Evidence map›Paper›PMID 33087570›Full record

ArticleProceedings of the National Academy of Sciences of the United States of America2020

Liquid drop of DNA libraries reveals total genome information.

Stanislav S Terekhov, Igor E Eliseev, Leyla A Ovchinnikova, Marsel R Kabilov, Andrey D Prjibelski, Alexey E Tupikin, Ivan V Smirnov, Alexey A Belogurov, Konstantin V Severinov, Yakov A Lomakin and 2 more

Abstract read
In one paragraph

Article in Proceedings of the National Academy of Sciences of the United States of America, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.

0numbers the graph read from it
0cells of the map it votes in
12citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

12 citing papers in PubMed.

  1. Review
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  7. Review
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  10. Modern Trends in Natural Antibiotic Discovery.Life (Basel, Switzerland) · 2023
    Review
  11. Review
  12. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

12 authors.

Stanislav S TerekhovShemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia.ORCID 0000-0003-2220-0452
Igor E EliseevNanobiotechnology Laboratory, Alferov University, St. Petersburg 194021, Russia.ORCID 0000-0002-3344-2513
Leyla A OvchinnikovaShemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia.ORCID 0000-0002-3086-0728
Marsel R KabilovInstitute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.ORCID 0000-0003-2777-0833
Andrey D PrjibelskiCenter for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 199004, Russia.ORCID 0000-0003-2816-4608
Alexey E TupikinInstitute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.ORCID 0000-0002-8194-0322
Ivan V SmirnovShemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia.ORCID 0000-0002-0384-6568
Alexey A BelogurovShemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia.ORCID 0000-0002-2033-9621
Konstantin V SeverinovInstitute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia.ORCID 0000-0001-9706-450X
Yakov A LomakinShemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; yasha.l@bk.ru sidney.altman@yale.edu gabibov@mx.ibch.ru.ORCID 0000-0002-3514-5395
Sidney AltmanDepartment of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520; yasha.l@bk.ru sidney.altman@yale.edu gabibov@mx.ibch.ru.ORCID 0000-0001-7287-0337
Alexander G GabibovShemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; yasha.l@bk.ru sidney.altman@yale.edu gabibov@mx.ibch.ru.ORCID 0000-0001-8665-3288

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Conventional "bulk" PCR often yields inefficient and nonuniform amplification of complex templates in DNA libraries, introducing unwanted biases. Amplification of single DNA molecules encapsulated in a myriad of emulsion droplets (emulsion PCR, ePCR) allows the mitigation of this problem. Different ePCR regimes were experimentally analyzed to identify the most robust techniques for enhanced amplification of DNA libraries. A phenomenological mathematical model that forms an essential basis for optimal use of ePCR for library amplification was developed. A detailed description by high-throughput sequencing of amplified DNA-encoded libraries highlights the principal advantages of ePCR over bulk PCR. ePCR outperforms PCR, reduces gross DNA errors, and provides a more uniform distribution of the amplified sequences. The quasi single-molecule amplification achieved via ePCR represents the fundamental requirement in case of complex DNA templates being prone to diversity degeneration and provides a way to preserve the quality of DNA libraries.

Indexed as

DNADNA PrimersEmulsionsGene LibraryGenomeHigh-Throughput Nucleotide SequencingHumansModels, TheoreticalNucleic Acid Amplification TechniquesPolymerase Chain ReactionTemplates, GeneticDNADNA PrimersEmulsionsdiversity degenerationemulsion PCR modelingquasi single-molecule amplificationtemplate mispairinguniform distribution of amplicons

Identifiers

PMID33087570
PMCPMC7959537

What OpenQuestion holds

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LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.