Draft:John SantaLucia, Jr.
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Comment: Well done on creating the draft, and it may potentially meet the relevant requirements (including WP:GNG, WP:ANYBIO, WP:NPROF) but presently it is not clear that it does. As other reviewers have noted, Wikipedia's basic requirement for entry is that the subject is notable. Essentially subjects are presumed notable if they have received significant coverage in multiple published secondary sources that are reliable, intellectually independent of each other, and independent of the subject. To properly create such a draft page, please see the articles ‘Your First Article’, ‘Referencing for Beginners’ and ‘Easier Referencing for Beginners’. Please note that many of the references are not from sources that are considered reliable for establishing notability. To do so requires reliable sources about SantaLucia rather than by SantaLucia.Additionally, the draft tends to read too much like a CV, which Wikipedia is not; and contains writing and spelling errors that are not of a standard appropriate for an encyclopedia. The draft does not appear to show that the subject has any notability beyond the average coverage in trade publications for similar academics and businessmen (see WP:ROTM). Also, if you have any connection to the subject, including being paid, you have a conflict of interest that you must declare on your Talk page (to see instructions on how to do this please click the link). Please familiarise yourself with these pages before amending the draft. If you feel you can meet these requirements, then please make the necessary amendments before resubmitting the page. It would help our volunteer reviewers by identifying, on the draft's talk page, the WP:THREE best sources that establish notability of the subject. It would also be helpful if you could please identify with specificity, exactly which criteria you believe the page meets (eg "I think the page now meets WP:ANYBIO criteria #3, because XXXXX"). Once you have implemented these suggestions, you may also wish to leave a note for me on my talk page and I would be happy to reassess. Cabrils (talk) 23:48, 26 July 2024 (UTC)
John SantaLucia Jr. is an American biophysical chemist known for his work on nucleic acid thermodynamics.[1]. He is an Emeritus Professor of Chemistry at Wayne State University in Detroit, Michigan[2], and the co-founder of DNA Software Inc[3].
Education and Early Career
[edit]John SantaLucia Jr. studied chemistry as an undergraduate at Clarkson University[2]. SantaLucia earned his Ph.D. in Chemistry from the University of Rochester in 1991, under Douglas H. Turner.[4]. He conducted postdoctoral research at the University of California, Berkeley, with Ignacio Tinoco Jr., focusing on RNA structural studies using isotope-edited NMR spectroscopy[5]. There he was an NIH Post-doctoral Fellow from 1991-1994[2]. In 1994, SantaLucia joined Wayne State University as an Assistant Professor[2].
Academic Career (1994-2021)
[edit]Thermodynamics of DNA
[edit]Between 1996 and 1998, he published several papers describing the nearest-neighbor method for DNA thermodynamics that collectively have been cited over 10,000 times[6][7][8][9][10][11]. He developed the HYTHER web server with his student, Dr. Nicolas Peyret, to predict the thermodynamic properties of DNA and RNA sequences, including melting temperatures (Tm) [12]. These parameters enable modern PCR, microarray hybridization, DNA sequencing, and DNA nanostructure technology[13][14] [15].
Nearest-neighbor parameters developed by SantaLucia are widely used in major software packages and Tm calculators including: UNAFold mFold[16] and DINAMelt[17], DNA Software VisualOMP[18], dnaMATE[19], Promega Tm for Oligos[20], ThermoFisher Tm calculator[21], Biosearch RealTimeDesign Software[22].
Structural Biology using NMR Spectroscopy and 3D Modeling
[edit]SantaLucia's group used NMR spectroscopy to determine the structures of ribosomal RNA segments - the 690 loop [23][24], 790 loop[25], 970 loop[26], A-site mutants[27], and helix 69 - from the large ribosome subunit[28][29][30]. The 690 loop was the first known example of a G-U mismatch structure with a sheared geometry, leading to the discovery that the mismatch could be substituted and still retain function in vivo[24].
This work led to the development of RNA123 3D structure prediction methods [31][32][33][34]
Organic Chemistry
[edit]SantaLucia’s work in organic synthesis includes the complete synthesis of 3-deaza-3methyl-deoxyadenosine (3mddA)[35] and 5-iodocytidine[36]. He also contributed an efficient method for synthesizing ester bonds[37]. SantaLucia also determined thermodynamic parameters for synthetic Hachimoji DNA base pairs invented by Steven A. Benner[38]. This latter collaboration was featured across news outlets, including Nature[39], Smithsonian Magazine[40], Wired[41], IFL Science[42], CNN[43], and an article by Carl Zimmer in The New York Times[44].
Commercial Career (2000 – Present)
[edit]In 2000, SantaLucia co-founded DNA Software Inc. to develop software for predicting nucleic acid behavior[3]. He led the development of the Visual-OMP program[45], improving PCR assay optimization, including an assay for detecting the 2009 H1N1 influenza pandemic[46]. Since 2010, he has published on the Alkhumra hemorrhagic fever virus genome[47] and PCR assays for Klebsiella and the gut microbiome[48].
Service and Awards
[edit]John SantaLucia Jr. served on the interagency “SPADA” (Stakeholder Panel on Agent Detection Assays) governmental panel, producing a 2020 report on modern molecular assay development[49].
In 2021, SantaLucia received the AOAC International Award for “Recognition of Technical and Scientific Excellence: COVID-19 Emergency Response Validation Program Advisory Group”[50]. SantaLucia's company, DNA Software, received the 2023 Technology Innovation Leadership Award for Multiplex PCR Solutions[51] from Frost & Sullivan.
References
[edit]- ^ "John SantaLucia, Jr. DNA Software, Inc". PMWC Precision Medicine World Conference. 2019-02-15. Retrieved 2024-07-26.
- ^ a b c d "College of Liberal Arts and Sciences". Wayne State University. 2017-04-10. Retrieved 2024-07-26.
- ^ a b "Team". DNA Software. 2024-07-25. Retrieved 2024-07-26.
- ^ SantaLucia J, Turner DH (1993). "Structure of (rGGCGAGCC)2 in solution from NMR and restrained molecular dynamics". Biochemistry. 32 (47): 12612–23. doi:10.1021/bi00210a009. PMID 8251479.
- ^ SantaLucia J, Shen L, Cai Z, Lewis H, Ignacio T (1995). "Synthesis and NMR of RNA with selective isotopic enrichment in the bases" (PDF). Nucleic Acids Research. 23 (23): 4913–4921. doi:10.1093/nar/23.23.4913. PMC 307483. PMID 8532537.
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: CS1 maint: multiple names: authors list (link) - ^ Xia, Tianbing; SantaLucia, John; Burkard, Mark E.; Kierzek, Ryszard; Schroeder, Susan J.; Jiao, Xiaoqi; Cox, Christopher; Turner, Douglas H. (1998-10-01). "Thermodynamic Parameters for an Expanded Nearest-Neighbor Model for Formation of RNA Duplexes with Watson−Crick Base Pairs". Biochemistry. 37 (42): 14719–14735. doi:10.1021/bi9809425. ISSN 0006-2960.
- ^ SantaLucia J, Allawi HT, Seneviratne PA (1996). "Improved nearest-neighbor parameters for predicting DNA duplex stability". Biochemistry. 35 (11): 3555–62. doi:10.1021/bi951907q. PMID 8639506.
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: CS1 maint: multiple names: authors list (link) - ^ Allawi HT, SantaLucia J (1997). "Thermodynamics and NMR of internal G.T mismatches in DNA". Biochemistry. 36 (34): 10581–94. doi:10.1021/bi962590c. PMID 9265640.
- ^ SantaLucia J (1998). "A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics". Proc Natl Acad Sci U S A. 95 (4): 1460–5. Bibcode:1998PNAS...95.1460S. doi:10.1073/pnas.95.4.1460. PMC 19045. PMID 9465037.
- ^ Allawi HT, SantaLucia J (1998). "Nearest neighbor thermodynamic parameters for internal G.A mismatches in DNA". Biochemistry. 37 (8): 2170–9. doi:10.1021/bi9724873. PMID 9485363.
- ^ Allawi HT, SantaLucia J (1998). "Nearest-neighbor thermodynamics of internal A.C mismatches in DNA: sequence dependence and pH effects". Biochemistry. 37 (26): 9435–44. doi:10.1021/bi9803729. PMID 9649326.
- ^ Peyret N, Seneviratne PA, Allawi HT, SantaLucia J (1999). "Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A.A, C.C, G.G, and T.T mismatches". Biochemistry. 38 (12): 3468–77. doi:10.1021/bi9825091. PMID 10090733.
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: CS1 maint: multiple names: authors list (link) - ^ SantaLucia J, Hicks D (2004). "The thermodynamics of DNA structural motifs". Annu Rev Biophys Biomol Struct. 33: 415–40. doi:10.1146/annurev.biophys.32.110601.141800. PMID 15139820.
- ^ SantaLucia J, Turner DH (1997). "Measuring the thermodynamics of RNA secondary structure formation". Biopolymers. 44 (3): 309–19. doi:10.1002/(SICI)1097-0282(1997)44:3<309::AID-BIP8>3.0.CO;2-Z. PMID 9591481.
- ^ Watkins NE, SantaLucia J (2005). "Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes". Nucleic Acids Res. 33 (19): 6258–67. doi:10.1093/nar/gki918. PMC 1277807. PMID 16264087.
- ^ "DNA Folding Form". www.unafold.org. Retrieved 2024-08-06.
- ^ "The DINAMelt Server". www.unafold.org. Retrieved 2024-08-06.
- ^ "Visual OMP™". DNA Software. Retrieved 2024-08-06.
- ^ "dnaMATE server". melolab.org. Retrieved 2024-08-06.
- ^ "Tm Calculator | Oligo melting temperature". www.promega.com. Retrieved 2024-08-06.
- ^ "Tm Calculator - US". www.thermofisher.com. Retrieved 2024-08-06.
- ^ "How is the Tm calculated in LGC Biosearch's Technologies' RealTimeDesign™ software?". LGC Biosearch Technologies. Retrieved 2024-08-06.
- ^ Morosyuk SV, Cunningham PR, SantaLucia J (2001). "Structure and function of the conserved 690 hairpin in Escherichia coli 16 S ribosomal RNA. II. NMR solution structure". J Mol Biol. 307 (1): 197–211. doi:10.1006/jmbi.2000.4431. PMID 11243814.
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: CS1 maint: multiple names: authors list (link) - ^ a b Morosyuk SV, SantaLucia J, Cunningham PR (2001). "Structure and function of the conserved 690 hairpin in Escherichia coli 16 S ribosomal RNA. III. Functional analysis of the 690 loop". J Mol Biol. 307 (1): 213–28. doi:10.1006/jmbi.2000.4432. PMID 11243815.
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: CS1 maint: multiple names: authors list (link) - ^ Lee K, Varma S, SantaLucia J, Cunningham PR (1997). "In vivo determination of RNA structure-function relationships: analysis of the 790 loop in ribosomal RNA". J Mol Biol. 269 (5): 732–43. doi:10.1006/jmbi.1997.1092. PMID 9223637.
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: CS1 maint: multiple names: authors list (link) - ^ Saraiya AA, Lamichhane TN, Chow CS, SantaLucia J, Cunningham PR (2008). "Identification and role of functionally important motifs in the 970 loop of Escherichia coli 16S ribosomal RNA". J Mol Biol. 376 (3): 645–57. doi:10.1016/j.jmb.2007.11.102. PMC 2262921. PMID 18177894.
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: CS1 maint: multiple names: authors list (link) - ^ Clos II, Lawrence J. NMR solution studies of 16S rRNA A-site functional mutants and binding of novel ligands. PhD Thesis. Wayne State University, 2007.
- ^ Desaulniers JP, Chang YC, Aduri R, Abeysirigunawardena SC, SantaLucia J, Chow CS (2008). "Pseudouridines in rRNA helix 69 play a role in loop stacking interactions". Org Biomol Chem. 6 (21): 3892–5. doi:10.1039/b812731j. PMID 18931791.
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: CS1 maint: multiple names: authors list (link) - ^ Sumita M, Jiang J, SantaLucia J, Chow CS (2012). "Comparison of solution conformations and stabilities of modified helix 69 rRNA analogs from bacteria and human". Biopolymers. 97 (2): 94–106. doi:10.1002/bip.21706. PMC 3269404. PMID 21858779.
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: CS1 maint: multiple names: authors list (link) - ^ Jiang J, Aduri R, Chow CS, SantaLucia J (2014). "Structure modulation of helix 69 from Escherichia coli 23S ribosomal RNA by pseudouridylations". Nucleic Acids Res. 42 (6): 3971–81. doi:10.1093/nar/gkt1329. PMC 3973299. PMID 24371282.
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: CS1 maint: multiple names: authors list (link) - ^ Aduri R, Psciuk BT, Saro P, Taniga H, Schlegel HB, SantaLucia J (2007). "AMBER Force Field Parameters for the Naturally Occurring Modified Nucleosides in RNA". J Chem Theory Comput. 3 (4): 1464–75. doi:10.1021/ct600329w. PMID 26633217.
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: CS1 maint: multiple names: authors list (link) - ^ Kazantsev AV, Rambo RP, Karimpour S, Santalucia J, Tainer JA, Pace NR (2011). "Solution structure of RNase P RNA". RNA. 17 (6): 1159–71. doi:10.1261/rna.2563511. PMC 3096047. PMID 21531920.
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: CS1 maint: multiple names: authors list (link) - ^ Sijenyi, F. et al. (2012). The RNA Folding Problems: Different Levels of sRNA Structure Prediction. In: Leontis, N., Westhof, E. (eds) RNA 3D Structure Analysis and Prediction. Nucleic Acids and Molecular Biology, vol 27. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-25740-7_6
- ^ Cruz JA, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cao S; et al. (2012). "RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction". RNA. 18 (4): 610–25. doi:10.1261/rna.031054.111. PMC 3312550. PMID 22361291.
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: CS1 maint: multiple names: authors list (link) - ^ Irani, Rostem J.; SantaLucia, John (1999). "The synthesis of 5-iodocytidine phosphoramidite for heavy atom derivatization of RNA". Tetrahedron Letters. 40 (51). Elsevier BV: 8961–8964. doi:10.1016/s0040-4039(99)01650-0. ISSN 0040-4039.
- ^ Irani, R.; SantaLucia, J. (1999). "The synthesis of 5-iodocytidine phosphoramidite for heavy atom derivatization of RNA". Tetrahedron Letters. 40 (51): 8961–8964. doi:10.1016/S0040-4039(99)01650-0. S2CID 96099503.
- ^ Dhimitruka, Ilirian; SantaLucia, John (2006-01-01). "Investigation of the Yamaguchi Esterification Mechanism. Synthesis of a Lux-S Enzyme Inhibitor Using an Improved Esterification Method". Organic Letters. 8 (1): 47–50. doi:10.1021/ol0524048. ISSN 1523-7060. PMID 16381564.
- ^ Hoshika, Shuichi; Leal, Nicole A.; Kim, Myong-Jung; Kim, Myong-Sang; Karalkar, Nilesh B.; Kim, Hyo-Joong; Bates, Alison M.; Watkins, Norman E.; SantaLucia, Holly A.; Meyer, Adam J.; DasGupta, Saurja; Piccirilli, Joseph A.; Ellington, Andrew D.; SantaLucia, John; Georgiadis, Millie M.; Benner, Steven A. (2019-02-22). "Hachimoji DNA and RNA: A genetic system with eight building blocks". Science. 363 (6429): 884–887. Bibcode:2019Sci...363..884H. doi:10.1126/science.aat0971. ISSN 0036-8075. PMC 6413494. PMID 30792304.
- ^ Warren, Matthew (2019-02-21). "Four new DNA letters double life's alphabet". Nature. 566 (7745): 436–436. doi:10.1038/d41586-019-00650-8.
- ^ Magazine, Smithsonian; Thulin, Lila. "Scientists Successfully Double the DNA Alphabet". Smithsonian Magazine. Retrieved 2024-08-06.
- ^ Molteni, Megan. "Doubling Our DNA Building Blocks Could Lead to New Life Forms". Wired. ISSN 1059-1028. Retrieved 2024-08-06.
- ^ "New Artificial DNA Has Doubled The Alphabet Of Life". IFLScience. 2019-02-22. Retrieved 2024-08-06.
- ^ Strickland, Ashley (2019-02-21). "Synthetic DNA could help with search for alien life". CNN. Retrieved 2024-08-06.
- ^ Zimmer, Carl (2019-02-21). "Genetic Alphabet". The New York Times. Retrieved 2024-07-26.
- ^ SantaLucia J (2007). Physical principles and visual-OMP software for optimal PCR design. Methods Mol Biol. Vol. 402. pp. 3–34. doi:10.1007/978-1-59745-528-2_1. ISBN 978-1-58829-725-9. PMID 17951788.
- ^ Medina RA, Rojas M, Tuin A, Huff S, Ferres M, Martinez-Valdebenito C; et al. (2011). "Development and characterization of a highly specific and sensitive SYBR green reverse transcriptase PCR assay for detection of the 2009 pandemic H1N1 influenza virus on the basis of sequence signatures". J Clin Microbiol. 49 (1): 335–44. doi:10.1128/JCM.01142-10. PMC 3020443. PMID 21084522.
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: CS1 maint: multiple names: authors list (link) - ^ Madani TA, Azhar EI, Abuelzein el-TM, Kao M, Al-Bar HM, Farraj SA; et al. (2014). "Complete genome sequencing and genetic characterization of Alkhumra hemorrhagic fever virus isolated from Najran, Saudi Arabia". Intervirology. 57 (5): 300–10. doi:10.1159/000362334. PMID 25096447.
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: CS1 maint: multiple names: authors list (link) - ^ Sun Y, Patel A, SantaLucia J, Roberts E, Zhao L, Kaye K; et al. (2021). "Measurement of Klebsiella Intestinal Colonization Density To Assess Infection Risk". mSphere. 6 (3): e0050021. doi:10.1128/mSphere.00500-21. PMC 8265666. PMID 34160234.
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: CS1 maint: multiple names: authors list (link) - ^ SantaLucia J, Sozhamannan S, Gans JD, Koehler JW, Soong R, Lin NJ; et al. (2020). "Appendix Q: Recommendations for Developing Molecular Assays for Microbial Pathogen Detection Using Modern In Silico Approaches". J AOAC Int. 103 (4): 882–899. doi:10.1093/jaoacint/qsaa045. PMC 8370429. PMID 33241357.
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: CS1 maint: multiple names: authors list (link) - ^ "Analytical science leaders honored at the 2021 AOAC INTERNATIONAL Annual Meeting". AOAC INTERNATIONAL. 2021-09-24. Retrieved 2024-07-26.
- ^ "2023 Award Recipients". Frost & Sullivan. Retrieved 2024-08-06.
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