Increasing the efficiency of SAGE adaptor ligation by directed ligation chemistry

Nucleic Acids Research
Austin P SoCharles A Haynes

Abstract

The ability of Serial Analysis of Gene Expression (SAGE) to provide a quantitative picture of global gene expression relies not only on the depth and accuracy of sequencing into the SAGE library, but also on the efficiency of each step required to generate the SAGE library from the starting mRNA material. The first critical step is the ligation of adaptors containing a Type IIS recognition sequence to the anchored 3' end cDNA population that permits the release of short sequence tags (SSTs) from defined sites within the 3' end of each transcript. Using an in vitro transcript as a template, we observed that only a small fraction of anchored 3' end cDNA are successfully ligated with added SAGE adaptors under typical reaction conditions currently used in the SAGE protocol. Although the introduction of approximately 500-fold molar excess of adaptor or the inclusion of 15% (w/v) PEG-8000 increased the yield of the adaptor-modified product, complete conversion to the desired adaptor:cDNA hetero-ligation product is not achieved. An alternative method of ligation, termed as directed ligation, is described which exploits a favourable mass-action condition created by the presence of NlaIII during ligation in combination with a novel SAGE...Continue Reading

References

Apr 1, 1991·Gene·W SzybalskiA J Podhajska
Mar 1, 1982·European Journal of Biochemistry·F M PohlA Karst
Oct 20, 1995·Science·V E VelculescuK W Kinzler
Jan 1, 1993·Annual Review of Biophysics and Biomolecular Structure·S B Zimmerman, A P Minton
Sep 30, 1994·Journal of Molecular Biology·D Louie, P Serwer
Apr 1, 1996·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·M D Adams
Jan 24, 1997·Cell·V E VelculescuK W Kinzler
Jan 23, 1999·Nature Genetics·R J LipshutzD J Lockhart
Aug 14, 1999·Nucleic Acids Research·A van den BergS Poppema
Dec 28, 1999·Proceedings of the National Academy of Sciences of the United States of America·B VirlonJ M Elalouf
Feb 19, 2000·Current Opinion in Biotechnology·C B Epstein, R A Butow
Aug 25, 2000·Genome Research·J StollbergC D Boyd
Sep 14, 2000·Proceedings of the National Academy of Sciences of the United States of America·J M AngelastroL A Greene
Oct 26, 2000·Trends in Genetics : TIG·V E VelculescuK W Kinzler
May 31, 2001·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·D FaulhammerL F Landweber
Jun 19, 2001·Nucleic Acids Research·E H MarguliesJ W Innis
Oct 9, 2001·Bioinformatics·J Colinge, G Feger
May 1, 2002·Nature Biotechnology·Saurabh SahaVictor E Velculescu
May 7, 2002·Nature Genetics·Martin J LercherLaurence D Hurst
Sep 6, 2002·Proceedings of the National Academy of Sciences of the United States of America·Jianjun ChenSan Ming Wang
Jan 10, 2003·Nucleic Acids Research·Richard J RobertsDana Macelis
Feb 8, 2003·Trends in Biotechnology·Kenneth R Boheler, Michael D Stern
Mar 4, 2003·Bioinformatics·Michael D SternKenneth R Boheler
Jul 25, 2003·Biochimica Et Biophysica Acta·Damien Hall, Allen P Minton

❮ Previous
Next ❯

Citations

Jul 8, 2009·Proceedings of the National Academy of Sciences of the United States of America·Benjamin StauchGisbert Schneider
Feb 26, 2009·Briefings in Bioinformatics·Nurcan TuncbagRuth Nussinov
Apr 22, 2008·Nucleic Acids Research·Efrat MashiachHaim J Wolfson
May 7, 2010·Nucleic Acids Research·Gary MacindoeDavid W Ritchie
May 13, 2010·Nucleic Acids Research·Efrat MashiachHaim J Wolfson
Jan 11, 2011·Protein Engineering, Design & Selection : PEDS·Jennifer C PaiJennifer A Maynard
Apr 18, 2009·BMC Genomics·Xing FuPhilipp Khaitovich
Nov 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Holger SondermannJohn Kuriyan
Feb 12, 2014·Proceedings of the National Academy of Sciences of the United States of America·Melody G CampbellMichael A Marletta
Nov 4, 2015·Brain : a Journal of Neurology·Rajnish KumarTaher Darreh-Shori
Dec 15, 2015·Molecular Biology and Evolution·Brantley D ColemanMikel Garcia-Marcos
Sep 12, 2015·Human Molecular Genetics·Moon-Yong ChaInhee Mook-Jung
Oct 13, 2006·Journal of Neurochemistry·Ira SuroliaSharmistha Sinha
Jul 24, 2015·Molecular Biology of the Cell·Kelly WatsonPatrick Brennwald
Sep 16, 2009·Comparative and Functional Genomics·Xiqiang LiuXiaofeng Zhou
Oct 22, 2014·Proceedings of the National Academy of Sciences of the United States of America·Hei-Man ChowJie Zhang
Jul 6, 2016·Nucleic Acids Research·Gururaj ShivangeRoy Anindya
Jan 25, 2019·The Journal of Biological Chemistry·Antony KamJames P Tam
Jan 24, 2019·The Journal of Biological Chemistry·Khue G NguyenDavid A Zaharoff
Feb 10, 2007·The Journal of Biological Chemistry·Onnik AgbulutCatherine Coirault
Jun 26, 2009·The Journal of Biological Chemistry·Maria A ArgiriadiDavid W Borhani
Jun 15, 2010·The Journal of Biological Chemistry·Tamara A DaileyHarry A Dailey
Sep 27, 2019·The Journal of Biological Chemistry·Zeenat FarooqMohammad Altaf
Nov 17, 2019·Proceedings of the National Academy of Sciences of the United States of America·Javier Delgado BlancoLuis Serrano
May 16, 2020·The Journal of Biological Chemistry·Jacob H ArtzPaul W King
Aug 15, 2014·The Journal of Biological Chemistry·Chun-Han HoAndrew H-J Wang
Nov 9, 2014·The Journal of Biological Chemistry·Alex C TuckerJorge C Escalante-Semerena
Mar 18, 2015·The Journal of Immunology : Official Journal of the American Association of Immunologists·Ivelisse MartinAna M Espino
Oct 6, 2007·The Journal of Biological Chemistry·Menachem J GunzburgGeoffrey J Howlett
Aug 26, 2015·The Journal of Biological Chemistry·Jason KenealeyS Patricia Becerra
May 12, 2018·The Journal of Biological Chemistry·Qingyu TangGuozhou Xu
May 17, 2012·The Journal of Biological Chemistry·Chong Wai LiewJulien Lescar

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.