Browsing by Subject "Nucleic Acid Conformation"
Now showing items 1-15 of 15
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A discrete chromatin loop in the mouse Tcra-Tcrd locus shapes the TCRδ and TCRα repertoires.
(Nat Immunol, 2015-10)The locus encoding the T cell antigen receptor (TCR) α-chain and δ-chain (Tcra-Tcrd) undergoes recombination of its variable-diversity-joining (V(D)J) segments in CD4(-)CD8(-) double-negative thymocytes and CD4(+)CD8(+) ... -
A Novel Genetic Variant in Long Non-coding RNA Gene NEXN-AS1 is Associated with Risk of Lung Cancer.
(Scientific reports, 2016-10-07)Lung cancer etiology is multifactorial, and growing evidence has indicated that long non-coding RNAs (lncRNAs) are important players in lung carcinogenesis. We performed a large-scale meta-analysis of 690,564 SNPs in 15,531 ... -
Computational Methods for RNA Structure Validation and Improvement.
(Methods Enzymol, 2015)With increasing recognition of the roles RNA molecules and RNA/protein complexes play in an unexpected variety of biological processes, understanding of RNA structure-function relationships is of high current importance. ... -
Cyanobacterial ribosomal RNA genes with multiple, endonuclease-encoding group I introns.
(BMC evolutionary biology, 2007-09-08)Group I introns are one of the four major classes of introns as defined by their distinct splicing mechanisms. Because they catalyze their own removal from precursor transcripts, group I introns are referred to as autocatalytic ... -
Development of universal antidotes to control aptamer activity.
(Nat Med, 2009-10)With an ever increasing number of people taking numerous medications, the need to safely administer drugs and limit unintended side effects has never been greater. Antidote control remains the most direct means to counteract ... -
Identification and utilization of arbitrary correlations in models of recombination signal sequences.
(Genome Biol, 2002)BACKGROUND: A significant challenge in bioinformatics is to develop methods for detecting and modeling patterns in variable DNA sequence sites, such as protein-binding sites in regulatory DNA. Current approaches sometimes ... -
Infrared Spectroscopic Observation of a G-C+ Hoogsteen Base Pair in the DNA:TATA-Box Binding Protein Complex Under Solution Conditions.
(Angewandte Chemie (International ed. in English), 2019-08)Hoogsteen DNA base pairs (bps) are an alternative base pairing to canonical Watson-Crick bps and are thought to play important biochemical roles. Hoogsteen bps have been reported in a handful of X-ray structures of protein-DNA ... -
Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A.
(Nucleic acids research, 2017-05)In the canonical DNA double helix, Watson-Crick (WC) base pairs (bps) exist in dynamic equilibrium with sparsely populated (∼0.02-0.4%) and short-lived (lifetimes ∼0.2-2.5 ms) Hoogsteen (HG) bps. To gain insights into transient ... -
Mitochondrial mutations in adenoid cystic carcinoma of the salivary glands.
(PLoS One, 2009-12-30)BACKGROUND: The MitoChip v2.0 resequencing array is an array-based technique allowing for accurate and complete sequencing of the mitochondrial genome. No studies have investigated mitochondrial mutation in salivary gland ... -
New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey.
(Nucleic Acids Res, 2015-04-20)Hoogsteen (HG) base pairs (bps) provide an alternative pairing geometry to Watson-Crick (WC) bps and can play unique functional roles in duplex DNA. Here, we use structural features unique to HG bps (syn purine base, HG ... -
New tools provide a second look at HDV ribozyme structure, dynamics and cleavage.
(Nucleic Acids Res, 2014-11-10)The hepatitis delta virus (HDV) ribozyme is a self-cleaving RNA enzyme essential for processing viral transcripts during rolling circle viral replication. The first crystal structure of the cleaved ribozyme was solved in ... -
Quantification of DNA cleavage specificity in Hi-C experiments.
(Nucleic Acids Res, 2016-01-08)Hi-C experiments produce large numbers of DNA sequence read pairs that are typically analyzed to deduce genomewide interactions between arbitrary loci. A key step in these experiments is the cleavage of cross-linked chromatin ... -
Sensitive and precise quantification of insulin-like mRNA expression in Caenorhabditis elegans.
(PLoS One, 2011-03-22)Insulin-like signaling regulates developmental arrest, stress resistance and lifespan in the nematode Caenorhabditis elegans. However, the genome encodes 40 insulin-like peptides, and the regulation and function of individual ... -
Surface-enhanced Raman scattering plasmonic enhancement using DNA origami-based complex metallic nanostructures.
(Nano letters, 2014-01)DNA origami is a novel self-assembly technique allowing one to form various two-dimensional shapes and position matter with nanometer accuracy. We use DNA origami templates to engineer surface-enhanced Raman scattering ... -
Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits.
(Genome Biol, 2013-08-23)WaRSwap is a randomization algorithm that for the first time provides a practical network motif discovery method for large multi-layer networks, for example those that include transcription factors, microRNAs, and non-regulatory ...
