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Article ; Online: Development of Software Workflow for the Rapid Detection of Cross-Linked Dipeptides.

Wecksler, Aaron T / Veale, Lawrie / Basanta-Sanchez, Maria / Bern, Marshall

Journal of the American Society for Mass Spectrometry

2022 Volume 33, Issue 3, Page(s) 598–602

Abstract: Detection and characterization of cross-linked peptides of unknown chemical nature and location is challenging. An analytical workflow based on the use ... ...

Abstract	Detection and characterization of cross-linked peptides of unknown chemical nature and location is challenging. An analytical workflow based on the use of
MeSH term(s)	Chromatography, Liquid/methods ; Cysteine/chemistry ; Cysteine/metabolism ; Dipeptides/analysis ; Dipeptides/chemistry ; Disulfides/chemistry ; Disulfides/metabolism ; Software ; Tandem Mass Spectrometry/methods ; Tryptophan/chemistry ; Tryptophan/metabolism ; Workflow
Chemical Substances	Dipeptides ; Disulfides ; Tryptophan (8DUH1N11BX) ; Cysteine (K848JZ4886)
Language	English
Publishing date	2022-02-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	1073671-2
ISSN	1879-1123 ; 1044-0305
ISSN (online)	1879-1123
ISSN	1044-0305
DOI	10.1021/jasms.1c00312
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Zs.MO 241: Show issues

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Article ; Online: Ultraviolet Photodissociation and Activated Electron Photodetachment Mass Spectrometry for Top-Down Sequencing of Modified Oligoribonucleotides.

Santos, Inês C / Lanzillotti, Michael / Shilov, Ignat / Basanta-Sanchez, Maria / Roushan, Abhishek / Lawler, Rose / Tang, Wilfred / Bern, Marshall / Brodbelt, Jennifer S

Journal of the American Society for Mass Spectrometry

2022 Volume 33, Issue 3, Page(s) 510–520

Abstract: With the increased development of new RNA-based therapeutics, the need for robust analytical methods for confirming sequences and mapping modifications has accelerated. Characterizing modified ribonucleic acids using mass spectrometry is challenging ... ...

Abstract	With the increased development of new RNA-based therapeutics, the need for robust analytical methods for confirming sequences and mapping modifications has accelerated. Characterizing modified ribonucleic acids using mass spectrometry is challenging because diagnostic fragmentation may be suppressed for modified nucleotides, thus hampering complete sequence coverage and the confident localization of modifications. Ultraviolet photodissociation (UVPD) has shown great potential for the characterization of nucleic acids due to extensive backbone fragmentation. Activated electron photodetachment dissociation (a-EPD) has also been used as an alternative to capitalize on the dominant charge-reduction pathway prevalent in UVPD, facilitate dissociation, and produce high abundances of fragment ions. Here, we compare higher-energy collisional activation (HCD), UVPD using 193 and 213 nm photons, and a-EPD for the top-down sequencing of modified nucleic acids, including methylated, phosphorothioate, and locked nucleic acid-modified DNA. The presence of these modifications alters the fragmentation pathways observed upon UVPD and a-EPD, and extensive backbone cleavage is observed that results in the production of fragment ions that retain the modifications and allow them to be pinpointed. LNA and 2'-
MeSH term(s)	Electrons ; Mass Spectrometry/methods ; Oligoribonucleotides/analysis ; Oligoribonucleotides/chemistry ; Oligoribonucleotides/radiation effects ; Photolysis ; Sequence Analysis/methods ; Ultraviolet Rays
Chemical Substances	Oligoribonucleotides
Language	English
Publishing date	2022-02-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	1073671-2
ISSN	1879-1123 ; 1044-0305
ISSN (online)	1879-1123
ISSN	1044-0305
DOI	10.1021/jasms.1c00340
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Zs.MO 241: Show issues

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Article: Shear Dependent LC Purification of an Engineered DNA Nanoswitch and Implications for DNA Origami

Halvorsen, Ken / Basanta-Sanchez Maria / Chandrasekaran Arun Richard / Kizer Megan E / Wang Xing

Analytical chemistry. 2017 June 06, v. 89, no. 11

2017

Abstract: As DNA nanotechnology matures, there is increasing need for fast, reliable, and automated purification methods. Here, we develop UHPLC methods to purify self-assembled DNA nanoswitches, which are formed using DNA origami approaches and are designed to ... ...

Abstract	As DNA nanotechnology matures, there is increasing need for fast, reliable, and automated purification methods. Here, we develop UHPLC methods to purify self-assembled DNA nanoswitches, which are formed using DNA origami approaches and are designed to change conformations in response to a binding partner. We found that shear degradation hindered LC purification of the DNA nanoswitches, removing oligonucleotides from the scaffold strand and causing loss of function. However, proper choice of column, flow rate, and buffers enabled robust and automated purification of DNA nanoswitches without loss of function in under a half hour. Applying our approach to DNA origami structures, we found that â¼400 nm long nanotubes degraded under the gentlest flow conditions while â¼40 nm diameter nanospheres remained intact even under aggressive conditions. These examples show how fluid stresses can affect different DNA nanostructures during LC purification and suggest that shear forces may be relevant for some applications of DNA nanotechnology. Further development of this approach could lead to fast and automated purification of DNA nanostructures of various shapes and sizes, which would be an important advance for the field.
Keywords	buffers ; DNA ; nanospheres ; nanotubes ; oligonucleotides ; purification methods ; ultra-performance liquid chromatography
Language	English
Dates of publication	2017-0606
Size	p. 5673-5677.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021%2Facs.analchem.7b00791
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Article ; Online: Shear Dependent LC Purification of an Engineered DNA Nanoswitch and Implications for DNA Origami.

Halvorsen, Ken / Kizer, Megan E / Wang, Xing / Chandrasekaran, Arun Richard / Basanta-Sanchez, Maria

Analytical chemistry

2017 Volume 89, Issue 11, Page(s) 5673–5677

Abstract	As DNA nanotechnology matures, there is increasing need for fast, reliable, and automated purification methods. Here, we develop UHPLC methods to purify self-assembled DNA nanoswitches, which are formed using DNA origami approaches and are designed to change conformations in response to a binding partner. We found that shear degradation hindered LC purification of the DNA nanoswitches, removing oligonucleotides from the scaffold strand and causing loss of function. However, proper choice of column, flow rate, and buffers enabled robust and automated purification of DNA nanoswitches without loss of function in under a half hour. Applying our approach to DNA origami structures, we found that ∼400 nm long nanotubes degraded under the gentlest flow conditions while ∼40 nm diameter nanospheres remained intact even under aggressive conditions. These examples show how fluid stresses can affect different DNA nanostructures during LC purification and suggest that shear forces may be relevant for some applications of DNA nanotechnology. Further development of this approach could lead to fast and automated purification of DNA nanostructures of various shapes and sizes, which would be an important advance for the field.
MeSH term(s)	Chromatography, High Pressure Liquid/methods ; DNA/chemistry ; DNA/isolation & purification ; Nanostructures ; Nanotechnology ; Nanotubes ; Nucleic Acid Conformation ; Shear Strength
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2017-05-08
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.7b00791
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Article: Synthesis and base pairing studies of geranylated 2-thiothymidine, a natural variant of thymidine

Wang, Rui / Ranganathan, Srivathsan V / Basanta-Sanchez, Maria / Shen, Fusheng / Chen, Alan / Sheng, Jia

Chemical communications. 2015 Nov. 3, v. 51, no. 91

2015

Abstract: The synthesis and base pairing of DNA duplexes containing the geranylated 2-thiothymidine have been investigated. This naturally existing hydrophobic modification could grant better base pairing stability to the T–G pair over normal T–A and other ... ...

Abstract	The synthesis and base pairing of DNA duplexes containing the geranylated 2-thiothymidine have been investigated. This naturally existing hydrophobic modification could grant better base pairing stability to the T–G pair over normal T–A and other mismatched pairs in the duplex context. This study provides a potential explanation for the different codon recognition preferences of the geranylated tRNAs.
Keywords	DNA ; chemical compounds ; chemical reactions ; hydrophobicity ; thymidine ; transfer RNA
Language	English
Dates of publication	2015-1103
Size	p. 16369-16372.
Publishing place	The Royal Society of Chemistry
Document type	Article
ZDB-ID	1472881-3
ISSN	1364-548X ; 1359-7345 ; 0009-241X
ISSN (online)	1364-548X
ISSN	1359-7345 ; 0009-241X
DOI	10.1039/c5cc07479g
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Article ; Online: Attomole quantification and global profile of RNA modifications: Epitranscriptome of human neural stem cells.

Basanta-Sanchez, Maria / Temple, Sally / Ansari, Suraiya A / D'Amico, Anna / Agris, Paul F

Nucleic acids research

2016 Volume 44, Issue 3, Page(s) e26

Abstract: Exploration of the epitranscriptome requires the development of highly sensitive and accurate technologies in order to elucidate the contributions of the more than 100 RNA modifications to cell processes. A highly sensitive and accurate ultra-high ... ...

Abstract	Exploration of the epitranscriptome requires the development of highly sensitive and accurate technologies in order to elucidate the contributions of the more than 100 RNA modifications to cell processes. A highly sensitive and accurate ultra-high performance liquid chromatography-tandem mass spectrometry method was developed to simultaneously detect and quantify 28 modified and four major nucleosides in less than 20 min. Absolute concentrations were calculated using extinction coefficients of each of the RNA modifications studied. A comprehensive RNA modifications database of UV profiles and extinction coefficient is reported within a 2.3-5.2 % relative standard deviation. Excellent linearity was observed 0.99227-0.99999 and limit of detection values ranged from 63.75 attomoles to 1.21 femtomoles. The analytical performance was evaluated by analyzing RNA modifications from 100 ng of RNA from human pluripotent stem cell-derived neural cells. Modifications were detected at concentrations four orders of magnitude lower than the corresponding parental nucleosides, and as low as 23.01 femtograms, 64.09 attomoles. Direct and global quantitative analysis of RNA modifications are among the advantages of this new approach.
MeSH term(s)	Cells, Cultured ; Chromatography, High Pressure Liquid/methods ; Gene Expression Profiling ; Humans ; Limit of Detection ; Neural Stem Cells/metabolism ; RNA/genetics ; RNA Processing, Post-Transcriptional ; Tandem Mass Spectrometry/methods ; Transcriptome
Chemical Substances	RNA (63231-63-0)
Language	English
Publishing date	2016-02-18
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkv971
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Article ; Online: Direct infusion analysis of nucleotide mixtures of very similar or identical elemental composition.

Quinn, Ryan / Basanta-Sanchez, Maria / Rose, Rebecca E / Fabris, Daniele

Journal of mass spectrometry : JMS

2013 Volume 48, Issue 6, Page(s) 703–712

Abstract: The challenges posed by the analysis of mono-nucleotide mixtures by direct infusion electrospray ionization were examined in the context of recent advances of mass spectrometry (MS) technologies. In particular, we evaluated the merits of high-resolution ... ...

Abstract	The challenges posed by the analysis of mono-nucleotide mixtures by direct infusion electrospray ionization were examined in the context of recent advances of mass spectrometry (MS) technologies. In particular, we evaluated the merits of high-resolution mass analysis, multistep gas-phase dissociation, and ion mobility determinations for the characterization of species with very similar or identical elemental composition. The high resolving power afforded by a linear trap quadrupole-orbitrap allowed the complete differentiation of overlapping isotopic distributions produced by nucleotides that differed by a single mass unit. Resolving (12)C signals from nearly overlapped (13)C contributions provided the exact masses necessary to calculate matching elemental compositions for unambiguous formulae assignment. However, it was the ability to perform sequential steps of gas-phase dissociation (i.e. MS(n)-type analysis) that proved more valuable for discriminating between truly isobaric nucleotides, such as the AMP/dGMP and UMP/ΨMP couples, which were differentiated in the mixture from their unique fragmentation patterns. The identification of diagnostic fragments enabled the deconvolution of dissociation spectra containing the products of coexisting isobars that could not be individually isolated in the mass-selection step. Approaches based on ion mobility spectrometry-MS provided another dimension upon which isobaric nucleotides could be differentiated according to their distinctive mobility behaviors. Subtle structural variations, such as the different positions of an oxygen atom in AMP/dGMP or the glycosidic bond in UMP/ΨMP, produced detectable differences in the respective ion mobility profiles, which enabled the differentiation of the isobaric couples in the mixture. Parallel activation of all ions emerging from the ion mobility element provided an additional dimension for differentiating these analytes on the basis of both mobility and fragmentation properties.
MeSH term(s)	Isotopes/chemistry ; Nucleotides/analysis ; Nucleotides/chemistry ; Nucleotides/isolation & purification ; Spectrometry, Mass, Electrospray Ionization/methods ; Tandem Mass Spectrometry
Chemical Substances	Isotopes ; Nucleotides
Language	English
Publishing date	2013-05-31
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1221763-3
ISSN	1096-9888 ; 1076-5174
ISSN (online)	1096-9888
ISSN	1076-5174
DOI	10.1002/jms.3207
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Zs.MO 220: Show issues

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Article ; Online: Surveillance for lower airway pathogens in mechanically ventilated patients by metabolomic analysis of exhaled breath: a case-control study.

Fowler, Stephen J / Basanta-Sanchez, Maria / Xu, Yun / Goodacre, Royston / Dark, Paul M

Thorax

2015 Volume 70, Issue 4, Page(s) 320–325

Abstract: Background: Healthcare associated infections, including ventilator associated pneumonia, are difficult to diagnose and treat, and are associated with significant morbidity, mortality and cost. We aimed to demonstrate proof of concept that breath ... ...

Abstract	Background: Healthcare associated infections, including ventilator associated pneumonia, are difficult to diagnose and treat, and are associated with significant morbidity, mortality and cost. We aimed to demonstrate proof of concept that breath volatile profiles were associated with the presence of clinically relevant pathogens in the lower respiratory tract. Methods: Patients with sterile brain injury requiring intubation and ventilation on the intensive care unit were eligible for inclusion. Serial clinical and breath data were obtained three times a week, from admission up to a maximum of 10 days. Bronchial lavage for semiquantitative culture was collected immediately prior to breath sampling. Breath samples were collected in triplicate for off-line analysis by thermal-desorption/gas chromatography/time-of-flight mass spectrometry. Breath data were recorded as retention time/mass ion pairs, and analysed (pathogen present vs absent) by ANOVA-mean centre principal component analysis. Results: Samples were collected from 46 patients (mean (SD) age 49 (19) years; 27 male). The dominant factors affecting breath sample analysis were the individual breath profile and duration of intubation. When these were taken into account, clear separation was seen between breath profiles at each time point by the presence/absence of pathogens. Loadings plots identified consistent metabolite peaks contributing to this separation at each time point. Conclusions: Breath volatile analysis is able to classify breath profiles of patients with and without significant pathogen load in the lower respiratory tract. If validated in independent cohorts, these findings could lead to development of rapid non-invasive point-of-care surveillance systems and diagnostics for lower respiratory tract infection in the intensive care unit.
MeSH term(s)	Adult ; Aged ; Breath Tests/methods ; Bronchoalveolar Lavage Fluid/microbiology ; Case-Control Studies ; Critical Care/methods ; Exhalation ; Female ; Humans ; Intensive Care Units ; Longitudinal Studies ; Male ; Metabolomics/methods ; Middle Aged ; Pneumonia, Ventilator-Associated/diagnosis ; Pneumonia, Ventilator-Associated/microbiology ; Population Surveillance/methods
Language	English
Publishing date	2015-04
Publishing country	England
Document type	Evaluation Studies ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	204353-1
ISSN	1468-3296 ; 0040-6376
ISSN (online)	1468-3296
ISSN	0040-6376
DOI	10.1136/thoraxjnl-2014-206273
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Article ; Online: Synthesis and base pairing studies of geranylated 2-thiothymidine, a natural variant of thymidine.

Wang, Rui / Ranganathan, Srivathsan V / Basanta-Sanchez, Maria / Shen, Fusheng / Chen, Alan / Sheng, Jia

Chemical communications (Cambridge, England)

2015 Volume 51, Issue 91, Page(s) 16369–16372

Abstract	The synthesis and base pairing of DNA duplexes containing the geranylated 2-thiothymidine have been investigated. This naturally existing hydrophobic modification could grant better base pairing stability to the T-G pair over normal T-A and other mismatched pairs in the duplex context. This study provides a potential explanation for the different codon recognition preferences of the geranylated tRNAs.
MeSH term(s)	Base Pairing ; Base Sequence ; Molecular Dynamics Simulation ; Nucleic Acid Denaturation ; Oligodeoxyribonucleotides/chemical synthesis ; Oligodeoxyribonucleotides/chemistry ; Terpenes/chemical synthesis ; Thymidine/analogs & derivatives ; Thymidine/chemical synthesis
Chemical Substances	Oligodeoxyribonucleotides ; Terpenes ; Thymidine (VC2W18DGKR)
Language	English
Publishing date	2015-11-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1472881-3
ISSN	1364-548X ; 1359-7345 ; 0009-241X
ISSN (online)	1364-548X
ISSN	1359-7345 ; 0009-241X
DOI	10.1039/c5cc07479g
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Article ; Online: Synthesis, base pairing and structure studies of geranylated RNA.

Wang, Rui / Vangaveti, Sweta / Ranganathan, Srivathsan V / Basanta-Sanchez, Maria / Haruehanroengra, Phensinee / Chen, Alan / Sheng, Jia

Nucleic acids research

2016 Volume 44, Issue 13, Page(s) 6036–6045

Abstract: Natural RNAs utilize extensive chemical modifications to diversify their structures and functions. 2-Thiouridine geranylation is a special hydrophobic tRNA modification that has been discovered very recently in several bacteria, such as Escherichia coli, ...

Abstract	Natural RNAs utilize extensive chemical modifications to diversify their structures and functions. 2-Thiouridine geranylation is a special hydrophobic tRNA modification that has been discovered very recently in several bacteria, such as Escherichia coli, Enterobacter aerogenes, Pseudomonas aeruginosa and Salmonella Typhimurium The geranylated residues are located in the first anticodon position of tRNAs specific for lysine, glutamine and glutamic acid. This big hydrophobic terpene functional group affects the codon recognition patterns and reduces frameshifting errors during translation. We aimed to systematically study the structure, function and biosynthesis mechanism of this geranylation pathway, as well as answer the question of why nature uses such a hydrophobic modification in hydrophilic RNA systems. Recently, we have synthesized the deoxy-analog of S-geranyluridine and showed the geranylated T-G pair is much stronger than the geranylated T-A pair and other mismatched pairs in the B-form DNA duplex context, which is consistent with the observation that the geranylated tRNA(Glu) UUC recognizes GAG more efficiently than GAA. In this manuscript we report the synthesis and base pairing specificity studies of geranylated RNA oligos. We also report extensive molecular simulation studies to explore the structural features of the geranyl group in the context of A-form RNA and its effect on codon-anticodon interaction during ribosome binding.
MeSH term(s)	Anticodon/genetics ; Codon/genetics ; DNA, B-Form/genetics ; Escherichia coli/genetics ; Hydrophobic and Hydrophilic Interactions ; Nucleic Acid Conformation ; Protein Biosynthesis/genetics ; RNA/genetics ; RNA/metabolism ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; Ribosomes/genetics ; Ribosomes/metabolism ; Thiouridine/analogs & derivatives ; Thiouridine/metabolism
Chemical Substances	2-thiouridine ; Anticodon ; Codon ; DNA, B-Form ; Thiouridine (13957-31-8) ; RNA (63231-63-0) ; RNA, Transfer (9014-25-9)
Language	English
Publishing date	2016-07-27
Publishing country	England
Document type	Journal Article
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkw544
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