeckman Jr., Andre B. Charette, Theodros Asberom, and Brian H. JohnstonCite this: J. Am. Chem. Soc. 1987, 109, 24, 7553–7555Publication Date (Print):November 1, 1987Publication History Published online1 May 2002Published inissue 1 November...

Treatment and prevention of hepatitis C virus (HCV) infections remain a major challenge for controlling this worldwide health problem; existing therapies are only partially effective no vaccine is currently available. RNA interference offers the potential novel therapeutic approach treating HCV infections. Toward end, we evaluated small hairpin interfering RNAs (shRNAs) targeting conserved internal ribosome entry site (IRES) element genome their ability to control gene expression in human...

Small hairpin RNAs (shRNAs) with 19-base-pair, or shorter, stems (short shRNAs [sshRNAs]) have been found to constitute a class whose mechanism of action appears be distinct from that small interfering (siRNAs) longer shRNAs. These sshRNAs can as active canonical siRNAs Their activity is affected by whether the antisense strand positioned 5′ 3′ loop (L R sshRNAs, respectively). Dicer seems not involved in processing although target gene suppression these hairpins through Ago2-mediated mRNA...

Discussion regarding the regulatory status of genome-edited crops has focused on precision editing and doubts feasibility analytical monitoring compliant with existing GMO regulations. Effective detection methods are important, both for enforcement traceability in case biosafety, environmental or socio-economic impacts. Here, we approach analysis question first time laboratory report successful development a quantitative PCR method commercialized crop, canola single base pair edit conferring...

Hepatitis C virus (HCV) is a leading cause of liver cirrhosis and hepatocellular carcinoma worldwide. Currently available treatment options are limited efficacy, there an urgent need for development alternative therapies. RNA interference (RNAi) natural mechanism by which small interfering (siRNA) or short hairpin (shRNA) can mediate degradation target molecule in sequence-specific manner. In this study, we screened vitro-transcribed 25-bp shRNAs targeting the internal ribosome entry site...

Recently, we reported for the first time development of pH-triggered nanoparticles functional delivery small interfering RNA (siRNA) to liver treatment hepatitis B virus infections in vivo. Here, report on systematic formulation and biophysical studies three different nanoparticle formulations looking ways improve capabilities our previous system. We demonstrate how pH-triggered, PEGylated siRNA stable with respect aggregation 80% serum can still release payload at pH 5.5 within 30 min. This...

Small hairpin RNAs (shRNAs) having duplex lengths of 25–29 bp are normally processed by Dicer into short interfering (siRNAs) before incorporation the RNA-induced silencing complex (RISC). However, shRNAs ≤19 [short (sshRNAs)] too for to excise their loops, raising questions about mechanism action. sshRNAs designated as L-type or R-type according whether loop is positioned 3′ 5′ guide sequence, respectively. Using nucleotide modifications that inhibit RNA cleavage, we show R- but not...

In diabetes-associated chronic wounds, the normal response to hypoxia is impaired and many cellular processes involved in wound healing are hindered. Central hypoxia-inducible factor-1α (HIF-1α), which activates multiple factors that enhance by promoting motility proliferation, new vessel formation, re-epithelialization. Prolyl hydroxylase domain-containing protein 2 (PHD2) regulates HIF-1α activity targeting it for degradation under normoxia. also upregulates microRNA miR-210, turn proteins...

Objective: To evaluate the efficacy of layer-by-layer (LbL) formulated therapeutic RNAs that inhibit PHD2 and microRNA-210 (miR-210), to improve impaired diabetic wound healing. Approach: We employed neuroischemic rabbit model Diabetes was induced in rabbits with alloxan, neuroischemia by ligating central neurovascular bundle each ear. Four 6-mm full-thickness wounds were creating on A technique conformally coat dressings a chemically modified antisense RNA (antimiR) against miR-210 an...

A significant limitation to the practical application of triplex DNA is its requirement for oligopurine tracts in target sequences. The repertoire triplex-forming sequences can potentially be expanded adjacent blocks purines and pyrimidines by allowing third strand pair with on alternate strands, while maintaining required polarities combining two major classes base triplets, Py · PuPy Pu PuPy. formation this fashion requires no unusual bases or backbone linkages strand. This approach has...

MicroRNAs (miRNAs) are important regulators of gene expression and have great potential as biomarkers, prognostic indicators, therapeutic targets. Determining the patterns these molecules is essential for elucidating their biogenesis, regulation, relation to disease, response therapy. Although PCR-based assays commonly used profiling miRNAs, small size, sequence heterogeneity, (in some cases) end modifications miRNAs constrain performance existing PCR methods. Here we introduce miR-ID, a...

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIntramolecular triple-helix formation at (PunPyn).cntdot.(PunPyn) tracts: recognition of alternate strands via Pu.cntdot.PuPy and Py.cntdot.PuPy base tripletsSumedha D. Jayasena Brian H. JohnstonCite this: Biochemistry 1992, 31, 2, 320–327Publication Date (Print):January 21, 1992Publication History Published online1 May 2002Published inissue 21 January...

Methods most commonly used for producing small interfering RNAs (siRNAs) or short hairpin (shRNAs) are chemical synthesis and intracellular expression from engineered vectors. For shRNAs, is very costly construction of vectors laborious. Synthesis by phage RNA polymerases their natural promoters results in a 5´-terminal triphosphate that can trigger an interferon (IFN) response. Moreover, due to the requirement 5´- GPuPuPu sequences transcription initiation, shRNA transcripts may have extra...