PCR-based techniques articles within Nature Communications

Featured

• Article
  24 August 2023 | Open Access

  A qPCR technology for direct quantification of methylation in untreated DNA

  Analysis of DNA methylation usually requires a chemical or an enzymatic pretreatment step. Here, the authors report a PCR-based technology for the detection of DNA methylation in untreated DNA, and present analytical and clinical results from methylation analysis of the MGMT promoter.

  • Kamilla Kolding Bendixen
  • , Maria Mindegaard
  •  & Rasmus Koefoed Petersen

• Article
  01 March 2023 | Open Access

  Sequence terminus dependent PCR for site-specific mutation and modification detection

  Rapid and facile detection of specific nucleic acid modifications could have numerous applications. Here the authors present Specific Terminal Mediated Polymerase Chain Reaction (STEM-PCR) as a generic and accessible approach, and demonstrate proof-of-principle cancer biomarker detection.

  • Gaolian Xu
  • , Hao Yang
  •  & Hongchen Gu

• Article
  23 October 2022 | Open Access

  Engineered helicase replaces thermocycler in DNA amplification while retaining desired PCR characteristics

  PCR is an essential method for the amplification and manipulation of nucleic acids, but the requirement for a thermocycler limits access. Here, authors engineer a helicase to replace the heating step of PCR with enzymatic unwinding, allowing the isothermal amplification of fragments up to 6 kb.

  • Momčilo Gavrilov
  • , Joshua Y. C. Yang
  •  & Taekjip Ha

• Article
  21 July 2022 | Open Access

  Detection of neutralizing antibodies against multiple SARS-CoV-2 strains in dried blood spots using cell-free PCR

  Neutralizing antibodies are critical for conferring immunity against SARS-CoV-2. Here, Dahn et al. report a PCR assay termed SONIA (Split-Oligonucleotide Neighboring Inhibition Assay) for measuring neutralizing antibodies against multiple SARS-CoV-2 strains in fingerprick dried blood spot samples.

  • Kenneth Danh
  • , Donna Grace Karp
  •  & Cheng-ting Tsai

• Article
  29 September 2021 | Open Access

  Unraveling the functional role of DNA demethylation at specific promoters by targeted steric blockage of DNA methyltransferase with CRISPR/dCas9

  The causal relationship between DNA demethylation and gene expression regulation has not yet been fully resolved. Here the authors develop a nuclease-dead Cas9 (dCas9) and gRNA site-specific targeting approach to physically block DNA methylation at specific promoters to cause DNA demethylation in cells and tackle this question.

  • Daniel M. Sapozhnikov
  •  & Moshe Szyf

• Article
  25 May 2021 | Open Access

  Multiplexed detection of SARS-CoV-2 and other respiratory infections in high throughput by SARSeq

  Massively parallel but cost-effective testing is essential to monitor the spread of pathogenic agents. Here the authors present SARSseq, which uses a dual indexing strategy in a multiplexed RT-PCR reaction to diagnose SARS-CoV-2 at scale.

  • Ramesh Yelagandula
  • , Aleksandr Bykov
  •  & Ulrich Elling

• Article
  20 November 2020 | Open Access

  An enhanced isothermal amplification assay for viral detection

  Current state-of-the-art diagnostics for infectious diseases are sensitive but require extensive equipment. Here the authors develop an enhanced recombinase polymerase amplification reaction for SARS-CoV-2 that allows for inexpensive and rapid testing with minimal equipment.

  • Jason Qian
  • , Sarah A. Boswell
  •  & Michael Springer

• Article
  02 September 2020 | Open Access

  Analysis of chromatin organization and gene expression in T cells identifies functional genes for rheumatoid arthritis

  Although genome-wide association studies have identified genetic variation contributing to disease risk, assigning causal genes is challenging. Here, the authors generate ATAC-seq, Hi-C, Capture Hi-C and RNA-seq data in stimulated CD4+ T cells to identify functional enhancers and demonstrate interactions of expression quantitative trait loci with target genes in rheumatoid arthritis.

  • Jing Yang
  • , Amanda McGovern
  •  & Stephen Eyre

• Article
  04 October 2019 | Open Access

  Dendronized fluorosurfactant for highly stable water-in-fluorinated oil emulsions with minimal inter-droplet transfer of small molecules

  Microdroplets are used as chemical and biological reactors; however, stability and inter-droplet transfer are major issues. Here, the authors report on the development of dendritic glycerol-based surfactants for the creation of stable microdroplets and demonstrate application for PCR, minimal emulsion, and cell encapsulation.

  • Mohammad Suman Chowdhury
  • , Wenshan Zheng
  •  & Rainer Haag

• Article
  06 November 2015 | Open Access

  Identification of DNA lesions using a third base pair for amplification and nanopore sequencing

  Genomic DNA lesions exist in low levels and cannot be amplified by standard PCR. Here, Riedlet al. report a method to amplify damaged DNA sites by replacing them via DNA repair with unnatural base pairs, which are subsequently identified by Sanger sequencing or α-hemolysin nanopore sequencing.

  • Jan Riedl
  • , Yun Ding
  •  & Cynthia J. Burrows

• Article | 25 October 2013

  Using synthetic templates to design an unbiased multiplex PCR assay

  Immunosequencing enables cost-effective sequencing of repertoires of immune cells, but it often suffers from amplification biases when attempting cell quantification. Here, the authors present a powerful multiplex PCR assay that allows for quantitative and unbiased analysis of frequency of different T cell receptors.

  • Christopher S. Carlson
  • , Ryan O. Emerson
  •  & Harlan Robins