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Academic literature on the topic 'DNA-encoded libraries'

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Published: 10 December 2022
Last updated: 14 March 2023

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Journal articles on the topic "DNA-encoded libraries"

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Dumelin, Christoph E, Jörg Scheuermann, Samu Melkko, and Dario Neri. "DNA-Encoded Chemical Libraries." QSAR & Combinatorial Science 25, no. 11 (November 2006): 1081–87. http://dx.doi.org/10.1002/qsar.200640104.

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Scheuermann, Jörg, Christoph E. Dumelin, Samu Melkko, and Dario Neri. "DNA-encoded chemical libraries." Journal of Biotechnology 126, no. 4 (December 2006): 568–81. http://dx.doi.org/10.1016/j.jbiotec.2006.05.018.

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Shi, Bingbing, Yu Zhou, and Xiaoyu Li. "Recent advances in DNA-encoded dynamic libraries." RSC Chemical Biology 3, no. 4 (2022): 407–19. http://dx.doi.org/10.1039/d2cb00007e.

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A brief review on the recent development of DNA-encoded dynamic libraries (DEDLs) is provided, highlighting their distinct features from traditional dynamic chemical libraries and static DNA-encoded libraries.
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Michael McCoy. "NovAliX invests in DNA-encoded libraries." C&EN Global Enterprise 98, no. 48 (December 21, 2020): 19. http://dx.doi.org/10.1021/cen-09848-buscon16.

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Franzini, Raphael M., and Cassie Randolph. "Chemical Space of DNA-Encoded Libraries." Journal of Medicinal Chemistry 59, no. 14 (February 25, 2016): 6629–44. http://dx.doi.org/10.1021/acs.jmedchem.5b01874.

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Connors, William H., Stephen P. Hale, and Nicholas K. Terrett. "DNA-encoded chemical libraries of macrocycles." Current Opinion in Chemical Biology 26 (June 2015): 42–47. http://dx.doi.org/10.1016/j.cbpa.2015.02.004.

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Scheuermann, Jörg, and Dario Neri. "Dual-pharmacophore DNA-encoded chemical libraries." Current Opinion in Chemical Biology 26 (June 2015): 99–103. http://dx.doi.org/10.1016/j.cbpa.2015.02.021.

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Reddavide, Francesco V., Weilin Lin, Sarah Lehnert, and Yixin Zhang. "DNA-Encoded Dynamic Combinatorial Chemical Libraries." Angewandte Chemie 127, no. 27 (May 26, 2015): 8035–39. http://dx.doi.org/10.1002/ange.201501775.

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Lerner, Richard A., and Dario Neri. "Reflections on DNA-encoded chemical libraries." Biochemical and Biophysical Research Communications 527, no. 3 (June 2020): 757–59. http://dx.doi.org/10.1016/j.bbrc.2020.04.080.

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Flood, Dillon T., Cian Kingston, Julien C. Vantourout, Philip E. Dawson, and Phil S. Baran. "DNA Encoded Libraries: A Visitor's Guide." Israel Journal of Chemistry 60, no. 3-4 (January 17, 2020): 268–80. http://dx.doi.org/10.1002/ijch.201900133.

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Dissertations / Theses on the topic "DNA-encoded libraries"

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Gironda, Martínez Adrián. "DNA-ENCODED CHEMICAL LIBRARIES: ADVANCES AND APPLICATIONS TO DRUG DIFFICULT TARGETS." Doctoral thesis, Università di Siena, 2022. http://hdl.handle.net/11365/1194175.

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The discovery of small organic ligands or biologics capable of modulating biological processes remains one of the biggest challenges in developing new medicines. Different technologies have been implemented over the last decades to ease this process and make it more efficient. In this regard, encoded display technologies have played a major role in the discovery of new antibodies, peptides, and proteins. However, the efficient exploitation of automated high-throughput screening to discover small organic ligands has mainly been limited to big pharmaceutical companies. DNA-Encoded Chemical Libraries (DELs) have emerged as a powerful and cost-effective alternative to solve this issue. The technology has been established during the last 25 years and has become one of the best methods to synthesize and screen libraries of unprecedented size, promising a bright future in the early drug discovery stages. DELs are collections of small molecules individually coupled to oligonucleotide fragments, serving as amplifiable identification barcodes. In the first part of this thesis new DEL designs, displaying molecules capable of targeting challenging therapeutic targets while keeping library-quality at the highest grade, were investigated. A novel single-pharmacophore library, termed AG-DEL, was synthesized. The library was constructed using split-and-pool procedures on single-stranded DNA. The modularity of this library design allowed the creation of different dual-pharmacophore libraries in an encoded self-assembling chemical library format (ESAC 2+1 and ESAC Plus). Furthermore, the new AG-DEL facilitated the use of novel screening methodologies (e.g., photo-crosslinking) to efficiently discover new small organic ligands. DEL synthesis mainly relies on the chemical diversity of building blocks and the efficiency of the chemical reactions to link them. Following this trend, many different groups have made great efforts during the last years to develop new mild and efficient DNA-compatible reactions. One of the most used reactions for DEL synthesis is the amide bond formation, thanks mainly to various reliable reaction protocols and the big commercially available collections of amino acids. Nevertheless, the current availability of DNA-compatible post-functionalization of amino acids is still quite limited due to some restrictions inherent to the presence of the DNA. In the second part of this thesis, a new DNA-compatible diazo-transfer reaction was successfully optimized and implemented. This reaction has shown to be efficient, both in reaction times and reaction yields, as well as to be mild and fully compatible with DNA, as demonstrated by subsequent enzyme-mediated ligation of the oligonucleotide template to a new fragment, and has served for the synthesis of new ESAC Plus libraries within our group. The modulation of protein-protein interactions (PPIs) represents another formidable challenge. These interactions are often characterized by large and flat protein surfaces that are composed of many different interacting groups. Therefore, these interactions are usually targeted using large macrocyclic peptides or antibodies. Notwithstanding this challenge, some examples have been reported during the last years in which small organic ligands or peptidomimetics were specifically designed for targeting this class of proteins. Some of these examples have successfully reached clinical trials and even marketing authorization, showing the critical importance of PPI modulators and indicating broad prospects. In PPI modulation, the discovery of ligands targeting cytokines is even more challenging, due to the small size and particularly flat surface of these proteins. Nevertheless, different small molecule ligands targeting cytokines have been described over the years. Among all these proteins, Interleukin-2 (IL2) represents one of the best examples. IL2 is a pro-inflammatory cytokine, that plays a crucial role in immunity, and different therapeutic approaches using IL2 are increasingly being used for the treatment of a variety of malignancies, like melanoma and renal cell carcinoma. However, the use of IL2 has been limited due to strong side effects related to the high doses of cytokine necessary to achieve a pharmacological effect. Side effects have been linked to the release of pro-inflammatory cytokines as well as to CD25-mediated endothelial damage induced by IL2 binding to endothelial surface receptors, leading to a vascular leak syndrome. The interaction between IL2 and its alpha subunit receptor (IL2Ra or CD25) activates immunosuppressive regulatory T cells (Tregs) and reduces its antitumor activity. Thus, avoiding the formation of the multimeric IL2/IL2R complex can enhance the antitumor response. The last chapter of this thesis was focused on the development of novel DEL-derived IL2 ligands capable of interacting at the CD25 binding domain of IL2. During these studies, a tumor-targeting antibody-IL2 fusion protein, L19-IL2, was used to find ligands masking the IL2 moiety. The ligands were optimized by a medicinal chemistry approach and characterized by fluorescence polarization. Furthermore, the best ligand showed binding at the CD25 binding epitope of IL2, as evidenced by competition experiments using an anti-IL2 antibody. The use of one of the discovered compounds or an affinity matured derivative can allow the generation of a new class of biopharmaceutical-small molecule complexes that localize at the site of the disease and regain activity of the cytokine only at the tumor site.
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McGregor, Lynn Marie. "Methods for the Identification of Ligand-Target Pairs from Combined Libraries of Targes and Ligands." Thesis, Harvard University, 2014. http://dissertations.umi.com/gsas.harvard:11370.

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Advances in genome and proteome research have led to a dramatic increase in the number of macromolecular targets of interest to the life sciences. A solution-phase method to simultaneously reveal all ligand-target binding pairs from a single solution containing libraries of ligands and targets could significantly increase the efficiency and effectiveness of target-oriented screening efforts. Here, we describe interaction-dependent PCR (IDPCR), a solution-phase method to identify binding partners from combined libraries of small-molecule ligands and targets in a single experiment. Binding between DNA-linked targets and DNA-linked ligands induces formation of an extendable duplex. Extension links codes identifying the ligand and target into one selectively amplifiable DNA molecule. In a model selection, IDPCR resulted in the enrichment of DNA encoding all five known protein-ligand pairs out of 67,599 possible sequences.
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Klika, Škopić Mateja [Verfasser], Daniel [Akademischer Betreuer] Rauh, and Herbert [Gutachter] Waldmann. "Development of synthesis methodology for DNA-encoded libraries / Mateja Klika Škopić ; Gutachter: Herbert Waldmann ; Betreuer: Daniel Rauh." Dortmund : Universitätsbibliothek Dortmund, 2017. http://d-nb.info/1160443076/34.

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Geylan, Gökçe. "Training Machine Learning-based QSAR models with Conformal Prediction on Experimental Data from DNA-Encoded Chemical Libraries." Thesis, Uppsala universitet, Institutionen för farmaceutisk biovetenskap, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-447354.

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DNA-encoded chemical libraries (DEL) allows an exhaustive chemical space sampling with a large-scale data consisting of compounds produced through combinatorial synthesis. This novel technology was utilized in the early drug discovery stages for robust hit identification and lead optimization. In this project, the aim was to build a Machine Learning- based QSAR model with conformal prediction for hit identification on two different target proteins, the DEL was assayed on. An initial investigation was conducted on a pilot project with 1000 compounds and the analyses and the conclusions drawn from this part were later applied to a larger dataset with 1.2 million compounds. With this classification model, the prediction of the compound activity in the DEL as well as in an external dataset was aimed to be analyzed with identification of the top hits to evaluate model’s performance and applicability. Support Vector Machine (SVM) and Random Forest (RF) models were built on both the pilot and the main datasets with different descriptor sets of Signature Fingerprints, RDKIT and CDK. In addition, an Autoencoder was used to supply data-driven descriptors on the pilot data as well. The Libsvm and the Liblinear implementations were explored and compared based on the models’ performances. The comparisons were made by considering the key concepts of conformal prediction such as the trade-off between validity and efficiency, observed fuzziness and the calibration against a range of significance levels. The top hits were determined by two sorting methods, credibility and p-value differences between the binary classes. The assignment of correct single-labels to the true actives over a wide range of significance levels regardless of the similarity of the test compounds to the training set was confirmed for the models. Furthermore, an accumulation of these true actives in the models’ top hit selections was observed according to the latter sorting method and additional investigations on the similarity and the building block enrichments in the top 50 and 100 compounds were conducted. The Tanimoto similarity demonstrated the model’s predictive power in selecting structurally dissimilar compounds while the building block enrichment analysis showed the selectivity of the binding pocket where the target protein B was determined to be more selective. All of these comparison methods enabled an extensive study on the model evaluation and performance. In conclusion, the Liblinear model with the Signature Fingerprints was concluded to give the best model performance for both the pilot and the main datasets with the considerations of the model performances and the computational power requirements. However, an external set prediction was not successful due to the low structural diversity in the DEL which the model was trained on.
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Grünzner, S., F. V. Reddavide, C. Steinfelder, M. Cui, M. Busek, U. Klotzbach, Y. Zhang, and F. Sonntag. "Lab-on-a-chip platform for high throughput drug discovery with DNAencoded chemical libraries." SPIE, 2017. https://tud.qucosa.de/id/qucosa%3A34877.

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The fast development of DNA-encoded chemical libraries (DECL) in the past 10 years has received great attention from pharmaceutical industries. It applies the selection approach for small molecular drug discovery. Because of the limited choices of DNA-compatible chemical reactions, most DNA-encoded chemical libraries have a narrow structural diversity and low synthetic yield. There is also a poor correlation between the ranking of compounds resulted from analyzing the sequencing data and the affinity measured through biochemical assays. By combining DECL with dynamical chemical library, the resulting DNA-encoded dynamic library (EDCCL) explores the thermodynamic equilibrium of reversible reactions as well as the advantages of DNA encoded compounds for manipulation/detection, thus leads to enhanced signal-to-noise ratio of the selection process and higher library quality. However, the library dynamics are caused by the weak interactions between the DNA strands, which also result in relatively low affinity of the bidentate interaction, as compared to a stable DNA duplex. To take advantage of both stably assembled dual-pharmacophore libraries and EDCCLs, we extended the concept of EDCCLs to heat-induced EDCCLs (hi-EDCCLs), in which the heat-induced recombination process of stable DNA duplexes and affinity capture are carried out separately. To replace the extremely laborious and repetitive manual process, a fully automated device will facilitate the use of DECL in drug discovery. Herein we describe a novel lab-on-a-chip platform for high throughput drug discovery with hi-EDCCL. A microfluidic system with integrated actuation was designed which is able to provide a continuous sample circulation by reducing the volume to a minimum. It consists of a cooled and a heated chamber for constant circulation. The system is capable to generate stable temperatures above 75 °C in the heated chamber to melt the double strands of the DNA and less than 15 °C in the cooled chamber, to reanneal the shuffled library. In the binding chamber (the cooled chamber) specific retaining structures are integrated. These hold back beads functionalized with the target protein, while the chamber is continuously flushed with library molecules. Afterwards the whole system can be flushed with buffer to wash out unspecific bound molecules. Finally the protein-loaded beads with attached molecules can be eluted for further investigation
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Parameswaran, Aishwarya. "DNA Encoded Libraries (DEGL) of Glycan Antigens to Detect Antibodies: An Approach Towards Next Generation Functional Glycomics." 2017. http://scholarworks.gsu.edu/chemistry_theses/101.

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Structure and functional study of glycans are highly challenging due to the difficulties in analyzing glycans and limited availability of samples for study. These limitations could be resolved by attaching DNA barcode to the glycan, which virtually represent glycan in further application, by increasing the sensitivity of detection by polymerase chain reaction (PCR), requiring minimal samples for analysis. Assuming bigger arena of DNA Encoded Glycan Libraries (DEGL) in future, we propose here a method for uniquely coding all glycans using computer program that can convert the structural information of glycans to DNA barcode. A unique and universal coding for glycans will benefit both synthesis and analysis of DEGLs. As a proof of principle study, a small DNA Encoded Glycan Library (DEGL) of blood and globo series glycan antigen and its application was demonstrated in detecting blood group and breast cancer from plasma.
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Books on the topic "DNA-encoded libraries"

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Brunschweiger, Andreas, and Damian W. Young, eds. DNA-Encoded Libraries. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-031-18629-5.

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Israel, David, and Yun Ding, eds. DNA-Encoded Chemical Libraries. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2545-3.

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Brunschweiger, Andreas, and Damian W. Young. DNA-Encoded Libraries. Springer International Publishing AG, 2022.

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Ding, Yun, and David Israel. DNA-Encoded Chemical Libraries. Springer, 2022.

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Jr, Robert A. Goodnow. A Handbook for DNA-Encoded Chemistry: Theory and Applications for Exploring Chemical Space and Drug Discovery. Wiley, 2014.

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Book chapters on the topic "DNA-encoded libraries"

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Mannocci, Luca. "DNA-encoded Chemical Libraries." In Diversity-Oriented Synthesis, 353–99. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2013. http://dx.doi.org/10.1002/9781118618110.ch11.

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Franzini, Raphael M. "DNA-Encoded Compound Libraries." In Drug Discovery and Development, 71–97. Third edition. | Boca Raton, Florida : CRC Press, 2019. |: CRC Press, 2019. http://dx.doi.org/10.1201/9781315113470-7.

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Scheuermann, Jörg, and Dario Neri. "Dual-Pharmacophore DNA-Encoded Chemical Libraries." In A Handbook for DNA-Encoded Chemistry, 349–55. Hoboken, NJ: John Wiley & Sons, Inc., 2014. http://dx.doi.org/10.1002/9781118832738.ch15.

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So, Sung-Sau. "Enumeration and Visualization of Large Combinatorial Chemical Libraries." In A Handbook for DNA-Encoded Chemistry, 247–79. Hoboken, NJ: John Wiley & Sons, Inc., 2014. http://dx.doi.org/10.1002/9781118832738.ch12.

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Creaser, Steffen P., and Raksha A. Acharya. "Exercises in the Synthesis of DNA-Encoded Libraries." In A Handbook for DNA-Encoded Chemistry, 123–51. Hoboken, NJ: John Wiley & Sons, Inc., 2014. http://dx.doi.org/10.1002/9781118832738.ch6.

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Kollmann, Christopher S. "Quantitation of DNA-Encoded Libraries by qPCR." In Methods in Molecular Biology, 135–42. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2545-3_17.

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Liu, Jian, and You Li. "Next Generation Sequencing of DNA-Encoded Libraries." In Methods in Molecular Biology, 173–85. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2545-3_21.

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Wartchow, Charles. "Theoretical Considerations of the Application of DNA-Encoded Libraries to Drug Discovery." In A Handbook for DNA-Encoded Chemistry, 213–30. Hoboken, NJ: John Wiley & Sons, Inc., 2014. http://dx.doi.org/10.1002/9781118832738.ch10.

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Li, Yizhou, Zheng Zhu, and Xiaoyu Li. "Chapter 8. Drug Discovery by DNA-encoded Libraries." In New Frontiers in Chemical Biology, 258–302. Cambridge: Royal Society of Chemistry, 2010. http://dx.doi.org/10.1039/9781849732178-00258.

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Li, You. "Translation of DNA Sequence to Chemical Structure in DNA-Encoded Libraries." In Methods in Molecular Biology, 187–94. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2545-3_22.

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Conference papers on the topic "DNA-encoded libraries"

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Grünzner, S., F. V. Reddavide, C. Steinfelder, M. Cui, M. Busek, U. Klotzbach, Y. Zhang, and F. Sonntag. "Lab-on-a-chip platform for high throughput drug discovery with DNA-encoded chemical libraries." In SPIE BiOS, edited by Bonnie L. Gray and Holger Becker. SPIE, 2017. http://dx.doi.org/10.1117/12.2253840.

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Ichinose, A., R. E. Bottenus, K. R. Loeb, and E. W. Davie. "ISOLATION AND CHARACTERIZATION OF THE GENES FOR THE a AND b SUBUNITS OF HUMAN COAGULATION FACTOR XIII." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644652.

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Factor XIII (plasma transglutaminase, fibrin stabilizing factor) is a plasma protein that plays an important role in the final stages of blood coagulation and fibrinolysis. The molecule occurs in blood as a tetramer (a2b2) consisting of two a. subunits and two b subunits. Recently, we have determined the amino acid sequences for both the a. and b subunits of human factor XIII by a combination of cDNA cloning and amino acid sequence analysis. cDNAs coding for the a (3.8 Kb) and b (2.2 Kb) subunits were used for the screening of human genomic DNA libraries. Among 12 × 106 recombinant phage, ∼30 have been shown to contain the sequences for the a subunit and ∼10 have been shown to contain the gene for the b subunit of factor XIII. The clones coding for the a. subunit span ∼90 Kb and have been characterized by restriction mapping. Southern blotting, and DNA sequencing. Both 5’ and 3’ ends of the genomic clones correspond to the 5’ and 3’portions of the cDNA for the a.subunit of factor XIII. The DNA sequence revealed that the activation peptide released ^thrombin (amino acid residues 137), the first putative Ca2+ binding region (around residue 251), the active Site Cys (amino acid residue 314), and the second putative Ca2+ binding region (around residue 473) are encoded by separate exons. Accordingly, the intervening sequences may separate the a subunit into functional and structural domains. The gene organization for the b subunit will also be presented. (Supported by NIH Grant HL 16919.)
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Chung, D. W., R. Asakai, and E. W. Davie. "THE ORGANIZATION OF THE HUMAN FACTOR XI GENE: CORRELATION OF INTRON AND EXON LOCATIONS WITH STRUCTURAL DOMAINS." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1642802.

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Factor XI (plasma thromboplastin antecedent) is a plasma glycoprotein that participates in the contact activation of blood coagulation. In the present study, the organization of the gene for human factor XI has been elucidated. The gene for human factor XI has been isolated from two independent human genomic λ phage libraries using a full length cDNA for human factor XI as a hybridization probe. Four overlapping recombinant λ phage containing the human factor XI gene have been isolated and characterized. Restriction mapping, Southern blotting and hybridization studies indicate that the entire gene for human factor XI is 25 kilobases in length. Overlapping regions of the gene have been subcloned and the DNA sequence of selective regions has been determined. These results show that the gene for factor XI is composed of 15 exons and 14 introns. Exon I codes for the 5′ noncoding sequences and exon II codes for the signal peptide of 18 amino acid residues. The four tandem repeats that constitute the heavy chain of factor XIa are each encoded by two consecutive exons (exons III and IV, V and VI, VII and VIII, IX and X). The location of the introns and the junction type among these four tandem repeats are strictly conserved. Exon XI, XII, XIII, XIV and XV code for the light chain of factor XIa that contains the serine protease part of the molecule. The location of the introns and the junction types in this region of the gene are identical to those in the corresponding regions of the genes for human tissue plasminogen activator and porcine urokinase. These results show that gene duplication and exon shuffling play a significant role in the evolution of the human factor XI gene. (Supported in part by NIH Grant HL 16919 and AHA Grant 82-221.)
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