Relevant bibliographies by topics / DNA binding

Academic literature on the topic 'DNA binding'

Author: Grafiati
Published: 4 June 2021
Last updated: 7 September 2023

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Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Journal articles on the topic "DNA binding":

1

PRENDERGAST, GEORGE, and EDWARD B. ZIFF. "DNA-binding motif." Nature 341, no. 6241 (October 1989): 392. http://dx.doi.org/10.1038/341392a0.

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Zilliacus, J., K. Dahlman-Wright, A. Wright, J. A. Gustafsson, and J. Carlstedt-Duke. "DNA binding specificity of mutant glucocorticoid receptor DNA-binding domains." Journal of Biological Chemistry 266, no. 5 (February 1991): 3101–6. http://dx.doi.org/10.1016/s0021-9258(18)49959-0.

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ZILLIACUS, JOHANNA, ANTHONY P. H. WRIGHT, ULF NORINDER, and JAN-ÅKE GUSTAFSSON. "DNA-Binding Specificity of Mutant Glucocorticoid Receptor DNA-Binding Domains." Annals of the New York Academy of Sciences 684, no. 1 Zinc-Finger P (June 1993): 253–56. http://dx.doi.org/10.1111/j.1749-6632.1993.tb32301.x.

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Dashwood, R. H., R. D. Combes, and J. Ashby. "DNA-binding studies with 6BT and 5I: implications for DNA-binding/carcinogenicity and DNA-binding/mutagenicity correlations." Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 198, no. 1 (March 1988): 61–68. http://dx.doi.org/10.1016/0027-5107(88)90040-1.

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Nafisi, Shohreh, Maryam Adelzadeh, Zeinab Norouzi, and Mohammad Nabi Sarbolouki. "Curcumin Binding to DNA and RNA." DNA and Cell Biology 28, no. 4 (April 2009): 201–8. http://dx.doi.org/10.1089/dna.2008.0840.

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Nafisi, Shohreh, Mahyar Bonsaii, Valerie Alexis, and James Glick. "Binding of 2-Acetylaminofluorene to DNA." DNA and Cell Biology 30, no. 11 (November 2011): 955–62. http://dx.doi.org/10.1089/dna.2011.1229.

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Kashanian, Soheila, Sanaz Javanmardi, Arash Chitsazan, Kobra Omidfar, and Maliheh Paknejad. "DNA-Binding Studies of Fluoxetine Antidepressant." DNA and Cell Biology 31, no. 7 (July 2012): 1349–55. http://dx.doi.org/10.1089/dna.2012.1657.

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HOLTH, LAUREL T., JIAN-MIN SUN, AMANDA S. COUTTS, LEIGH C. MURPHY, and JAMES R. DAVIE. "Estrogen Receptor Diminishes DNA-Binding Activities of Chicken GATA-1 and CACCC-Binding Proteins." DNA and Cell Biology 16, no. 12 (December 1997): 1477–82. http://dx.doi.org/10.1089/dna.1997.16.1477.

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Rasimas, Joseph J., Anthony E. Pegg, and Michael G. Fried. "DNA-binding Mechanism ofO6-Alkylguanine-DNA Alkyltransferase." Journal of Biological Chemistry 278, no. 10 (December 20, 2002): 7973–80. http://dx.doi.org/10.1074/jbc.m211854200.

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RICH, ALEXANDER. "Z-DNA and Z-DNA-binding proteins." Biochemical Society Transactions 14, no. 2 (April 1, 1986): 202. http://dx.doi.org/10.1042/bst0140202.

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Journal articles Dissertations / Theses Books

Dissertations / Theses on the topic "DNA binding":

1

Pérez-Breva, Luis. "DNA binding economies." Thesis, Massachusetts Institute of Technology, 2007. http://hdl.handle.net/1721.1/42057.

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Abstract:
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2007.
This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Includes bibliographical references (p. 195-204).
This thesis develops a new scalable modeling framework at the interface of game theory and machine learning to recover economic structures from limited slices of data. Inference using economic models has broad applicability in machine learning. Economic structures underlie a surprisingly broad array of problems including signaling and molecular control in biology, drug development, neural structures, distributed control, recommender problems, social networking, as well as market dynamics. We demonstrate the framework with an application to genetic regulation. Genetic regulation determines how DNA is read and interpreted, is responsible for cell specialization, reaction to drugs, metabolism, etc. Improved understanding of regulation has potential to impact research on genetic diseases including cancer. Genetic regulation relies on coordinate binding of regulators along DNA. Understanding how binding arrangements are achieved and their effect on regulation is challenging since it is not always possible to study regulatory processes in isolation. Indeed, observing the action of regulators is an experimental and computational challenge. We need causal genome-wide models that can work with existing high-throughput observations. We abstract DNA binding as an economy and develop fast algorithms to predict average binding arrangements as competitive equilibria. The framework supports viewing regulation as a succession of regulatory states. We complete the framework with algorithms to infer causal structure from high-throughput observations. Learning here deviates from work in learning in games, it is closer to the economic theory of revealed preferences. Our algorithms predict the effect of experimental perturbations and can be used to refine experimental hypotheses. We show that the economic approach reproduces known behavior of a genetic switch (-phage), and that it can complete the map of coordinate binding in yeast.
by Luis Pérez-Breva.
Ph.D.
2

Umurtak, H. B. "Studies on DNA-binding peptides]." Thesis, University of Southampton, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.235192.

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Pokhrel, Pujan. "Prediction of DNA-Binding Proteins and their Binding Sites." ScholarWorks@UNO, 2018. https://scholarworks.uno.edu/honors_theses/114.

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Abstract:
DNA-binding proteins play an important role in various essential biological processes such as DNA replication, recombination, repair, gene transcription, and expression. The identification of DNA-binding proteins and the residues involved in the contacts is important for understanding the DNA-binding mechanism in proteins. Moreover, it has been reported in the literature that the mutations of some DNA-binding residues on proteins are associated with some diseases. The identification of these proteins and their binding mechanism generally require experimental techniques, which makes large scale study extremely difficult. Thus, the prediction of DNA-binding proteins and their binding sites from sequences alone is one of the most challenging problems in the field of genome annotation. Since the start of the human genome project, many attempts have been made to solve the problem with different approaches, but the accuracy of these methods is still not suitable to do large scale annotation of proteins. Rather than relying solely on the existing machine learning techniques, I sought to combine those using novel “stacking technique” and used the problem-specific architectures to solve the problem with better accuracy than the existing methods. This thesis presents a possible solution to the DNA-binding proteins prediction problem which performs better than the state-of-the-art approaches.
4

Sando, Shinsuke. "RATIONAL DESIGN OF DNA-BINDING MOLECULES AND DNA PHOTOCLEAVERS." 京都大学 (Kyoto University), 2001. http://hdl.handle.net/2433/150700.

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Komori, Hirofumi. "Structural studies on DNA-binding proteins : DNA replication initiator and DNA photolyase." 京都大学 (Kyoto University), 2002. http://hdl.handle.net/2433/150005.

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Geary, Joella Suzanne. "DNA binding proteins of archaeal viruses." Thesis, Montana State University, 2008. http://etd.lib.montana.edu/etd/2008/geary/GearyJ1208.pdf.

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Archaea are single-celled organisms comprising the third domain of life. The Achaeal species Sulfolobus are infected by the Fuselloviridae virus family: SSV1, SSV2, SSV-RH, and SSV-K. The genomes of these viruses have been annotated and contain putative DNA-binding proteins. The purpose of this work is to identify DNA sequences bound by the SSV1 putative DNA-binding protein C43. C43 protein was cloned, expressed, purified, and assayed at various temperatures for interaction with three SSV1 DNA sequences. C43 binds the T5-promoter, T6-promoter, and C43-promoter sequentially and consistently. Additionally, C43 protein is functional at temperatures of 50°C and 65°C. Thus, C43 appears to be an important regulator of the Fuselloviridae SSV1 viral genome.
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Bisset, Louise Clair. "Fluorescence of a DNA-binding protein." Thesis, University of Newcastle Upon Tyne, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.320129.

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Bullen, Gemma Anne. "Anthracene tagged biomolecules for DNA binding." Thesis, University of Birmingham, 2015. http://etheses.bham.ac.uk//id/eprint/6369/.

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Within this thesis, the use of anthracene to perform various applications within biomolecules is assessed. Anthracene displays two interesting photo properties which make it an appealing molecule for incorporation; fluorescence and photodimerisation. The former is utilised to develop a single nucleotide polymorphism detection assay which is shown to allow for determination of the base present in a complementary strand of DNA. In addition to this, the photodimerisation properties of anthracene are used within a protein for the first time. This is utilised to develop a photoswitched binding protein, allowing for control of DNA binding of the protein. Further to this, the photodimerisation properties are utilised within oligonucleotides to achieve structural control of a G-quadruplex as well as photo-triggered release of single stranded DNA.
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Weinberg, Richard Lawrence. "The binding of p53 to DNA." Thesis, University of Cambridge, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.615988.

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Walavalkar, Ninad. "Structural basis of DNA binding complexes." VCU Scholars Compass, 2013. http://scholarscompass.vcu.edu/etd/3162.

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Abstract:
The nucleosome remodeling and deacetylase (NuRD) complex is an abundant deacetylase complex, which couples histone deacetylation and chromatin remodeling ATPase activities, and has a broad cellular and tissue distribution. Although the working model of how this complex forms and functions is not well known, we have demonstrated that the coiled-coil interaction between two proteins (MBD2 and p66α) is critical for DNA methylation dependent gene silencing in vivo. Chapter one: ‘Unique features of the anti-parallel, heterodimeric coiled-coil interaction between methyl-cytosine binding domain 2 (MBD2) homologues and p66α dictate high affinity binding’ describes this unique coiled coil interaction. Coiled-coils were studied using a variety of biophysical techniques including analytical ultracentrifugation (AUC), isothermal titration calorimetry (ITC) and circular dichroism (CD). Results were compared across homologues and mutation studies were carried out to test our hypotheses. The studies reported in this chapter add to our understanding of coiled-coil interaction and thereby facilitate development of small peptide based drugs which target such interactions in nature.A number of proteins have been identified in humans that specifically bind to methylated CpG via a methyl binding domain (MBD). The human genome encodes at least five MBD proteins: MeCP2 and MBD1 through MBD4, which are homologous in their methyl binding domains but not many similarities are seen outside the MBD. Out of the five MBDs, MBD4 has a c-terminal glycosylase domain through which it recognizes mCpG.TpG mismatch and is important for base excision repair system. Chapter two: ‘Dynamic behavior of MBD4 in methylated DNA recognition’ focuses on MBD4 and its preference for DNA methylation mark. Techniques of surface plasmon resonance (SPR), nuclear magnetic resonance (NMR) spectroscopy are used to study binding affinity for variations of methylated DNA mark. Chemical exchange studies are used to demonstrate how MBD4 scans for methylation mark and these studies have added a new dimension to our understanding of how MBD proteins ‘read’ DNA methylation marks. Chapter three: ‘Solving the solution structure of MBD domain of MBD4 on methylated DNA by NMR’ describes a process of structure determination using NMR spectroscopy. The focus of this chapter is not on developing a new technique but rather on using current resources to solve a protein structure, which can be used to further understand our biological system. Here, I have discussed the workflow used to determine a final three-dimensional structure starting from sample preparation, data collection, data analysis to structure calculation.
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Books on the topic "DNA binding":

1

Oliveira, Marcos T., ed. Single Stranded DNA Binding Proteins. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1290-3.

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Keck, James L., ed. Single-Stranded DNA Binding Proteins. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-032-8.

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Waring, Michael J., ed. Sequence-specific DNA Binding Agents. Cambridge: Royal Society of Chemistry, 2006. http://dx.doi.org/10.1039/9781847555304.

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J, Waring Michael, and Royal Society of Chemistry (Great Britain), eds. Sequence-specific DNA binding agents. Cambridge: RSC Publishing, 2006.

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K, Docherty, ed. Gene transcription: DNA binding proteins. Chichester: Wiley, 1996.

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Wibley, Jane Elizabeth. DNA binding proteins: Structures and predictions. Manchester: University of Manchester, 1996.

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Kevin, Docherty, ed. Gene transcription: DNA binding proteins: Essential techniques. Chichester: Wiley, 1996.

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Preston, Nicola Susan. Structure and DNA binding of HMG boxes. Portsmouth: Universityof Portsmouth, School of Biological Sciences, 1996.

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Cruickshank, Jennifer. The DNA binding mechanism of the Epstein-Barr origin binding protein, EBNA1. Ottawa: National Library of Canada, 1999.

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Rodgers, David S. Circular dichroism: Theory and spectroscopy. Hauppauge, N.Y: Nova Science Publishers, 2011.

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Book chapters on the topic "DNA binding":

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ANITA, C., H. BIGGER, and ANTHONY DIPPLE. "Carcinogen-DNA Binding." In ACS Symposium Series, 187–208. Washington, D.C.: American Chemical Society, 1985. http://dx.doi.org/10.1021/bk-1985-0277.ch015.

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Zhitkovich, Anatoly. "Chromium Binding to DNA." In Encyclopedia of Metalloproteins, 630–35. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-1533-6_3.

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Marceau, Aimee H. "Functions of Single-Strand DNA-Binding Proteins in DNA Replication, Recombination, and Repair." In Single-Stranded DNA Binding Proteins, 1–21. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-032-8_1.

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Lambert, Bernard, and Jean-Bernard Le Pecq. "Pharmacology of DNA Binding Drugs." In DNA—Ligand Interactions, 141–57. Boston, MA: Springer US, 1987. http://dx.doi.org/10.1007/978-1-4684-5383-6_9.

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Lu, Duo. "Analyzing Interactions Between SSB and Proteins by the Use of Fluorescence Anisotropy." In Single-Stranded DNA Binding Proteins, 155–59. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-032-8_10.

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Walsh, Brian W., Justin S. Lenhart, Jeremy W. Schroeder, and Lyle A. Simmons. "Far Western Blotting as a Rapid and Efficient Method for Detecting Interactions Between DNA Replication and DNA Repair Proteins." In Single-Stranded DNA Binding Proteins, 161–68. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-032-8_11.

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Page, Asher N., and Nicholas P. George. "Methods for Analysis of SSB–Protein Interactions by SPR." In Single-Stranded DNA Binding Proteins, 169–74. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-032-8_12.

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Inoue, Jin, and Tsutomu Mikawa. "Use of Native Gels to Measure Protein Binding to SSB." In Single-Stranded DNA Binding Proteins, 175–82. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-032-8_13.

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Bernstein, Douglas A. "Identification of Small Molecules That Disrupt SSB–Protein Interactions Using a High-Throughput Screen." In Single-Stranded DNA Binding Proteins, 183–91. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-032-8_14.

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Hass, Cathy S., Ran Chen, and Marc S. Wold. "Detection of Posttranslational Modifications of Replication Protein A." In Single-Stranded DNA Binding Proteins, 193–204. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-032-8_15.

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Conference papers on the topic "DNA binding":

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Srhar, Sania, Amna Arshad, and Ahsan Raza. "Protien-DNA binding sites Prediction." In 2021 International Conference on Innovative Computing (ICIC). IEEE, 2021. http://dx.doi.org/10.1109/icic53490.2021.9692990.

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Bhardwaj, N., R. E. Langlois, Guijun Zhao, and Hui Lu. "Structure Based Prediction of Binding Residues on DNA-binding Proteins." In 2005 IEEE Engineering in Medicine and Biology 27th Annual Conference. IEEE, 2005. http://dx.doi.org/10.1109/iembs.2005.1617004.

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Fan, Yue, Mark A. Kon, and Charles DeLisi. "Ensemble Machine Methods for DNA Binding." In 2008 Seventh International Conference on Machine Learning and Applications. IEEE, 2008. http://dx.doi.org/10.1109/icmla.2008.114.

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Andersson, Johanna, Shiming Li, Per Lincoln, and Joakim Andréasson. "Light controlled DNA-binding of spiropyrans." In XIVth Symposium on Chemistry of Nucleic Acid Components. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 2008. http://dx.doi.org/10.1135/css200810305.

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Chang, Yao-Lin, Huai-Kuang Tsai, Cheng-Yan Kao, Yung-Chian Chen, and Jinn-Moon Yang. "Evolutionary conservation of DNA-contact residues in DNA-binding domains." In Second International Multi-Symposiums on Computer and Computational Sciences (IMSCCS 2007). IEEE, 2007. http://dx.doi.org/10.1109/imsccs.2007.24.

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Wong, Ka-Chun. "Data Analytics for Protein-DNA Binding Interactions." In 2015 IEEE International Conference on Systems, Man, and Cybernetics (SMC). IEEE, 2015. http://dx.doi.org/10.1109/smc.2015.278.

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Barash, Yoseph, Gal Elidan, Nir Friedman, and Tommy Kaplan. "Modeling dependencies in protein-DNA binding sites." In the seventh annual international conference. New York, New York, USA: ACM Press, 2003. http://dx.doi.org/10.1145/640075.640079.

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Swavey, Shawn, Rodd L. Williams, Zhenglai Fang, Matthew Milkevitch, and Karen J. Brewer. "DNA binding of supramolecular mixed-metal complexes." In Complex Adaptive Structures, edited by William B. Spillman, Jr. SPIE, 2001. http://dx.doi.org/10.1117/12.446779.

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Wang, You-Xin, Hong-Hong Fang, Zhong-Xin Xiao, Li-Juan Wu, Man-Shu Song, and Wei Wang. "Novel Method to Screen DNA Binding Proteins for a Given DNA Fragment." In 2015 International Conference on Medicine and Biopharmaceutical. WORLD SCIENTIFIC, 2016. http://dx.doi.org/10.1142/9789814719810_0093.

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Ihmels, Heiko, Katja Faulhaber, and Kathrin Wissel. "DNA-Binding and DNA-Photodamaging Properties of Indolo[2,3-b]-Quinolizinium Bromide." In The 4th International Electronic Conference on Synthetic Organic Chemistry. Basel, Switzerland: MDPI, 2000. http://dx.doi.org/10.3390/ecsoc-4-01906.

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Reports on the topic "DNA binding":

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Hanke, Andreas. DNA Conforming Dynamics and Protein Binding. Fort Belvoir, VA: Defense Technical Information Center, December 2006. http://dx.doi.org/10.21236/ada461014.

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Chiang, Shu-Yuan. DNA Binding Drugs Targeting the Regulatory DNA Binding Site of the ETS Domain Family Transcription Factor. Fort Belvoir, VA: Defense Technical Information Center, July 1998. http://dx.doi.org/10.21236/ada352305.

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Wood, Sheila J. Predictive Binding Parameters for DNA-DNA Association within a Fluid Stream. Fort Belvoir, VA: Defense Technical Information Center, July 1997. http://dx.doi.org/10.21236/ada328050.

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Hanke, Andreas. Regulation of DNA Metabolism by DNA-Binding Proteins Probed by Single Molecule Spectroscopy. Fort Belvoir, VA: Defense Technical Information Center, December 2006. http://dx.doi.org/10.21236/ada459264.

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Wang, Yong-Dong. DNA Binding Drugs Targeting the Regulatory DNA Binding Site of the ETS Domain Family Transcription Factor Associated With Human Breast Cancer. Fort Belvoir, VA: Defense Technical Information Center, July 2000. http://dx.doi.org/10.21236/ada392560.

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Wang, Yong-Dong. DNA Binding Drugs Targeting the Regulatory DNA Binding Site of the ETS Domain Family Transcription Factor Associated With Human Breast Cancer. Fort Belvoir, VA: Defense Technical Information Center, July 1999. http://dx.doi.org/10.21236/ada381309.

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Yaswen, Paul. Functional Analysis of BORIS, A Novel DNA Binding Protein. Fort Belvoir, VA: Defense Technical Information Center, April 2006. http://dx.doi.org/10.21236/ada448330.

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Yaswen, Paul. Functional Analysis of BORIS, a Novel DNA Binding Protein. Fort Belvoir, VA: Defense Technical Information Center, March 2005. http://dx.doi.org/10.21236/ada435433.

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Chen, Fu-Ming. Sequence-Specific and Synergistic Binding of Drugs to DNA. Fort Belvoir, VA: Defense Technical Information Center, October 1995. http://dx.doi.org/10.21236/ada306436.

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Chen, Fu-Ming. Sequence-Specific and Synergistic Binding of Drugs to DNA. Fort Belvoir, VA: Defense Technical Information Center, October 1999. http://dx.doi.org/10.21236/ada392011.

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