Literature DB >> 19897384

A role for the MS analysis of nucleic acids in the post-genomics age.

Daniele Fabris1.   

Abstract

The advances of mass spectrometry in the analysis of nucleic acids have tracked very closely the exciting developments of instrumentation and ancillary technologies, which have taken place over the years. However, their diffusion in the broader life sciences community has been and will be linked to the ever evolving focus of biomedical research and its changing demands. Before the completion of the Human Genome Project, great emphasis was placed on sequencing technologies that could help accomplish this project of exceptional scale. After the publication of the human genome, the emphasis switched toward techniques dedicated to the exploration of sequences not coding for actual protein products, which amount to the vast majority of transcribed elements. The broad range of capabilities offered by mass spectrometry is rapidly advancing this platform to the forefront of the technologies employed for the structure-function investigation of these noncoding elements. Increasing focus on the characterization of functional assemblies and their specific interactions has prompted a re-evaluation of what has been traditionally construed as nucleic acid analysis by mass spectrometry. Inspired by the accelerating expansion of the broader field of nucleic acid research, new applications to fundamental biological studies and drug discovery will help redefine the evolving role of MS-analysis of nucleic acids in the post-genomics age. 2010. Published by Elsevier Inc.

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Year:  2009        PMID: 19897384     DOI: 10.1016/j.jasms.2009.09.006

Source DB:  PubMed          Journal:  J Am Soc Mass Spectrom        ISSN: 1044-0305            Impact factor:   3.109


  160 in total

1.  Measuring dissociation constants of RNA and aminoglycoside antibiotics by electrospray ionization mass spectrometry.

Authors:  K A Sannes-Lowery; R H Griffey; S A Hofstadler
Journal:  Anal Biochem       Date:  2000-05-01       Impact factor: 3.365

Review 2.  Analysis of protein-nucleic acid interactions by photochemical cross-linking and mass spectrometry.

Authors:  Hanno Steen; Ole Nørregaard Jensen
Journal:  Mass Spectrom Rev       Date:  2002 May-Jun       Impact factor: 10.946

Review 3.  DNA sequencing by mass spectrometry.

Authors:  K K Murray
Journal:  J Mass Spectrom       Date:  1996-11       Impact factor: 1.982

4.  Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression.

Authors:  Wade Winkler; Ali Nahvi; Ronald R Breaker
Journal:  Nature       Date:  2002-10-16       Impact factor: 49.962

Review 5.  Indirect mass spectrometric methods for characterizing and sequencing oligonucleotides.

Authors:  P A Limbach
Journal:  Mass Spectrom Rev       Date:  1996       Impact factor: 10.946

6.  Mechanism of alkylation of nucleic acids by nitrosodimethylamine.

Authors:  W Lijinsky; J Loo; A E Ross
Journal:  Nature       Date:  1968-06-22       Impact factor: 49.962

7.  Studies of non-covalent interactions of actinomycin D with single-stranded oligodeoxynucleotides by ion spray mass spectrometry and tandem mass spectrometry.

Authors:  Y L Hsieh; Y T Li; J D Henion; B Ganem
Journal:  Biol Mass Spectrom       Date:  1994-05

8.  Ultrafast sequencing of oligodeoxyribonucleotides by FAB-mass spectrometry.

Authors:  L Grotjahn; R Frank; H Blöcker
Journal:  Nucleic Acids Res       Date:  1982-08-11       Impact factor: 16.971

9.  Interpretation of oligonucleotide mass spectra for determination of sequence using electrospray ionization and tandem mass spectrometry.

Authors:  J Ni; C Pomerantz; J Rozenski; Y Zhang; J A McCloskey
Journal:  Anal Chem       Date:  1996-07-01       Impact factor: 6.986

10.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:  Ewan Birney; John A Stamatoyannopoulos; Anindya Dutta; Roderic Guigó; Thomas R Gingeras; Elliott H Margulies; Zhiping Weng; Michael Snyder; Emmanouil T Dermitzakis; Robert E Thurman; Michael S Kuehn; Christopher M Taylor; Shane Neph; Christoph M Koch; Saurabh Asthana; Ankit Malhotra; Ivan Adzhubei; Jason A Greenbaum; Robert M Andrews; Paul Flicek; Patrick J Boyle; Hua Cao; Nigel P Carter; Gayle K Clelland; Sean Davis; Nathan Day; Pawandeep Dhami; Shane C Dillon; Michael O Dorschner; Heike Fiegler; Paul G Giresi; Jeff Goldy; Michael Hawrylycz; Andrew Haydock; Richard Humbert; Keith D James; Brett E Johnson; Ericka M Johnson; Tristan T Frum; Elizabeth R Rosenzweig; Neerja Karnani; Kirsten Lee; Gregory C Lefebvre; Patrick A Navas; Fidencio Neri; Stephen C J Parker; Peter J Sabo; Richard Sandstrom; Anthony Shafer; David Vetrie; Molly Weaver; Sarah Wilcox; Man Yu; Francis S Collins; Job Dekker; Jason D Lieb; Thomas D Tullius; Gregory E Crawford; Shamil Sunyaev; William S Noble; Ian Dunham; France Denoeud; Alexandre Reymond; Philipp Kapranov; Joel Rozowsky; Deyou Zheng; Robert Castelo; Adam Frankish; Jennifer Harrow; Srinka Ghosh; Albin Sandelin; Ivo L Hofacker; Robert Baertsch; Damian Keefe; Sujit Dike; Jill Cheng; Heather A Hirsch; Edward A Sekinger; Julien Lagarde; Josep F Abril; Atif Shahab; Christoph Flamm; Claudia Fried; Jörg Hackermüller; Jana Hertel; Manja Lindemeyer; Kristin Missal; Andrea Tanzer; Stefan Washietl; Jan Korbel; Olof Emanuelsson; Jakob S Pedersen; Nancy Holroyd; Ruth Taylor; David Swarbreck; Nicholas Matthews; Mark C Dickson; Daryl J Thomas; Matthew T Weirauch; James Gilbert; Jorg Drenkow; Ian Bell; XiaoDong Zhao; K G Srinivasan; Wing-Kin Sung; Hong Sain Ooi; Kuo Ping Chiu; Sylvain Foissac; Tyler Alioto; Michael Brent; Lior Pachter; Michael L Tress; Alfonso Valencia; Siew Woh Choo; Chiou Yu Choo; Catherine Ucla; Caroline Manzano; Carine Wyss; Evelyn Cheung; Taane G Clark; James B Brown; Madhavan Ganesh; Sandeep Patel; Hari Tammana; Jacqueline Chrast; Charlotte N Henrichsen; Chikatoshi Kai; Jun Kawai; Ugrappa Nagalakshmi; Jiaqian Wu; Zheng Lian; Jin Lian; Peter Newburger; Xueqing Zhang; Peter Bickel; John S Mattick; Piero Carninci; Yoshihide Hayashizaki; Sherman Weissman; Tim Hubbard; Richard M Myers; Jane Rogers; Peter F Stadler; Todd M Lowe; Chia-Lin Wei; Yijun Ruan; Kevin Struhl; Mark Gerstein; Stylianos E Antonarakis; Yutao Fu; Eric D Green; Ulaş Karaöz; Adam Siepel; James Taylor; Laura A Liefer; Kris A Wetterstrand; Peter J Good; Elise A Feingold; Mark S Guyer; Gregory M Cooper; George Asimenos; Colin N Dewey; Minmei Hou; Sergey Nikolaev; Juan I Montoya-Burgos; Ari Löytynoja; Simon Whelan; Fabio Pardi; Tim Massingham; Haiyan Huang; Nancy R Zhang; Ian Holmes; James C Mullikin; Abel Ureta-Vidal; Benedict Paten; Michael Seringhaus; Deanna Church; Kate Rosenbloom; W James Kent; Eric A Stone; Serafim Batzoglou; Nick Goldman; Ross C Hardison; David Haussler; Webb Miller; Arend Sidow; Nathan D Trinklein; Zhengdong D Zhang; Leah Barrera; Rhona Stuart; David C King; Adam Ameur; Stefan Enroth; Mark C Bieda; Jonghwan Kim; Akshay A Bhinge; Nan Jiang; Jun Liu; Fei Yao; Vinsensius B Vega; Charlie W H Lee; Patrick Ng; Atif Shahab; Annie Yang; Zarmik Moqtaderi; Zhou Zhu; Xiaoqin Xu; Sharon Squazzo; Matthew J Oberley; David Inman; Michael A Singer; Todd A Richmond; Kyle J Munn; Alvaro Rada-Iglesias; Ola Wallerman; Jan Komorowski; Joanna C Fowler; Phillippe Couttet; Alexander W Bruce; Oliver M Dovey; Peter D Ellis; Cordelia F Langford; David A Nix; Ghia Euskirchen; Stephen Hartman; Alexander E Urban; Peter Kraus; Sara Van Calcar; Nate Heintzman; Tae Hoon Kim; Kun Wang; Chunxu Qu; Gary Hon; Rosa Luna; Christopher K Glass; M Geoff Rosenfeld; Shelley Force Aldred; Sara J Cooper; Anason Halees; Jane M Lin; Hennady P Shulha; Xiaoling Zhang; Mousheng Xu; Jaafar N S Haidar; Yong Yu; Yijun Ruan; Vishwanath R Iyer; Roland D Green; Claes Wadelius; Peggy J Farnham; Bing Ren; Rachel A Harte; Angie S Hinrichs; Heather Trumbower; Hiram Clawson; Jennifer Hillman-Jackson; Ann S Zweig; Kayla Smith; Archana Thakkapallayil; Galt Barber; Robert M Kuhn; Donna Karolchik; Lluis Armengol; Christine P Bird; Paul I W de Bakker; Andrew D Kern; Nuria Lopez-Bigas; Joel D Martin; Barbara E Stranger; Abigail Woodroffe; Eugene Davydov; Antigone Dimas; Eduardo Eyras; Ingileif B Hallgrímsdóttir; Julian Huppert; Michael C Zody; Gonçalo R Abecasis; Xavier Estivill; Gerard G Bouffard; Xiaobin Guan; Nancy F Hansen; Jacquelyn R Idol; Valerie V B Maduro; Baishali Maskeri; Jennifer C McDowell; Morgan Park; Pamela J Thomas; Alice C Young; Robert W Blakesley; Donna M Muzny; Erica Sodergren; David A Wheeler; Kim C Worley; Huaiyang Jiang; George M Weinstock; Richard A Gibbs; Tina Graves; Robert Fulton; Elaine R Mardis; Richard K Wilson; Michele Clamp; James Cuff; Sante Gnerre; David B Jaffe; Jean L Chang; Kerstin Lindblad-Toh; Eric S Lander; Maxim Koriabine; Mikhail Nefedov; Kazutoyo Osoegawa; Yuko Yoshinaga; Baoli Zhu; Pieter J de Jong
Journal:  Nature       Date:  2007-06-14       Impact factor: 49.962

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  15 in total

Review 1.  Recent technical and biological development in the analysis of biomarker N-deoxyguanosine-C8-4-aminobiphenyl.

Authors:  Zhidan Chen; Yuesheng Zhang; Paul Vouros
Journal:  J Chromatogr B Analyt Technol Biomed Life Sci       Date:  2018-04-24       Impact factor: 3.205

2.  A Novel and Intuitive Method of Displaying and Interacting with Mass Difference Information: Application to Oligonucleotide Drug Impurities.

Authors:  Stilianos G Roussis
Journal:  J Am Soc Mass Spectrom       Date:  2015-04-03       Impact factor: 3.109

Review 3.  Advances and challenges in analytical characterization of biotechnology products: mass spectrometry-based approaches to study properties and behavior of protein therapeutics.

Authors:  Igor A Kaltashov; Cedric E Bobst; Rinat R Abzalimov; Guanbo Wang; Burcu Baykal; Shunhai Wang
Journal:  Biotechnol Adv       Date:  2011-05-17       Impact factor: 14.227

4.  Ultraviolet Photodissociation Mass Spectrometry for Analysis of Biological Molecules.

Authors:  Jennifer S Brodbelt; Lindsay J Morrison; Inês Santos
Journal:  Chem Rev       Date:  2019-12-18       Impact factor: 60.622

5.  Imidazole Derivatives Improve Charge Reduction and Stabilization for Native Mass Spectrometry.

Authors:  Julia A Townsend; James E Keener; Zachary M Miller; James S Prell; Michael T Marty
Journal:  Anal Chem       Date:  2019-11-05       Impact factor: 6.986

6.  Design and application of an easy to use oligonucleotide mass calculation program.

Authors:  Jiong Yang; Peter Leopold; Roy Helmy; Craig Parish; Becky Arvary; Bing Mao; Fanyu Meng
Journal:  J Am Soc Mass Spectrom       Date:  2013-06-06       Impact factor: 3.109

Review 7.  Tandem mass spectrometry for characterization of covalent adducts of DNA with anticancer therapeutics.

Authors:  Catherine Silvestri; Jennifer S Brodbelt
Journal:  Mass Spectrom Rev       Date:  2012-11-13       Impact factor: 10.946

Review 8.  The analysis of DNA adducts: the transition from (32)P-postlabeling to mass spectrometry.

Authors:  Joshua J Klaene; Vaneet K Sharma; James Glick; Paul Vouros
Journal:  Cancer Lett       Date:  2012-09-04       Impact factor: 8.679

9.  Footprints of Nanoscale DNA-Silver Cluster Chromophores via Activated-Electron Photodetachment Mass Spectrometry.

Authors:  Molly S Blevins; Dahye Kim; Christopher M Crittenden; Soonwoo Hong; Hsin-Chih Yeh; Jeffrey T Petty; Jennifer S Brodbelt
Journal:  ACS Nano       Date:  2019-11-27       Impact factor: 15.881

10.  Facile Improvement of Negative Ion Mode Electrospray Ionization Using Capillary Vibrating Sharp-Edge Spray Ionization.

Authors:  Chong Li; Kushani Attanayake; Stephen J Valentine; Peng Li
Journal:  Anal Chem       Date:  2020-01-15       Impact factor: 6.986

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