Cryo-EM Structure of a 3D DNA-Origami Object
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An RNA Holliday Junction? Structural and Dynamic Considerations of the Bacteriophage T4 Gene 60 Interruption
J. Mol. Biol. (1990) 213, 199-201 COMMUNICATIONS An RNA Holliday Junction? Structural and Dynamic Considerations of the Bacteriophage T4 Gene 60 Interruption Donald H. Burke-Agiiero and John E. Hearst Department of Chemistry University of California, Laboratory of Chemical Biodynamics Lawrence Berkeley Laboratory, Berkeley, CA 94720, U.S.A. (Received 20 June 1988; accepted 20 November 1989) A novel interrupted gene motif has been reported in which a 50-nucleotide insertion into bacteriophage T4 gene 60 appears to be present in the message at the time of translation, yet it is not translated. We present here a dynamic model for how translation may be occurring in the neighborhood of the interruption. The model involves formation of an RNA structure with similarities to a Holliday junction, followed by migration of the branch point in a strand exchange between message and interruption. The advantage of this model over previous ones is that at no time is a new tRNA required to pair with a discontinuous template. Huang et al. (1988) have reported a novel gene tion; the order of events is not important to this interruption motif in gene 60 of bacteriophage T4, model. More extensive branch migration is hindered in which a 50-nucleotide intervening segment is by the lack of sequence homology between the neither removed nor translated. The sequence of the message and the dumbbell outside these five bases. interruption suggests that it can be folded to bring When tRNA G~y moves into the P site, the template the translated codons on either side of the inter- 3' to Gly46 will now be in position to receive the ruption into close proximity (Fig. -
Holliday Junction Resolvases
Downloaded from http://cshperspectives.cshlp.org/ on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press Holliday Junction Resolvases Haley D.M. Wyatt and Stephen C. West London Research Institute, Cancer Research UK, Clare Hall Laboratories, South Mimms, Herts EN6 3LD, United Kingdom Correspondence: [email protected] Four-way DNA intermediates, called Holliday junctions (HJs), can form during meiotic and mitotic recombination, and their removal is crucial for chromosome segregation. A group of ubiquitous and highly specialized structure-selective endonucleases catalyze the cleavage of HJs into two disconnected DNA duplexes in a reaction called HJ resolution. These enzymes, called HJ resolvases, have been identified in bacteria and their bacteriophages, archaea, and eukaryotes. In this review, we discuss fundamental aspects of the HJ structure and their interaction with junction-resolving enzymes. This is followed by a brief discussion of the eubacterial RuvABC enzymes, which provide the paradigm for HJ resolvases in other organisms. Finally, we review the biochemical and structural properties of some well-char- acterized resolvases from archaea, bacteriophage, and eukaryotes. omologous recombination (HR) is an es- homologous strand as a template for DNA syn- Hsential process that promotes genetic di- thesis. Recombination then proceeds in one of versity during meiosis (see Lam and Keeney several different ways, some of which involve 2014; Zickler and Kleckner 2014). However, in second-end capture, such that the other resect- somatic cells, HR plays a key role in conserv- ed 30 end anneals to the displaced strand of the ing genetic information by facilitating DNA re- D-loop (Szostak et al. -
Programming Structured DNA Assemblies to Probe Biophysical Processes
Programming Structured DNA Assemblies to Probe Biophysical Processes The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Wamhoff, Eike-Christian et al. “Programming Structured DNA Assemblies to Probe Biophysical Processes.” Annual Review of Biophysics 48 (2019): 395-419 © 2019 The Author(s) As Published 10.1146/ANNUREV-BIOPHYS-052118-115259 Publisher Annual Reviews Version Author's final manuscript Citable link https://hdl.handle.net/1721.1/125280 Terms of Use Creative Commons Attribution-Noncommercial-Share Alike Detailed Terms http://creativecommons.org/licenses/by-nc-sa/4.0/ HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Annu Rev Manuscript Author Biophys. Author Manuscript Author manuscript; available in PMC 2020 February 22. Published in final edited form as: Annu Rev Biophys. 2019 May 06; 48: 395–419. doi:10.1146/annurev-biophys-052118-115259. Programming Structured DNA Assemblies to Probe Biophysical Processes Eike-Christian Wamhoff, James L. Banal, William P. Bricker, Tyson R. Shepherd, Molly F. Parsons, Rémi Veneziano, Matthew B. Stone, Hyungmin Jun, Xiao Wang, Mark Bathe Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; Abstract Structural DNA nanotechnology is beginning to emerge as a widely accessible research tool to mechanistically study diverse biophysical processes. Enabled by scaffolded DNA origami in which a long single strand of DNA is weaved throughout an entire target nucleic acid assembly to ensure its proper folding, assemblies of nearly any geometric shape can now be programmed in a fully automatic manner to interface with biology on the 1–100-nm scale. -
Bottom-Up Self-Assembly Based on DNA Nanotechnology
nanomaterials Review Bottom-Up Self-Assembly Based on DNA Nanotechnology 1, 1, 1 1 1,2,3, Xuehui Yan y, Shujing Huang y, Yong Wang , Yuanyuan Tang and Ye Tian * 1 College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, China; [email protected] (X.Y.); [email protected] (S.H.); [email protected] (Y.W.); [email protected] (Y.T.) 2 Shenzhen Research Institute of Nanjing University, Shenzhen 518000, China 3 Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, China * Correspondence: [email protected] These authors contributed equally to this work. y Received: 9 September 2020; Accepted: 12 October 2020; Published: 16 October 2020 Abstract: Manipulating materials at the atomic scale is one of the goals of the development of chemistry and materials science, as it provides the possibility to customize material properties; however, it still remains a huge challenge. Using DNA self-assembly, materials can be controlled at the nano scale to achieve atomic- or nano-scaled fabrication. The programmability and addressability of DNA molecules can be applied to realize the self-assembly of materials from the bottom-up, which is called DNA nanotechnology. DNA nanotechnology does not focus on the biological functions of DNA molecules, but combines them into motifs, and then assembles these motifs to form ordered two-dimensional (2D) or three-dimensional (3D) lattices. These lattices can serve as general templates to regulate the assembly of guest materials. In this review, we introduce three typical DNA self-assembly strategies in this field and highlight the significant progress of each. -
Insights Into Holliday Junction Resolution and Chromosome Segregation in Yeast
September 17, 2012 SCIENCE SPOTLIGHT Insights into Holliday Junction Resolution and Chromosome Segregation in Yeast September 17, 2012 ME Arnegard Homologous DNA recombination is the highly conserved process by which similar or identical nucleotide sequences are exchanged between two DNA molecules. In all eukaryotes – from yeast to humans – this kind of genetic recombination serves two critical functions during meiosis, the class of cell division that leads to the formation of gametes such as sperm and eggs in the case of humans, or spores in yeast: Homologous recombination promotes the genetic diversity of gametes by allowing crossing-over between homologous chromosomes, and it is also critical to accurate chromosome segregation during meiosis. Anomalies in recombination often result in the complete loss of chromosomes during meiosis, or in chromosomal rearrangements such as deletions or translocations, which in turn can lead to birth defects or cancer. All current models for crossing-over involve two key intermediate structures: DNA double strand breaks (DSBs) and Holliday junctions (HJs). DSBs are the initiating events in crossing-over that are caused by Rec12 in fission yeast, whereas HJs are the crossed-strand structures by which DNA molecules from two homologous chromosomes become intertwined (see figure). At the Fred Hutchinson Cancer Research Center, the laboratory of Dr. Gerald Smith (Basic Sciences Division) has made many advances toward understanding a complex pathway composed of dozens of proteins that promote homologous recombination in fission yeast (Schizosaccharomyces pombe) by moving or pairing chromosomes, or forming or repairing DSBs. In a previous study, for example, Cromie et al. (2006) provided strong evidence that HJs in fission yeast are 'resolved' (i.e., precisely cut and reconnected into two independent helices) solely by the endonucleolytic activity of the partner proteins Mus81 and Eme1. -
Using Modular Preformed DNA Origami Building Blocks to Fold Dynamic 3D Structures
Using Modular Preformed DNA Origami Building Blocks to Fold Dynamic 3D Structures Thesis Presented in Partial Fulfillment of the Requirements for the Degree Master of Science in the Graduate School of The Ohio State University By Gunter Eickert, B.S. Graduate Program in Mechanical Engineering The Ohio State University 2014 Thesis Committee: Carlos Castro, Advisor Haijun Su Copyright by Gunter Erick Eickert 2014 Abstract DNA origami is a bottom-up approach that takes advantage of DNA’s structure and lock key sequencing to build nano scale machines and structures. By introducing specific single stranded DNA (ssDNA) “staples”, a ssDNA “scaffold” can be folded into a desired 2D or 3D structure. Using this method, a variety of shapes have been formed, including tetrahedrons and octahedrons. These structures have been explored as drug carriers, enzyme platforms, signal markers, and for other medical and research uses. However, each of these structures must be specifically designed and often pertain to only one particular application. A DNA origami structure that functions as a building block was designed to allow for the creation of several different 3D structures without the need for a lengthy design process. An annealing process called a thermal ramp was then used to fold the structures. The building block was made of four equilateral triangles arranged into a parallelogram. This is ideal since a parallelogram can be used to form three of the five platonic solids, in addition to many non-platonic shapes. The parallelogram was successfully folded into a tetrahedron and an octahedron by introducing staples that bound to overhangs on its edges. -
Working with Molecular Genetics Chapter 8. Recombination of DNA CHAPTER 8 RECOMBINATION of DNA
Working with Molecular Genetics Chapter 8. Recombination of DNA CHAPTER 8 RECOMBINATION OF DNA The previous chapter on mutation and repair of DNA dealt mainly with small changes in DNA sequence, usually single base pairs, resulting from errors in replication or damage to DNA. The DNA sequence of a chromosome can change in large segments as well, by the processes of recombination and transposition. Recombination is the production of new DNA molecule(s) from two parental DNA molecules or different segments of the same DNA molecule; this will be the topic of this chapter. Transposition is a highly specialized form of recombination in which a segment of DNA moves from one location to another, either on the same chromosome or a different chromosome; this will be discussed in the next chapter. Types and examples of recombination At least four types of naturally occurring recombination have been identified in living organisms (Fig. 8.1). General or homologous recombination occurs between DNA molecules of very similar sequence, such as homologous chromosomes in diploid organisms. General recombination can occur throughout the genome of diploid organisms, using one or a small number of common enzymatic pathways. This chapter will be concerned almost entirely with general recombination. Illegitimate or nonhomologous recombination occurs in regions where no large- scale sequence similarity is apparent, e.g. translocations between different chromosomes or deletions that remove several genes along a chromosome. However, when the DNA sequence at the breakpoints for these events is analyzed, short regions of sequence similarity are found in some cases. For instance, recombination between two similar genes that are several million bp apart can lead to deletion of the intervening genes in somatic cells. -
Protein-Assisted Room-Temperature Assembly of Rigid, Immobile Holliday Junctions and Hierarchical DNA Nanostructures
molecules Article Protein-Assisted Room-Temperature Assembly of Rigid, Immobile Holliday Junctions and Hierarchical DNA Nanostructures 1,2, 3,4, 1, Saminathan Ramakrishnan y, Sivaraman Subramaniam y, Charlotte Kielar z, Guido Grundmeier 1 , A. Francis Stewart 3,4 and Adrian Keller 1,* 1 Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098 Paderborn, Germany; [email protected] (S.R.); [email protected] (C.K.); [email protected] (G.G.) 2 Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA 3 Biotechnology Center, Department of Genomics, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany; [email protected] (S.S.); [email protected] (A.F.S.) 4 Cluster of Excellence Physics of Life, Technische Universität Dresden, 01062 Dresden, Germany * Correspondence: [email protected] These authors contributed equally to this work. y Present address: Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, z Bautzner Landstraße 400, 01328 Dresden, Germany. Academic Editor: Ramon Eritja Received: 29 September 2020; Accepted: 30 October 2020; Published: 3 November 2020 Abstract: Immobile Holliday junctions represent not only the most fundamental building block of structural DNA nanotechnology but are also of tremendous importance for the in vitro investigation of genetic recombination and epigenetics. Here, we present a detailed study on the room-temperature assembly of immobile Holliday junctions with the help of the single-strand annealing protein Redβ. Individual DNA single strands are initially coated with protein monomers and subsequently hybridized to form a rigid blunt-ended four-arm junction. We investigate the efficiency of this approach for different DNA/protein ratios, as well as for different DNA sequence lengths. -
The Crystal Structures of DNA Holliday Junctions P Shing Ho* and Brandt F Eichman†
302 The crystal structures of DNA Holliday junctions P Shing Ho* and Brandt F Eichman† Nearly 40 years ago, Holliday proposed a four-stranded Molecular models of the four-way junction complex or junction as the central intermediate in the general It is now generally accepted that there are two structural mechanism of genetic recombination. During the past two forms of the Holliday junction (reviewed in [9•]). Low salt years, six single-crystal structures of such DNA junctions have conditions favor an open-X form, in which the four arms been determined by three different research groups. These are extended in a square planar geometry (Figure 1b), structures all essentially adopt the antiparallel stacked-X thereby minimizing the repulsion between the negatively conformation, but can be classified into three distinct charged phosphates concentrated at the junction. This is categories: RNA–DNA junctions; ACC trinucleotide junctions; also the form observed in complexes with the enzymes and drug-induced junctions. Together, these structures provide RuvA [10,11,12•] and Cre [13]. insight into how local and distant interactions help to define the detailed and general physical features of Holliday junctions In contrast, the presence of multivalent cations effective- at the atomic level. ly shields these negative charges, allowing the arms to coaxially pair and stack into the more compact stacked-X Addresses junction (Figure 1c). Before the recent crystal studies, *Department of Biochemistry and Biophysics, ALS 2011, Oregon the most detailed models of four-way junctions were State University, Corvallis, Oregon 97331, USA; derived from studies using gel electrophoresis, fluores- e-mail: [email protected] cence resonance energy transfer, NMR spectroscopy and †Department of Biological Chemistry and Molecular Pharmacology, • Harvard Medical School, Boston, Massachusetts 02115, USA atomic force microscopy [9 ]. -
Implications of Metastable Nicks and Nicked Holliday Junctions in Processing Joint Molecules in Mitosis and Meiosis
G C A T T A C G G C A T genes Concept Paper Implications of Metastable Nicks and Nicked Holliday Junctions in Processing Joint Molecules in Mitosis and Meiosis Félix Machín 1,2,3 1 Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain; [email protected] 2 Instituto de Tecnologías Biomédicas, Universidad de la Laguna, 38200 Tenerife, Spain 3 Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, 35450 Las Palmas de Gran Canaria, Spain Received: 22 October 2020; Accepted: 9 December 2020; Published: 12 December 2020 Abstract: Joint molecules (JMs) are intermediates of homologous recombination (HR). JMs rejoin sister or homolog chromosomes and must be removed timely to allow segregation in anaphase. Current models pinpoint Holliday junctions (HJs) as a central JM. The canonical HJ (cHJ) is a four-way DNA that needs specialized nucleases, a.k.a. resolvases, to resolve into two DNA molecules. Alternatively, a helicase–topoisomerase complex can deal with pairs of cHJs in the dissolution pathway. Aside from cHJs, HJs with a nick at the junction (nicked HJ; nHJ) can be found in vivo and are extremely good substrates for resolvases in vitro. Despite these findings, nHJs have been neglected as intermediates in HR models. Here, I present a conceptual study on the implications of nicks and nHJs in the final steps of HR. I address this from a biophysical, biochemical, topological, and genetic point of view. My conclusion is that they ease the elimination of JMs while giving genetic directionality to the final products. -
Gradient-Mixing LEGO Robots for Purifying DNA Origami Nanostructures of Multiple Components by Rate-Zonal Centrifugation
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.02.450731; this version posted July 4, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Gradient-mixing LEGO robots for purifying DNA origami nanostructures of multiple components by rate-zonal centrifugation Jason Sentosaa,b,1, Brian Hornec,1, Franky Djutantaa,d,1,2, Dominic Showkeirc,1, Robert Rezvania,c, and Rizal F. Hariadi ID a,d,1 aBiodesign Center for Molecular Design and Biomimetics (at the Biodesign Institute) at Arizona State University, Tempe, AZ 85287, USA.; bDepartment of Biomedical Engineering, Georgia Institute of Technology, GA; cDepartment of Physics, Arizona State University, AZ.; dSchool for Engineering of Matter, Transport and Energy, Arizona State University, AZ. 1These authors contributed equally. 2To whom correspondence should be addressed. E-mail: [email protected] AND [email protected] This manuscript was compiled on July 4, 2021 Abstract DNA origami purification is critical in emerging applications of functionalized DNA nanostructures from basic fundamental biophysics, nanorobots to therapeutics. Advances in DNA origami purification have led to the establishment of rate-zonal centrifugation (RZC) as a scalable, high-yield, and contamination-free approach to purifying DNA origami nanostructures. In RZC purification, a linear density gradient is created using viscous agents, such as glycerol and sucrose, to separate molecules based on their mass and shape during high-rpm centrifugation. However, current methods for creating density gradients are typically time-consuming because of their reliance on slow passive diffusion. -
Atomic Force Microscopy Studies of DNA Origami Nanostructures: from Structural Stability to Molecular Patterning
Atomic force microscopy studies of DNA origami nanostructures: from structural stability to molecular patterning Dissertation zur Erlangung des Grades „Doktor rerum naturalium“ an der Universität Paderborn Fakultät für Naturwissenschaften Department Chemie von Saminathan Ramakrishnan Geb. 22.04.1989 in Aranthangi, India Gutachter: PD Dr. Adrian Keller Adjunct Professor, PhD Veikko Linko Eingereicht am: Tag der Verteidigung: ii Contents Abstract ............................................................................................................................................ 1 1. Introduction .................................................................................................................................. 3 1.1 Genetic material ...................................................................................................................... 3 1.2 DNA as a genetic material ...................................................................................................... 3 1.3 Molecular structure of nucleic acids ....................................................................................... 4 1.4 Nanotechnology and Atomic Force Microscopy (AFM)........................................................ 7 1.5 DNA nanotechnology ........................................................................................................... 11 1.6 DNA origami ........................................................................................................................ 14 1.7 Structural stability of