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Marmarelis ME, Scholes DG, McGrath CM, Priore SF, Roth JJ, Feldman M, Morrissette JJD, Litzky L, Deshpande C, Thompson JC, Doucette A, Gabriel PE, Sun L, Singh AP, Cohen RB, Langer CJ, Carpenter EL, Aggarwal C. Brief Report: Impact of Reflex Testing on Tissue-Based Molecular Genotyping in Patients With Advanced Non-Squamous Non-Small Cell Lung Cancer. Clin Lung Cancer 2024; 25:262-265.e2. [PMID: 38582618 DOI: 10.1016/j.cllc.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/01/2024] [Accepted: 03/05/2024] [Indexed: 04/08/2024]
Affiliation(s)
- Melina E Marmarelis
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
| | - Dylan G Scholes
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Penn Center for Cancer Care Innovation, University of Pennsylvania, Philadelphia, PA
| | - Cindy M McGrath
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Philadelphia, PA
| | - Salvatore F Priore
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Philadelphia, PA
| | - Jacquelyn J Roth
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Philadelphia, PA
| | - Michael Feldman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Philadelphia, PA
| | | | - Leslie Litzky
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Philadelphia, PA
| | - Charu Deshpande
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, Philadelphia, PA
| | - Jeffrey C Thompson
- Department of Pulmonary Medicine and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Abigail Doucette
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA; Penn Center for Cancer Care Innovation, University of Pennsylvania, Philadelphia, PA
| | - Peter E Gabriel
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA; Penn Center for Cancer Care Innovation, University of Pennsylvania, Philadelphia, PA; Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Lova Sun
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
| | - Aditi P Singh
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
| | - Roger B Cohen
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
| | - Corey J Langer
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
| | - Erica L Carpenter
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
| | - Charu Aggarwal
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA; Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA; Penn Center for Cancer Care Innovation, University of Pennsylvania, Philadelphia, PA.
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Landsburg DJ, Caponetti GC, Bagg A, Schuster SJ, Nasta S, Gerson JM, Frank DM, Barta SK, Svoboda J, Bhattacharyya S, Qualtieri JN, Lim MS, Chong EA, Roth J, Priore SF, Deihimi S, Morrissette JJ. Clinical laboratory mutation analysis performed on aggressive B cell non-Hodgkin lymphoma patient biopsies. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.e19561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e19561 Background: Results from comprehensive genomic analysis performed on aggressive B cell non-Hodgkin lymphomas (aBNHL) patient (pt) biopsies (bx) have identified mutations (mut) which may be predictive of pt survival. However, results from mut analysis (MA) performed on aBNHL pt bx in clinical laboratories are not well-described. Methods: Bx diagnostic of non-Burkitt aBNHL obtained from 7/2015-2/2021 with MA performed in the Penn Center for Personalized Diagnostics clinical laboratory using 3 consecutive versions of lymphoma sequencing panels were retrospectively analyzed. Mut tested varied by panel. Mut detected with variant allele frequency (VAF) ≥10% were included. Results: MA was performed on 293 aBNHL pt bx with a successful assay for 270 (7.8% failure rate). Request for MA was made by interpreting hematopathologist 93% and treating clinician 7%. Median turnaround time (TAT) from receipt of bx to result report was 18 (range 8-53) days. Notable pt characteristics included prior/concurrent indolent lymphoma (IL) 31% and prior systemic therapy received for IL and/or aBNHL 38%. Notable bx characteristics included bx type paraffin-embedded tissue 85% and bone marrow 12%, histologic classification diffuse large B cell lymphoma 86% and high grade B cell lymphoma 13%, cell of origin (COO) by Hans algorithm non-germinal center B (non-GCB) 51% and GCB 44%, known double expressor lymphoma 30%, known MYC rearrangement 18%, known double hit lymphoma 9% and any mut detected with VAF ≥10% 82%. Number and percentage of mut occurring in ≥10% of bx (minimum tested bx for mut ≥92) with associated COO are listed in the table. Subset analysis of 147 bx obtained from pts with newly-diagnosed aBNHL (15% with previously-untreated IL) had similar bx characteristics to the entire population were analyzed for the presence of mut reported in poor-prognosis COO-associated classifications: Cluster 5 for non-GCB and Cluster 3 for GCB (PMID: 29713087), double-hit signature (DHITsig) for GCB (PMID: 30523716) and molecular high grade (MHG) for GCB (PMID: 30523719). For 77 non-GCB bx, 19% had Cluster 5 mut. For 59 GCB bx, 56% had at least one of Cluster 3, DHITsig or MHG mut. Conclusions: Clinical laboratory MA performed on nearly 300 aBNHL pt bx was highly successful with a short TAT and demonstrated recurrent gene mut associated with aBNHL development. In the subset of bx from previously-untreated pts, MA identified mut associated with poor-prognosis genetic subtypes of aBNHL.[Table: see text]
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Affiliation(s)
- Daniel J Landsburg
- Division of Hematology/Oncology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Gabriel C. Caponetti
- Division of Hematopathology, Department of Pathology, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Adam Bagg
- Division of Hematopathology, Department of Pathology, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Stephen J. Schuster
- Division of Hematology/Oncology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Sunita Nasta
- Division of Hematology/Oncology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - James M. Gerson
- Division of Hematology/Oncology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Dale M. Frank
- Division of Hematopathology, Department of Pathology, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Stefan K. Barta
- Division of Hematology/Oncology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Jakub Svoboda
- Division of Hematology/Oncology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Siddharth Bhattacharyya
- Division of Hematopathology, Department of Pathology, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Julianne N Qualtieri
- Division of Hematopathology, Department of Pathology, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Megan S. Lim
- Division of Hematopathology, Department of Pathology, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Elise A. Chong
- Division of Hematology/Oncology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Jacquelyn Roth
- Division of Precision and Computational Diagnostics, Department of Pathology, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Salvatore F. Priore
- Division of Precision and Computational Diagnostics, Department of Pathology, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Safoora Deihimi
- Division of Precision and Computational Diagnostics, Department of Pathology, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Jennifer J. Morrissette
- Division of Precision and Computational Diagnostics, Department of Pathology, Hospital of the University of Pennsylvania, Philadelphia, PA
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Priore SF, Schwartz LE, Epstein JI. An expanded immunohistochemical profile of osteoclast-rich undifferentiated carcinoma of the urinary tract. Mod Pathol 2018; 31:984-988. [PMID: 29410491 DOI: 10.1038/s41379-018-0012-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 09/06/2017] [Accepted: 12/03/2017] [Indexed: 11/09/2022]
Abstract
Osteoclast-rich undifferentiated carcinoma of the urinary tract (ORUCUT) is a rare tumor composed of ovoid to spindle-shaped mononuclear cells with intermixed or focally clustered osteoclast-like giant cells. Previous studies have demonstrated that the mononuclear cells are neoplastic cells, while the giant cells are reactive cells of histiocytic lineage. The association between these tumors and classic urothelial carcinomas suggest that the mononuclear cells are derived from urothelial cells; however, no studies have been conducted to assess the immunohistochemical profile of ORUCUT with more specific urothelial markers. This study identified 21 cases of ORUCUT and performed immunohistochemistry for GATA3, uroplakin II, and thrombomodulin along with pancytokeratin (AE1/3) on all cases. Mononuclear cells stained positive in 20 cases (95%) for GATA3 and 19 cases (90%) for thrombomodulin. None of the mononuclear cells were positive for uroplakin II and only three cases showed focal positivity for AE1/3. The osteoclast-like giant cells were negative for GATA3, uroplakin II, thrombomodulin, and AE1/3, providing additional support to a reactive origin for these cells. Additionally, 15 cases (71%) were associated with either in situ or invasive urothelial carcinoma. This study provides an expanded immunohistochemical profile for ORUCUT and more definitively supports a urothelial origin for this tumor.
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Affiliation(s)
- Salvatore F Priore
- Department of Pathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lauren E Schwartz
- Department of Pathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jonathan I Epstein
- Departments of Pathology, Oncology, and Urology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA.
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Abstract
Influenza A is a negative-sense RNA virus with an eight-segment genome. Some segments encode more than one polypeptide product, but how the virus accesses alternate internal open reading frames (ORFs) is not completely understood. In segment 2, ribosomal scanning produces two internal ORFs, PB1-F2 and N40. Here, chemical mapping reveals a Mg(2+)-dependent pseudoknot structure that includes the PB1-F2 and N40 start codons. The results suggest that interactions of the ribosome with the pseudoknot may affect the level of translation for PB1-F2 and N40.
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Affiliation(s)
- Salvatore F Priore
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, New York 14627, United States
| | - Andrew D Kauffmann
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, New York 14627, United States
| | - Jayson R Baman
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, New York 14627, United States
| | - Douglas H Turner
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, New York 14627, United States
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Priore SF, Kierzek E, Kierzek R, Baman JR, Moss WN, Dela-Moss LI, Turner DH. Secondary structure of a conserved domain in the intron of influenza A NS1 mRNA. PLoS One 2013; 8:e70615. [PMID: 24023714 PMCID: PMC3759394 DOI: 10.1371/journal.pone.0070615] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 06/22/2013] [Indexed: 12/04/2022] Open
Abstract
Influenza A virus is a segmented single-stranded (−)RNA virus that causes substantial annual morbidity and mortality. The transcriptome of influenza A is predicted to have extensive RNA secondary structure. The smallest genome segment, segment 8, encodes two proteins, NS1 and NEP, via alternative splicing. A conserved RNA domain in the intron of segment 8 may be important for regulating production of NS1. Two different multi-branch loop structures have been proposed for this region. A combination of in vitro chemical mapping and isoenergetic microarray techniques demonstrate that the consensus sequence for this region folds into a hairpin conformation. These results provide an alternative folding for this region and a foundation for designing experiments to probe its functional role in the influenza life cycle.
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Affiliation(s)
- Salvatore F. Priore
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Jayson R. Baman
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
| | - Walter N. Moss
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
| | - Lumbini I. Dela-Moss
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
| | - Douglas H. Turner
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
- * E-mail:
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Priore SF, Moss WN, Turner DH. Influenza B virus has global ordered RNA structure in (+) and (-) strands but relatively less stable predicted RNA folding free energy than allowed by the encoded protein sequence. BMC Res Notes 2013; 6:330. [PMID: 23958134 PMCID: PMC3765861 DOI: 10.1186/1756-0500-6-330] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 07/03/2013] [Indexed: 12/03/2022] Open
Abstract
Background Influenza A virus contributes to seasonal epidemics and pandemics and contains Global Ordered RNA structure (GORS) in the nucleoprotein (NP), non-structural (NS), PB2, and M segments. A related virus, influenza B, is also a major annual public health threat, but unlike influenza A is very selective to human hosts. This study extends the search for GORS to influenza B. Findings A survey of all available influenza B sequences reveals GORS in the (+) and (−)RNAs of the NP, NS, PB2, and PB1 gene segments. The results are similar to influenza A, except GORS is observed for the M1 segment of influenza A but not for PB1. In general, the folding free energies of human-specific influenza B RNA segments are less stable than allowable by the encoded amino acid sequence. This is consistent with findings in influenza A, where human-specific influenza RNA folds are less stable than avian and swine strains. Conclusions These results reveal fundamental molecular similarities and differences between Influenza A and B and suggest a rational basis for choosing segments to target with therapeutics and for viral attenuation for live vaccines by altering RNA folding stability.
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Affiliation(s)
- Salvatore F Priore
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, NY 14627-0216, USA.
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Abstract
The 3′ splice site of the influenza A segment 7 transcript is utilized to produce mRNA for the critical M2 ion-channel protein. In solution a 63 nt fragment that includes this region can adopt two conformations: a pseudoknot and a hairpin. In each conformation, the splice site, a binding site for the SF2/ASF exonic splicing enhancer and a polypyrimidine tract, each exists in a different structural context. The most dramatic difference occurs for the splice site. In the hairpin the splice site is between two residues that are involved in a 2 by 2 nucleotide internal loop. In the pseudoknot, however, these bases are canonically paired within one of the pseudoknotted helices. The conformational switching observed in this region has implications for the regulation of splicing of the segment 7 mRNA. A measure of stability of the structures also shows interesting trends with respect to host specificity: avian strains tend to be the most stable, followed by swine and then human.
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Affiliation(s)
- Walter N Moss
- Department of Chemistry and Center for RNA Biology, University of Rochester; Rochester, NY, USA
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Moss WN, Dela-Moss LI, Kierzek E, Kierzek R, Priore SF, Turner DH. The 3' splice site of influenza A segment 7 mRNA can exist in two conformations: a pseudoknot and a hairpin. PLoS One 2012; 7:e38323. [PMID: 22685560 PMCID: PMC3369869 DOI: 10.1371/journal.pone.0038323] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 05/03/2012] [Indexed: 12/29/2022] Open
Abstract
The 3′ splice site of influenza A segment 7 is used to produce mRNA for the M2 ion-channel protein, which is critical to the formation of viable influenza virions. Native gel analysis, enzymatic/chemical structure probing, and oligonucleotide binding studies of a 63 nt fragment, containing the 3′ splice site, key residues of an SF2/ASF splicing factor binding site, and a polypyrimidine tract, provide evidence for an equilibrium between pseudoknot and hairpin structures. This equilibrium is sensitive to multivalent cations, and can be forced towards the pseudoknot by addition of 5 mM cobalt hexammine. In the two conformations, the splice site and other functional elements exist in very different structural environments. In particular, the splice site is sequestered in the middle of a double helix in the pseudoknot conformation, while in the hairpin it resides in a two-by-two nucleotide internal loop. The results suggest that segment 7 mRNA splicing can be controlled by a conformational switch that exposes or hides the splice site.
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Affiliation(s)
- Walter N. Moss
- Department of Chemistry, Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
| | - Lumbini I. Dela-Moss
- Department of Chemistry, Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Noskowskiego, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Noskowskiego, Poland
| | - Salvatore F. Priore
- Department of Chemistry, Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
| | - Douglas H. Turner
- Department of Chemistry, Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
- * E-mail:
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Abstract
Influenza A is a significant public health threat, partially because of its capacity to readily exchange gene segments between different host species to form novel pandemic strains. An understanding of the fundamental factors providing species barriers between different influenza hosts would facilitate identification of strains capable of leading to pandemic outbreaks and could also inform vaccine development. Here, we describe the difference in predicted RNA secondary structure stability that exists between avian, swine and human coding regions. The results predict that global ordered RNA structure exists in influenza A segments 1, 5, 7 and 8, and that ranges of free energies for secondary structure formation differ between host strains. The predicted free energy distributions for strains from avian, swine, and human species suggest criteria for segment reassortment and strains that might be ideal candidates for viral attenuation and vaccine development.
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Affiliation(s)
- Salvatore F. Priore
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
| | - Walter N. Moss
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
| | - Douglas H. Turner
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
- * E-mail:
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Abstract
Influenza A is a negative sense RNA virus of significant public health concern. While much is understood about the life cycle of the virus, knowledge of RNA secondary structure in influenza A virus is sparse. Predictions of RNA secondary structure can focus experimental efforts. The present study analyzes coding regions of the eight viral genome segments in both the (+) and (-) sense RNA for conserved secondary structure. The predictions are based on identifying regions of unusual thermodynamic stabilities and are correlated with studies of suppression of synonymous codon usage (SSCU). The results indicate that secondary structure is favored in the (+) sense influenza RNA. Twenty regions with putative conserved RNA structure have been identified, including two previously described structured regions. Of these predictions, eight have high thermodynamic stability and SSCU, with five of these corresponding to current annotations (e.g., splice sites), while the remaining 12 are predicted by the thermodynamics alone. Secondary structures with high conservation of base-pairing are proposed within the five regions having known function. A combination of thermodynamics, amino acid and nucleotide sequence comparisons along with SSCU was essential for revealing potential secondary structures.
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Affiliation(s)
- Walter N Moss
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, New York 14627-0216, USA
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Priore SF, Pogozelski WK, Macula A. MOLECULAR COMPUTATION: A DNA‐BASED MODEL FOR SOLVING MATHEMATICAL PROBLEMS. FASEB J 2006. [DOI: 10.1096/fasebj.20.4.a101-d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | - Anthony Macula
- Department of MathematicsState University of New York College at GeneseoGeneseoNY14454
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