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  1. No Access


    A Novel Method to Quantify RNA–Protein Interactions In Situ Using FMTRIP and Proximity Ligation

    RNA binding proteins (RBP) and small RNAs regulate the editing, localization, stabilization, translation, and degradation of ribonucleic acids (RNAs) through their interactions with specific cis-acting element...

    C. Zurla, J. Jung, E. L. Blanchard, P. J. Santangelo Ph.D. in Enhancer RNAs (2017)

  2. No Access


    Bioinformatics Pipeline for Transcriptome Sequencing Analysis

    The development of High Throughput Sequencing (HTS) for RNA profiling (RNA-seq) has shed light on the diversity of transcriptomes. While RNA-seq is becoming a de facto standard for monitoring the population of...

    Sarah Djebali Ph.D., Valentin Wucher, Sylvain Foissac, Christophe Hitte in Enhancer RNAs (2017)

  3. No Access


    Clonetegration Using OSIP Plasmids: One-Step DNA Assembly and Site-Specific Genomic Integration in Bacteria

    Clonetegration is a method for site-specific insertion of DNA into prokaryotic chromosomes, based on bacteriophage integrases. The method combines DNA cloning/assembly and chromosomal integration into a single...

    Lun Cui, Keith E. Shearwin in Synthetic DNA (2017)

  4. No Access


    Cellular Fractionation and Isolation of Chromatin-Associated RNA

    In eukaryotic cells, the synthesis, processing, and functions of RNA molecules are confined to distinct subcellular compartments. Biochemical fractionation of cells prior to RNA isolation thus enables the anal...

    Thomas Conrad, Ulf Andersson Ørom Ph.D. in Enhancer RNAs (2017)

  5. No Access


    Targeted Gene Activation Using RNA-Guided Nucleases

    The discovery of the prokaryotic CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) system and its adaptation for targeted manipulation of DNA in diverse species has revol...

    Alexander Brown, Wendy S. Woods, Pablo Perez-Pinera M.D., Ph.D. in Enhancer RNAs (2017)

  6. No Access


    A Guide to Using STITCHER for Overlapping Assembly PCR Applications

    Overlapping PCR is commonly used in many molecular applications that include stitching PCR fragments together, generating fluorescent transcriptional and translational fusions, inserting mutations, making dele...

    Damien M. O’Halloran in Synthetic DNA (2017)

  7. No Access


    Gene Deletion by Synthesis in Yeast

    Targeted gene deletion is a useful tool for understanding the function of a gene and its protein product. We have developed an efficient and robust gene deletion approach in yeast that employs oligonucleotide-...

    Jinsil Kim, Dong-Uk Kim, Kwang-Lae Hoe in Synthetic DNA (2017)

  8. No Access


    Visualization of Enhancer-Derived Noncoding RNA

    Enhancers are principal regulators that allow spatiotemporal tissue-specific control of gene expression. While mounting evidence suggests that enhancer-derived long noncoding RNAs (long ncRNAs), including enha...

    Youtaro Shibayama, Stephanie Fanucchi, Musa M. Mhlanga Ph.D. in Enhancer RNAs (2017)

  9. No Access


    Shuffle Optimizer: A Program to Optimize DNA Shuffling for Protein Engineering

    DNA shuffling is a powerful tool to develop libraries of variants for protein engineering. Here, we present a protocol to use our freely available and easy-to-use computer program, Shuffle Optimizer. Shuffle O...

    John N. Milligan, Daniel J. Garry in Synthetic DNA (2017)

  10. No Access


    Simultaneous Removal of Multiple DNA Segments by Polymerase Chain Reactions

    Precise DNA manipulation is a key enabling technology for synthetic biology. Approaches based on restriction digestion are often limited by the presence of certain restriction enzyme recognition sites. Recent ...

    Vishnu Krishnamurthy, Kai Zhang Ph.D. in Synthetic DNA (2017)

  11. No Access


    Mapping Long Noncoding RNA Chromatin Occupancy Using Capture Hybridization Analysis of RNA Targets (CHART)

    Capture Hybridization Analysis of RNA Targets (CHART) has recently been developed to map the genome-wide binding profile of chromatin-associated RNAs. This protocol uses a small number of 22–28 nucleotide biot...

    Keith W. Vance Ph.D. in Enhancer RNAs (2017)

  12. No Access


    SpeedyGenes: Exploiting an Improved Gene Synthesis Method for the Efficient Production of Synthetic Protein Libraries for Directed Evolution

    Gene synthesis is a fundamental technology underpinning much research in the life sciences. In particular, synthetic biology and biotechnology utilize gene synthesis to assemble any desired DNA sequence, which...

    Andrew Currin, Neil Swainston, Philip J. Day, Douglas B. Kell in Synthetic DNA (2017)

  13. No Access


    Immobilized MutS-Mediated Error Removal of Microchip-Synthesized DNA

    Applications of microchip-synthesized oligonucleotides for de novo gene synthesis are limited primarily by their high error rates. The mismatch binding protein MutS, which can specifically recognize and bind t...

    Wen Wan, Dongmei Wang, Xiaolian Gao, Jiong Hong in Synthetic DNA (2017)

  14. No Access


    Deciphering Noncoding RNA and Chromatin Interactions: Multiplex Chromatin Interaction Analysis by Paired-End Tag Sequencing (mChIA-PET)

    Genomic DNA is dynamically associated with protein factors and folded to form chromatin fibers. The 3-dimensional (3D) configuration of the chromatin will enable the distal genetic elements to come into close ...

    Jocelyn Choy, Melissa J. Fullwood Ph.D. in Enhancer RNAs (2017)

  15. No Access


    Enzymatic Synthesis of Single-Stranded Clonal Pure Oligonucleotides

    Single-stranded oligonucleotides, or oligodeoxyribonucleotides (ODNs), are very important in several fields of science such as molecular biology, diagnostics, nanotechnology, and gene therapy. They are usually...

    Cosimo Ducani, Björn Högberg in Synthetic DNA (2017)

  16. No Access


    Global Run-On Sequencing (GRO-Seq)

    Transcription occurring at gene loci results in accumulation of mature RNA molecules (i.e., mRNAs) that can be easily assayed by RT-PCR or RNA sequencing. However, the steady-state level of RNA does not accura...

    Alessandro Gardini Ph.D. in Enhancer RNAs (2017)

  17. No Access


    PaperClip: A Simple Method for Flexible Multi-Part DNA Assembly

    Joining DNA sequences to create linear and circular constructs is a basic requirement in molecular biology. Here we describe PaperClip, a recently developed method, which enables assembly of multiple DNA seque...

    Maryia Trubitsyna, Chao-Kuo Liu, Alejandro Salinas, Alistair Elfick in Synthetic DNA (2017)

  18. No Access


    Evaluating the Stability of mRNAs and Noncoding RNAs

    Changes in RNA stability have an important impact in the gene expression regulation. Different methods based on the transcription blockage with RNA polymerase inhibitors or metabolic labeling of newly synthesi...

    Ana Carolina Ayupe, Eduardo M. Reis Ph.D. in Enhancer RNAs (2017)

  19. No Access


    In Silico Promoter Recognition from deepCAGE Data

    The accurate identification of transcription start regions corresponding to the promoters of known genes, novel coding, and noncoding transcripts, as well as enhancer elements, is a crucial step towards a comp...

    Xinyi Yang, Annalisa Marsico Ph.D. in Enhancer RNAs (2017)

  20. No Access


    The Polymerase Step Reaction (PSR) Method for Gene and Library Synthesis

    Current gene synthesis methods often incorporate a PCR-amplifying step in order to yield sufficient final product that is detectable and resolvable from multiple off-products. This amplification step can cause...

    Brian S. DeDecker in Synthetic DNA (2017)

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