Abstract:
:Understanding the interactions between small interfering RNAs (siRNAs) and the RNA-induced silencing complex (RISC), the key protein complex of RNA interference (RNAi), is of great importance to the development of siRNAs with improved biological and potentially therapeutic function. Although various chemically modified siRNAs have been reported, relatively few studies with modified nucleobases exist. Here we describe the synthesis and hybridization properties of siRNAs bearing size-expanded RNA (xRNA) nucleobases and their use as a novel and systematic set of steric probes in RNAi. xRNA nucleobases are expanded by 2.4 Å using benzo-homologation and retain canonical Watson-Crick base-pairing groups. Our data show that the modified siRNA duplexes display small changes in melting temperature (+1.4 to -5.0 °C); substitutions near the center are somewhat destabilizing to the RNA duplex, while substitutions near the ends are stabilizing. RNAi studies in a dual-reporter luciferase assay in HeLa cells revealed that xRNA nucleobases in the antisense strand reduce activity at some central positions near the seed region but are generally well tolerated near the ends. Most importantly, we observed that xRNA substitutions near the 3'-end increased activity over that of wild-type siRNAs. The data are analyzed in terms of site-dependent steric effects in RISC. Circular dichroism experiments show that single xRNA substitutions do not significantly distort the native A-form helical structure of the siRNA duplex, and serum stability studies demonstrated that xRNA substitutions protect siRNAs against nuclease degradation.
journal_name
ACS Chem Bioljournal_title
ACS chemical biologyauthors
Hernández AR,Peterson LW,Kool ETdoi
10.1021/cb300174csubject
Has Abstractpub_date
2012-08-17 00:00:00pages
1454-61issue
8eissn
1554-8929issn
1554-8937journal_volume
7pub_type
杂志文章abstract::The emergence of multidrug-resistant Staphylococcus aureus strains has become a serious clinical problem. Iron is absolutely required for the bacterial growth, virulence associated with colonization, and survival from the host immune system. The FeoB protein is a major iron permease in bacterial ferrous iron transport...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/acschembio.0c00842
更新日期:2021-01-15 00:00:00
abstract::The arabinosyltransferases responsible for the biosynthesis of the arabinan domains of two abundant heteropolysaccharides of the cell envelope of all mycobacterial species, lipoarabinomannan and arabinogalactan, are validated drug targets. Using a cell envelope preparation from Mycobacterium smegmatis as the enzyme so...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/acschembio.6b00093
更新日期:2016-06-17 00:00:00
abstract::Combinatorial libraries built with severely restricted chemical diversity have yielded highly functional synthetic binding proteins. Structural analyses of these minimalist binding sites have revealed the dominant role of large tyrosine residues for mediating molecular contacts and of small serine/glycine residues for...
journal_title:ACS chemical biology
pub_type: 杂志文章,评审
doi:10.1021/cb800314v
更新日期:2009-05-15 00:00:00
abstract::Synthetic biology is the realization of systems with desired behavior using biological materials. A recent addition to the field is a bipartite consortium of the bacterium Escherichia coli in which each species harbors complementary gene circuits that actuate only when both are present above a critical density. This b...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/cb700256w
更新日期:2008-01-18 00:00:00
abstract::The display and analysis of proteins expressed on biological surfaces has become an attractive tool for the study of molecular interactions in enzymology, protein engineering, and high-throughput screening. Among the growing number of established display systems, retroviruses offer a unique and fully mammalian platfor...
journal_title:ACS chemical biology
pub_type: 杂志文章,评审
doi:10.1021/cb100285n
更新日期:2011-01-21 00:00:00
abstract::Rediscovery of known compounds and time consumed in identification, especially high molecular weight compounds with complex structure, have let down interest in drug discovery. In this study, whole-genome analysis of microbe and Global Natural Products Social (GNPS) molecular networking helped in initial understanding...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/acschembio.0c00026
更新日期:2020-03-20 00:00:00
abstract::The plant hormone auxin is a master regulator of plant growth and development. By regulating rates of cell division and elongation and triggering specific patterning events, indole 3-acetic acid (IAA) regulates almost every aspect of plant development. The perception of auxin involves the formation of a ternary comple...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/cb200404c
更新日期:2012-03-16 00:00:00
abstract::Beta-peptides (beta-amino acid oligomers) that mimic the amphiphilic, helical, and cationic properties of natural antimicrobial peptides have previously been shown to display antifungal activity against planktonic Candida albicans cells. Beta-peptides offer several advantages over conventional peptides composed of alp...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/cb900093r
更新日期:2009-07-17 00:00:00
abstract::Tumor heterogeneity has hampered the development of novel effective therapeutic options for aggressive cancers, including the deadly primary adult brain tumor glioblastoma (GBM). Intratumoral heterogeneity is partially attributed to the tumor initiating cell (TIC) subset that contains highly tumorigenic, stem-like cel...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/acschembio.8b00251
更新日期:2018-08-17 00:00:00
abstract::Dihydrofolate reductase (DHFR) is a potential drug target for Trypanosoma brucei, a human parasite, which is the causative agent for African sleeping sickness. No drug is available against this target, since none of the classical antifolates such as pyrimethamine (PYR), cycloguanil, or trimethoprim are effective as se...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/cb200124r
更新日期:2011-09-16 00:00:00
abstract::Agonists and antagonists of the nicotinic acetylcholine receptor (nAChR) are used to treat nicotine addiction, neuromuscular disorders, and neurological diseases. In designing small molecule therapeutics with the nAChR as a target, it is useful to identify chemical parameters that correlate with ability to activate th...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/cb800189y
更新日期:2008-11-21 00:00:00
abstract::Terpene synthases (TS) are classified into two broad types, Class I and II, based on the chemical strategy for initial carbocation formation and motif sequences of the catalytic site. We have recently identified a new class of enzymes, Class IB, showing the acceptability of long (C20-C35) prenyl-diphosphates as substr...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/acschembio.0c00145
更新日期:2020-06-19 00:00:00
abstract::Endocytosis is a key process in cellular delivery of macromolecules by molecular transporters, although the mechanism of internalization remains unclear. Here, we probe the cellular uptake of streptavidin using biotinylated guanidinoneomycin (biotinGNeo), a low molecular weight guanidinium-rich molecular transporter. ...
journal_title:ACS chemical biology
pub_type: 信件
doi:10.1021/cb400172h
更新日期:2013-07-19 00:00:00
abstract::Synthetic compounds for controlling or creating human immunity have the potential to revolutionize disease treatment. Motivated by challenges in this arena, we report herein a strategy to target metastatic cancer cells for immune-mediated destruction by targeting the urokinase-type plasminogen activator receptor (uPAR...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/cb200374e
更新日期:2012-02-17 00:00:00
abstract::Numerous cytochrome P450 (CYP) 2B6 substrates including drugs and environmental chemicals are halogenated. To assess the role of halogen-π bonds in substrate selectivity and orientation in the active site, structures of four CYP2B6 monoterpenoid complexes were solved by X-ray crystallography. Bornyl bromide exhibited ...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/acschembio.7b00056
更新日期:2017-05-19 00:00:00
abstract::N-Acetylneuraminic acid lyase (NAL) is a Class I aldolase that catalyzes the reversible condensation of pyruvate with N-acetyl-d-mannosamine (ManNAc) to yield the sialic acid N-acetylneuraminic acid (Neu5Ac). Aldolases are finding increasing use as biocatalysts for the stereospecific synthesis of complex molecules. In...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/cb500067z
更新日期:2014-04-18 00:00:00
abstract::In a process called quorum sensing, bacteria produce and secrete certain signaling compounds (called autoinducers) that bind to receptors on other bacteria and activate transcription of certain genes. A clever genetic selection yields a new quorum-sensing transcriptional regulator that marches to the beat of a differe...
journal_title:ACS chemical biology
pub_type: 杂志文章,评审
doi:10.1021/cb6003417
更新日期:2006-08-22 00:00:00
abstract::Ammonia lyases catalyze the formation of α,β-unsaturated bonds by the elimination of ammonia from their substrates. This conceptually straightforward reaction has been the emphasis of many studies, with the main focus on the catalytic mechanism of these enzymes and/or the use of these enzymes as catalysts for the synt...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/cb3002792
更新日期:2012-10-19 00:00:00
abstract::Endothelial progenitor cells (EPCs) and endothelial cells (ECs) play a vital role in endothelialization and vascularization for tissue regeneration. Various EPC/EC targeting biomolecules have been investigated to improve tissue regeneration with limited success often due to their limited functional specificity and str...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/acschembio.7b00118
更新日期:2017-04-21 00:00:00
abstract::Cysteine residues on proteins play key roles in catalysis and regulation. These functional cysteines serve as active sites for nucleophilic and redox catalysis, sites of allosteric regulation, and metal-binding ligands on proteins from diverse classes including proteases, kinases, metabolic enzymes, and transcription ...
journal_title:ACS chemical biology
pub_type: 杂志文章,评审
doi:10.1021/cb3005269
更新日期:2013-02-15 00:00:00
abstract::Current therapeutic interventions for both heart disease and heart failure are largely insufficient and associated with undesired side effects. Biomedical research has emphasized the role of sarcomeric protein function for the normal performance and energy efficiency of the heart, suggesting that directly targeting th...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/acschembio.0c00908
更新日期:2021-01-15 00:00:00
abstract::Light-activated protein domains provide a convenient, modular, and genetically encodable sensor for optogenetics and optobiology. Although these domains have now been deployed in numerous systems, the precise mechanism of photoactivation and the accompanying structural dynamics that modulate output domain activity rem...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/acschembio.0c00543
更新日期:2020-10-16 00:00:00
abstract::Phosphoinositides are critical cell-signal mediators present on the plasma membrane. The dynamic change of phosphoinositide concentrations on the membrane including clustering and declustering mediates signal transduction. The importance of phosphoinositides is scored by the fact that they participate in almost all ce...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/acschembio.6b00067
更新日期:2016-07-15 00:00:00
abstract::Large-scale quantification of protein O-linked β- N-acetylglucosamine (O-GlcNAc) modification in a site-specific manner remains a key challenge in studying O-GlcNAc biology. Herein, we developed an isotope-tagged cleavable linker (isoTCL) strategy, which enabled isotopic labeling of O-GlcNAc through bioorthogonal conj...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/acschembio.8b00414
更新日期:2018-08-17 00:00:00
abstract::Membrane curvature and lipid composition regulates important biological processes within a cell. Currently, several proteins have been reported to sense and/or induce membrane curvatures, e.g., Synaptotagmin-1 and Amphiphysin. However, the large protein scaffold of these curvature sensors limits their applications in ...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/cb300429e
更新日期:2013-01-18 00:00:00
abstract::Phosphorylation-dependent protein-protein interaction has rarely been targeted in medicinal chemistry. Thymoquinone, a naturally occurring antitumor agent, disrupts prephosphorylated substrate recognition by the polo-box domain of polo-like kinase 1, a key mitotic regulator responsible for various carcinogenesis when ...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/cb3004379
更新日期:2013-02-15 00:00:00
abstract::Photo- or optoacoustics (OA) imaging is increasingly being used as a non-invasive imaging method that can simultaneously reveal structure and function in deep tissue. However, the most frequent transgenic OA labels are current fluorescent proteins that are not optimized for OA imaging. Thus, they lack OA signal streng...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/acschembio.9b00299
更新日期:2019-09-20 00:00:00
abstract::The epidermal growth-factor-like domain A (EGF-A) of the low-density lipoprotein (LDL) receptor is a promising lead for therapeutic inhibition of proprotein convertase subtilisin/kexin type 9 (PCSK9). However, the clinical potential of EGF-A is limited by its suboptimal affinity for PCSK9. Here, we use phage display t...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/acschembio.0c00991
更新日期:2021-01-29 00:00:00
abstract::As part of the central core domain of the ribosome, helix 69 of 23S rRNA participates in an important intersubunit bridge and contacts several protein translation factors. Helix 69 is believed to play key roles in protein synthesis. Even though high-resolution crystal structures of the ribosome exist, the solution dyn...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/cb200497q
更新日期:2012-05-18 00:00:00
abstract::Several C-β-d-glucopyranosyl azoles have recently been uncovered as among the most potent glycogen phosphorylase (GP) catalytic site inhibitors discovered to date. Toward further exploring their translational potential, ex vivo experiments have been performed for their effectiveness in reduction of glycogenolysis in h...
journal_title:ACS chemical biology
pub_type: 杂志文章
doi:10.1021/acschembio.9b00172
更新日期:2019-07-19 00:00:00