Nanoparticle‐Mediated DNA and Mrna Delivery
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Design of Nucleic Acid Strands with Long Low-Barrier Folding Pathways
Nat Comput DOI 10.1007/s11047-016-9587-9 Design of nucleic acid strands with long low-barrier folding pathways Anne Condon1 · Bonnie Kirkpatrick2 · Ján Maˇnuch1 © The Author(s) 2017. This article is published with open access at Springerlink.com Abstract A major goal of natural computing is to design fully developed, that exploit base pairing interactions of biomolecules, such as nucleic acid sequences, that can be nucleic acids. Prominent examples include DNA strand dis- used to perform computations. We design sequences of placement systems (DSDs) (Seelig et al. 2006) and RNA nucleic acids that are “guaranteed” to have long folding origami systems (Geary and Andersen 2014). Our work here pathways relative to their length. This particular sequences is motivated by the goal of computing with a single RNA with high probability follow low-barrier folding pathways sequence as the nucleic acids of the sequence interact with that visit a large number of distinct structures. Long fold- each other. ing pathways are interesting, because they demonstrate that RNA sequences form folded structures in which pairs of natural computing can potentially support long and com- nucleic acids biochemically bond to each other. These bonds plex computations. Formally, we provide the first scalable change the physical energy of the sequence, and a given designs of molecules whose low-barrier folding pathways, sequence prefers to assume low-energy folded structures. with respect to a simple, stacked pair energy model, grow Folding is a dynamic process, constrained by kinetics, dur- superlinearly with the molecule length, but for which all sig- ing which an RNA sequence will move through a sequence nificantly shorter alternative folding pathways have an energy of structures with each differing from the previous one by barrier that is 2 − times that of the low-barrier pathway for the addition or removal of a single base pair. -
Algorithms for Nucleic Acid Sequence Design
Algorithms for Nucleic Acid Sequence Design Thesis by Joseph N. Zadeh In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy California Institute of Technology Pasadena, California 2010 (Defended December 8, 2009) ii © 2010 Joseph N. Zadeh All Rights Reserved iii Acknowledgements First and foremost, I thank Professor Niles Pierce for his mentorship and dedication to this work. He always goes to great lengths to make time for each member of his research group and ensures we have the best resources available. Professor Pierce has fostered a creative environment of learning, discussion, and curiosity with a particular emphasis on quality. I am grateful for the tremendously positive influence he has had on my life. I am fortunate to have had access to Professor Erik Winfree and his group. They have been very helpful in pushing the limits of our software and providing fun test cases. I am also honored to have two other distinguished researchers on my thesis committee: Stephen Mayo and Paul Rothemund. All of the work presented in this thesis is the result of collaboration with extremely talented individuals. Brian Wolfe and I codeveloped the multiobjective design algorithm (Chapter 3). Brian has also been instru- mental in finessing details of the single-complex algorithm (Chapter 2) and contributing to the parallelization of NUPACK’s core routines. I would also like to thank Conrad Steenberg, the NUPACK software engineer (Chapter 4), who has significantly improved the performance of the site and developed robust secondary structure drawing code. Another codeveloper on NUPACK, Justin Bois, has been a good friend, mentor, and reliable coding partner. -
A Global Sampling Approach to Designing and Reengineering RNA
i “rnaensign” — 2017/7/1 — 22:02 — page 1 — #1 i i i Published online ?? Nucleic Acids Research, ??, Vol. ??, No. ?? 1–11 doi:10.1093/nar/gkn000 Aglobalsamplingapproachtodesigningandreengineering RNA secondary structures 1,2, 1, 3 1 1 Alex Levin ⇤,MieszkoLis ⇤,YannPonty ,CharlesW.O’Donnell ,SrinivasDevadas , 1,2, 1,2,4, Bonnie Berger †,J´erˆomeWaldisp¨uhl † 1 Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA. and 2 Department of Mathematics, MIT, Cambridge, MA 02139, USA. and 3 Laboratoire d’Informatique, Ecole´ Polytechnique, Palaiseau, France. and 4 School of Computer Science, McGill University, Montreal, QC H2A 3A7, Canada. Received ??; Revised ??; Accepted ?? ABSTRACT mechanisms (1), reprogramming cellular behavior (2), and designing logic circuits (3). The development of algorithms for designing artificial Here, we aim to design RNA sequences that fold into RNA sequences that fold into specific secondary structures specific secondary structures (a.k.a. inverse folding). Even has many potential biomedical and synthetic biology in this case, efficient computational formulations remain applications. To date, this problem remains computationally difficult, with no exact solutions known. Instead, the solutions difficult, and current strategies to address it resort available today rely on local search strategies and heuristics. to heuristics and stochastic search techniques. The Indeed, the computational difficulty of the RNA design most popular methods consist of two steps: First a problem was proven by M. Schnall-Levin et al. (4). random seed sequence is generated; next, this seed is One of the first and most widely known programs for progressively modified (i.e. mutated) to adopt the desired the RNA inverse folding problem is RNAinverse (5). -
Chad A. Mirkin, Ph.D
Chad A. Mirkin, Ph.D. Controlling the architecture of bio- or nonbio-materials in nanometer length scale and the application of such structures in the development of new technologies in diverse areas, such as chemical and biological sensing, gene regulation, lithography, catalysis, optics, and energy generation, storage, and conversion, are recognized to be one of the hottest research area. Chad Mirkin, who is a chemist, chemical engineer, and world-renowned expert in nanoscience, has contributed significantly in this field. He has pioneered the use of nanoparticle-biomolecule conjugates as synthons in materials science, their novel applications to extra- and intra-cellular diagnostic and therapeutic tools, and Dip-Pen Nanolithography. A common strategy used by Mirkin’s group is the use of the unique properties of spherical nucleic acids (SNAs), spherical arrangements of nucleic acids with or without organic or inorganic nanoparticle cores, to enable the synthesis of novel materials and development of highly sensitive probes for chemical and medical purposes. He is one of today’s most celebrated chemists for his discovery and development of SNAs and many medical diagnostic and therapeutic technologies, the invention of Dip-Pen Nanolithography (recognized by National Geographic as one of the top 100 scientific discoveries that changed the world), and significant contributions to supramolecular chemistry, nanoelectronics, and nanooptics. He is the author of over 700 manuscripts and over 1000 patents worldwide (over 300 issued), and the founder of six companies including Nanosphere, Nanolnk, AuraSense, Exicure, TERA-print, and CDJ, which are commercializing nanotechnology applications in the life science and semiconductor industries. He was an eight-year Member of the President’s Council of Advisors on Science & Technology (PCAST, Obama Administration), and the only chemist to be elected to all three US National Academies. -
Remarks by the Chair Chemistry Department
Chemistry Department Newsletter Summer 2004 Volume 2 http://www.dickinson.edu/departments/chem Remarks by the Chair Professor David Crouch Remarks by the Chair …..1 The Chemistry Department at Dickinson has enjoyed a most exciting year! New academic initiatives, major grants received, visiting faculty, Faculty Reports………2-4 renovations to Althouse and planning for the next phase of construction at Scholarly Research…….4-5 Dickinson have been part of the ways we have spent our time outside of the Department News……...5-7 classroom. The chemistry class of 2004 is moving on to some prestigious graduate and professional programs. One colleague was promoted to full 2004 Department Awards..7 professor and another has become a first time parent. A chemistry alum Class of 2004………..….…8 visited in the fall to tell us of his groundbreaking work in nanotechnology Recent Grad Spotlight…8-9 and returned in May to be honored by his alma mater with an honorary degree. This newsletter will fill in many of these details. But I’d like to Alumni News…………10-11 highlight three of them. Over the last few years, the possibility of developing an interdisciplinary major in neuroscience has been the subject of informal discussions around campus. In the fall, a committee was formed to formally prepare a proposed neuroscience major and, given chemistry’s role as the central science, it’s not surprising that two members of the chemistry department were involved. In the spring semester, the new major was officially adopted and the first neuroscience majors are being declared at Dickinson. The major consists of courses in psychology, biology and chemistry and new neuroscience courses at the 100 and 400 level are in development. -
(12) United States Patent (10) Patent No.: US 7.058,515 B1 Selifonov Et Al
US007058515B1 (12) United States Patent (10) Patent No.: US 7.058,515 B1 Selifonov et al. (45) Date of Patent: *Jun. 6, 2006 (54) METHODS FOR MAKING CHARACTER (56) References Cited STRINGS, POLYNUCLEOTIDES AND POLYPEPTIDES HAVING DESRED CHARACTERISTICS U.S. PATENT DOCUMENTS 4.959,312 A 9, 1990 Sirokin (75) Inventors: Sergey A. Selifonov, Los Altos, CA 4,994,379 A 2/1991 Chang (US); Willem P. C. Stemmer, Los 5,023,171 A 6, 1991 Ho et al. ....................... 435/6 Gatos, CA (US); Claes Gustafsson, 5,043,272 A 8/1991 Hartly et al. Belmont, CA (US); Matthew Tobin, 5,066,584 A 11/1991 Gyllensten et al. San Jose, CA (US); Stephen del 5,264,563 A 11/1993 Huse Cardayre, Belmont, CA (US); Phillip SE A Rhen A. Patten, Menlo Park, CA (US); 3.) A 96 MTS al. Jeremy Minshull, Menlo Park, CA 5.512.463 A 4/1996 Stemmer ................... 435,912 (US); Lorraine J. Giver, Sunnyvale, 5.514.588 A 5/1996 Varadaraj.................... 435/262 CA (US) 5,519,319 A 5/1996 Smith et al. 5,521,077 A 5/1996 Kholsa et al. (73) Assignee: Maxygen, Inc., Redwood City, CA 5,565,350 A 10, 1996 Kmiec (US) 5,580,730 A 12/1996 Okamoto 5,605,793 A 2/1997 Stemmer ....................... 435/6 (*) Notice: Subject to any disclaimer, the term of this 5,612.205 A 3/1997 Kay et al. patent is extended or adjusted under 35 3. 6. 3. Site U.S.C. 154(b) by 0 days. 5,717,085w - A 2f1998 Little et al.a This patent is Subject to a terminal dis- 29, Stil 435/6 claimer. -
A Rule-Based Modelling and Simulation Tool for DNA Strand Displacement Systems
This is an electronic reprint of the original article. This reprint may differ from the original in pagination and typographic detail. Gautam, Vinay; Long, Shiting; Orponen, Pekka RuleDSD: A rule-based modelling and simulation tool for DNA strand displacement systems Published in: Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies DOI: 10.5220/0008979101580167 Published: 01/01/2020 Document Version Peer reviewed version Published under the following license: CC BY-NC-ND Please cite the original version: Gautam, V., Long, S., & Orponen, P. (2020). RuleDSD: A rule-based modelling and simulation tool for DNA strand displacement systems. In E. De Maria, A. Fred, & H. Gamboa (Eds.), Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies: Volume 3 BIOINFORMATICS (pp. 158-167) https://doi.org/10.5220/0008979101580167 This material is protected by copyright and other intellectual property rights, and duplication or sale of all or part of any of the repository collections is not permitted, except that material may be duplicated by you for your research use or educational purposes in electronic or print form. You must obtain permission for any other use. Electronic or print copies may not be offered, whether for sale or otherwise to anyone who is not an authorised user. Powered by TCPDF (www.tcpdf.org) RuleDSD: A Rule-based Modelling and Simulation Tool for DNA Strand Displacement Systems Vinay Gautam a, Shiting Long and Pekka Orponen b Department of Computer Science, Aalto University, 00076 Aalto, Finland fvinay.gautam, shiting.long, pekka.orponeng@aalto.fi Keywords: DNA Strand Displacement, DSD Modelling and Simulation, PySB, Rule-based Model, BioNetGen. -
Design of Nucleic Acid Sequences for DNA Computing Based on a Thermodynamic Approach
Title Design of nucleic acid sequences for DNA computing based on a thermodynamic approach Author(s) Tanaka, Fumiaki; Kameda, Atsushi; Yamamoto, Masahito; Ohuchi, Azuma Nucleic Acids Research, 33(3), 903-911 Citation https://doi.org/10.1093/nar/gki235 Issue Date 2005 Doc URL http://hdl.handle.net/2115/64504 Type article File Information gki235.pdf Instructions for use Hokkaido University Collection of Scholarly and Academic Papers : HUSCAP Published online February 8, 2005 Nucleic Acids Research, 2005, Vol. 33, No. 3 903–911 doi:10.1093/nar/gki235 Design of nucleic acid sequences for DNA computing based on a thermodynamic approach Fumiaki Tanaka1,*, Atsushi Kameda2, Masahito Yamamoto1,2 and Azuma Ohuchi1,2 1Graduate School of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo 060-8628, Japan and 2CREST, Japan Science and Technology Corporation, 4-1-8, Honmachi, Kawaguchi, Saitama, 332-0012, Japan Received October 19, 2004; Revised and Accepted January 20, 2005 ABSTRACT order to satisfy the constraints based on the physicochemical properties of nucleic acids. In particular, it is essential to We have developed an algorithm for designing prevent undesired hybridization. In DNA computing, multiple multiple sequences of nucleic acids that have a sequences need to be designed that do not hybridize non- uniform melting temperature between the sequence specifically with each other (10,11), while in RNA secondary and its complement and that do not hybridize non- structure design, a single sequence needs to be designed that specifically with each other based on the minimum folds into the desired secondary structure (12–15). For free energy (DGmin). -
2013 CIRC Poster Session Abstracts
3rd Annual Center for Integrated Research Computing Poster Session! May 10, 2013 2013 Annual Poster Session ! 1 3rd Annual Center for Integrated Research Computing Poster Session! May 10, 2013 Computational Design and Characterization of 2-D tendency to cross- and self-hybridize. These features are observed in Photonic Crystal Geometries for Biosensing RNA sequences with known structure. We demonstrate that pre- James E. Baker and Benjamin L. Miller selected sequences accelerate the design of structures that are mimics Physics and Astronomy of biologically relevant structures. This is implemented as a new Dermatology structure design component of RNAstructure (http:// Biochemistry and Biophysics rna.urmc.rochester.edu/RNAstructure.html). This work is a Biomedical Engineering collaboration with Celadon Laboratories, Inc. (http:// The importance of early disease diagnosis both for initiating www.celadonlabs.com/). successful clinical treatment and preventing disease transmission continues to drive the development of rapid, ultrasensitive, label-free Next Generation Sequence Analysis of the Transcriptional biosensors. Sensors based on two-dimensional photonic bandgap Response to Neonatal Hyperoxia crystal structures, in particular, have the potential for single- Soumyaroop Bhattacharya, Chin-Yi Chu, Zhongyang Zhou, Min Yee, pathogen detection capabilities. In order to achieve such high Ashley M. Lopez, Valerie A. Lunger, Bradley Buczynski, Gloria S. sensitivity, the geometric structure of the photonic crystal must be Pryhuber, Michael A. O’Reilly, and Thomas J. Mariani designed in a way that pathogen binding is evident in the optical Pediatrics transmission spectrum of the crystal. Computational modeling methods allow us to simulate the electric field profiles and Rationale: Bronchopulmonary Dysplasia (BPD) is a major transmission spectra that we expect to observe for different photonic complication of preterm birth associated with significant morbidity. -
2018 FACULTY RECOGNITION DINNER the Honorees
The 31st Annual FACULTY RECOGNITION DINNER Kellogg Global Hub October 25, 2018 The 31st Annual FACULTY RECOGNITION DINNER is hosted by President Morton Schapiro and Provost Jonathan Holloway. It honors members of the Northwestern faculty who have brought distinction to the University by earning important external recognition in the past year. The multidisciplinary Faculty Honors Committee reviewed award recipients identified by the deans and department chairs, selecting the most prestigious awards for University recognition. Each subcommittee reviewed awards in its respective fields. Arts and Humanities Life and Medical Chris Abani Sciences Richard Kieckhefer Serdar Bulun Sara Maza Bob Lamb Saul Morson Amy Rosenzweig Natasha Trethewey Clyde Yancy Engineering and Physical Social Sciences Sciences David Austen-Smith Yonggang Huang Shari Diamond Bryna Kra Jamie Druckman Tobin Marks Jan Eberly Chad Mirkin Larry Hedges Greg Olson Joel Mokyr Monica Olvera de la Cruz John Rogers Richard Silverman The Honorees Jan Achenbach Zdeněk Bažant Honorary Doctor of Science ASME Medal Clarkson University American Society of Mechanical Engineers Emma Adam Foreign Member Lyle Spencer Research Award Academy of Athens Spencer Foundation Alfred M. Freudenthal Medal Erik Andersen American Society of Civil Engineers Faculty Early Career Development (CAREER) Award Karl Bilimoria National Science Foundation President Association for Academic Surgery Torben Andersen Fellow Michelle Birkett Society for Economic Measurement Inaugural Member National Academies of Sciences, -
Computer-Aided Design Software for Custom Nucleic Acid Nanostructures
Aalto University School of Science Degree Programme in Computer Science and Engineering Juhana Kommeri Computer-aided design software for cus- tom nucleic acid nanostructures Master's Thesis Espoo, October 2, 2016 Supervisors: Professor Mauri Kostiainen Advisor: Ph.D., Docent Veikko Linko Aalto University School of Science ABSTRACT OF Degree Programme in Computer Science and Engineering MASTER'S THESIS Author: Juhana Kommeri Title: Computer-aided design software for custom nucleic acid nanostructures Date: October 2, 2016 Pages: 72 Major: Media technology Code: T-111 Supervisors: Professor Mauri Kostiainen Advisor: Ph.D., Docent Veikko Linko The past decade has witnessed significant improvement in the techniques for as- sembling nucleic acid molecules into desired nanostructures. Today, structural DNA nanotechnology is seen as an attractive field by many multidisciplinary researchers who are impressed on the ability to position and control molecules with nanometer-level accuracy. The rationally designed DNA structures possess a tremendous potential in many bionanotechnological applications, and therefore the complexity of the designed structures is constantly increasing. To follow this trend and to enable straightforward design of such structures, powerful and ver- satile computer-aided design software and simulation tools are urgently needed. In this thesis various design software for creating nucleic acid nanostructures are assessed against predefined criteria. Using these software, exemplary DNA designs are created, and the features of the software are described. The aim of this comparison is to give a comprehensive overview of the currently available software and help a reader to decide which software to use for each particular purpose. In addition, a specific plugin for the most commonly used software caDNAno is created. -
AAAFM-UCLA, 2019 August Aug 19-22, 2019, UCLA Prof. Chad Mirkin
AAAFM-UCLA, 2019 August Aug 19-22, 2019, UCLA Prof. Chad Mirkin H-Index (Google Scholar): 163 Director, International Institute for Nanotechnology, Northwestern University Dr. Chad A. Mirkin is the Director of the International Institute for Nanotechnology, the George B. Rathmann Professor of Chemistry, Professor of Chemical and Biological Engineering, Professor of Biomedical Engineering, Professor of Materials Science and Engineering, and Professor of Medicine. Professor Mirkin is a chemist and a world renowned nanoscience expert, who is known for his development of nanoparticle-based biodetection schemes, the invention of Dip-Pen Nanolithography, and contributions to supramolecular chemistry, nanoelectronics and nanooptics. He is the author of over 380 manuscripts and over 350 patents and applications, and the founder of two companies, Nanosphere and NanoInk, which are commercializing nanotechnology applications in the life science and semiconductor industries. Currently, he is listed as the third most cited chemist in the world, and is the top most cited nanomedicine researcher in the world. At present, he is a member of the President Obama’s Council of Advisors for Science and Technology. Dr. Mirkin has been recognized for his accomplishments with over 50 national and international awards. These include the Lemelson-MIT Prize, Havinga Medal, the Gustavus John Esselen Award, the Biomedical Engineering Society’s Distinguished Achievement Award, a Department of Defense NSSEFF Award, the Pittsburgh Analytical Chemistry Award, the ACS