1
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Katrivas L, Makarovsky A, Kempinski B, Randazzo A, Improta R, Rotem D, Porath D, Kotlyar AB. Ag +-Mediated Folding of Long Polyguanine Strands to Double and Quadruple Helixes. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:663. [PMID: 38668157 PMCID: PMC11055002 DOI: 10.3390/nano14080663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/03/2024] [Accepted: 04/07/2024] [Indexed: 04/29/2024]
Abstract
Metal-mediated base pairing of DNA has been a topic of extensive research spanning over more than four decades. Precise positioning of a single metal ion by predetermining the DNA sequence, as well as improved conductivity offered by the ions, make these structures interesting candidates in the context of using DNA in nanotechnology. Here, we report the formation and characterization of conjugates of long (kilo bases) homoguanine DNA strands with silver ions. We demonstrate using atomic force microscopy (AFM) and scanning tunneling microscope (STM) that binding of silver ions leads to folding of homoguanine DNA strands in a "hairpin" fashion to yield double-helical, left-handed molecules composed of G-G base pairs each stabilized by a silver ion. Further folding of the DNA-silver conjugate yields linear molecules in which the two halves of the double helix are twisted one against the other in a right-handed fashion. Quantum mechanical calculations on smaller molecular models support the helical twist directions obtained by the high resolution STM analysis. These long guanine-based nanostructures bearing a chain of silver ions have not been synthesized and studied before and are likely to possess conductive properties that will make them attractive candidates for nanoelectronics.
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Affiliation(s)
- Liat Katrivas
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and Nanotechnology Center, Tel Aviv University, Ramat Aviv, Tel-Aviv 6997801, Israel; (L.K.); (B.K.)
| | - Anna Makarovsky
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 7610001, Israel; (A.M.); (D.R.)
| | - Benjamin Kempinski
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and Nanotechnology Center, Tel Aviv University, Ramat Aviv, Tel-Aviv 6997801, Israel; (L.K.); (B.K.)
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Napoli, Italy;
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini-CNR (IBB-CNR), Via De Amicis 95, I-80145 Napoli, Italy;
| | - Dvir Rotem
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 7610001, Israel; (A.M.); (D.R.)
| | - Danny Porath
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 7610001, Israel; (A.M.); (D.R.)
| | - Alexander B. Kotlyar
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and Nanotechnology Center, Tel Aviv University, Ramat Aviv, Tel-Aviv 6997801, Israel; (L.K.); (B.K.)
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2
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Bethur E, Guha R, Zhao Z, Katz BB, Ashby PD, Zeng H, Copp SM. Formation and Nanomechanical Properties of Silver-Mediated Guanine DNA Duplexes in Aqueous Solution. ACS NANO 2024; 18:3002-3010. [PMID: 38227309 PMCID: PMC10832345 DOI: 10.1021/acsnano.3c08008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/04/2024] [Accepted: 01/10/2024] [Indexed: 01/17/2024]
Abstract
Silver cations can mediate base pairing of guanine (G) DNA oligomers, yielding linear parallel G-Ag+-G duplexes with enhanced stabilities compared to those of canonical DNA duplexes. To enable their use in programmable DNA nanotechnologies, it is critical to understand solution-state formation and the nanomechanical stiffness of G-Ag+-G duplexes. Using temperature-controlled circular dichroism (CD) spectroscopy, we find that heating mixtures of G oligomers and silver salt above 50 °C fully destabilizes G-quadruplex structures and converts oligomers to G-Ag+-G duplexes. Electrospray ionization mass spectrometry supports that G-Ag+-G duplexes form at stoichiometries of 1 Ag+ per base pair, and CD spectroscopy suggests that as the Ag+/base stoichiometry increases further, G-Ag+-G duplexes undergo additional morphological changes. Using liquid-phase atomic force microscopy, we find that this excess Ag+ enables assembly of long fiberlike structures with ∼2.5 nm heights equivalent to a single DNA duplex but with lengths that far exceed a single duplex. Finally, using the conditions established to form single G-Ag+-G duplexes, we use a surface forces apparatus (SFA) to compare the solution-phase stiffness of single G-Ag+-G duplexes with dG-dC Watson-Crick-Franklin duplexes. SFA shows that G-Ag+-G duplexes are 1.3 times stiffer than dG-dC duplexes, confirming gas-phase ion mobility spectrometry measurements and computational predictions. These findings may guide the development of structural DNA nanotechnologies that rely on silver-mediated base pairing.
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Affiliation(s)
- Eshana Bethur
- Department
of Materials Science and Engineering, University
of California, Irvine, California 92697, United States
| | - Rweetuparna Guha
- Department
of Materials Science and Engineering, University
of California, Irvine, California 92697, United States
| | - Ziqian Zhao
- Department
of Chemical and Materials Engineering, University
of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Benjamin B. Katz
- Department
of Chemistry, University of California, Irvine, California 92697, United States
| | - Paul D. Ashby
- Molecular
Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Hongbo Zeng
- Department
of Chemical and Materials Engineering, University
of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Stacy M. Copp
- Department
of Materials Science and Engineering, University
of California, Irvine, California 92697, United States
- Department
of Physics and Astronomy, University of
California, Irvine, California 92697, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697, United States
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3
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Gustavsson T, Markovitsi D. The Ubiquity of High-Energy Nanosecond Fluorescence in DNA Duplexes. J Phys Chem Lett 2023; 14:2141-2147. [PMID: 36802626 DOI: 10.1021/acs.jpclett.2c03884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
During the past few years, several studies reported that a significant part of the intrinsic fluorescence of DNA duplexes decays with surprisingly long lifetimes (1-3 ns) at wavelengths shorter than the ππ* emission of their monomeric constituents. This high-energy nanosecond emission (HENE), hardly discernible in the steady-state fluorescence spectra of most duplexes, was investigated by time-correlated single-photon counting. The ubiquity of HENE contrasts with the paradigm that the longest-lived excited states correspond to low-energy excimers/exciplexes. Interestingly, the latter were found to decay faster than the HENE. So far, the excited states responsible for HENE remain elusive. In order to foster future studies for their characterization, this Perspective presents a critical summary of the experimental observations and the first theoretical approaches. Moreover, some new directions for further work are outlined. Finally, the obvious need for computations of the fluorescence anisotropy considering the dynamic conformational landscape of duplexes is stressed.
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Affiliation(s)
- Thomas Gustavsson
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191 Gif-sur-Yvette, France
| | - Dimitra Markovitsi
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000, 91405 Orsay, France
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4
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Vittala SK, Zhao Y, Han D. Programmed Assembly of DNA Templates by Silver Nanowires. Chempluschem 2022; 87:e202100478. [PMID: 35014201 DOI: 10.1002/cplu.202100478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/20/2021] [Indexed: 12/16/2022]
Abstract
DNA origami templates are known to exhibit many advantages to integrate functional components at desirable locations for nanoelectronic applications. In order to immobilize conducting or semiconducting species in a bottom-up approach, the programmed assembly of DNA templates is of utmost necessity. This report demonstrates the silver nanowires enabled bridging of two linear DNA origami (DO) nanostructures by utilizing the host-guest interaction of biotin-STV and sequence-specific silver metallization of poly(dG-dC) DNA nanowires (in 10 % yield) using (dA)10 coated AgNPs (15 nm). The enzymatic synthesis of 750 bp, 1500 bp and 3000 bp bis-biotinylated poly(dG-dC), facile synthesis of 1 : 1 biotin-STV and silver-nanowire bridged DNA templates were characterized by gel electrophoresis, atomic force microscope imaging techniques. The strategy utilized here provides a method that can precisely connect heterogeneous templates towards bottom-up fabrication of practical nanoelectronics.
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Affiliation(s)
- Sandeepa K Vittala
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Yumeng Zhao
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Da Han
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
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5
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Fardian-Melamed N, Katrivas L, Rotem D, Kotlyar A, Porath D. Electronic Level Structure of Novel Guanine Octuplex DNA Single Molecules. NANO LETTERS 2021; 21:8987-8992. [PMID: 34694812 DOI: 10.1021/acs.nanolett.1c02269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Throughout the past few decades, guanine quadruplex DNA structures have attracted much interest both from a fundamental material science perspective and from a technologically oriented perspective. Novel guanine octuplex DNA, formed from coiled quadruplex DNA, was recently discovered as a stable and rigid DNA-based nanostructure. A detailed electronic structure study of this new nanomaterial, performed by scanning tunneling spectroscopy on a subsingle-molecule level at cryogenic temperature, is presented herein. The electronic levels and lower energy gap of guanine octuplex DNA compared to quadruplex DNA dictate higher transverse conductivity through guanine octads than through guanine tetrads.
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Affiliation(s)
- Natalie Fardian-Melamed
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Liat Katrivas
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, and The Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Dvir Rotem
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Alexander Kotlyar
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, and The Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Danny Porath
- Institute of Chemistry and The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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6
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Vittala SK, Han D. DNA-Guided Assemblies toward Nanoelectronic Applications. ACS APPLIED BIO MATERIALS 2020; 3:2702-2722. [PMID: 35025404 DOI: 10.1021/acsabm.9b01178] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sandeepa Kulala Vittala
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Da Han
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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7
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Katrivas L, Kempinski B, Kuchuk K, Sivan U, Kotlyar A. Multiply Modified Repeating DNA Templates for Production of Novel DNA-Based Nanomaterial. Bioconjug Chem 2019; 30:2201-2208. [PMID: 31343869 DOI: 10.1021/acs.bioconjchem.9b00433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here, we report synthesis of long (thousands of base pairs), uniform double-stranded (ds) DNA comprising short (6-15 base pairs) tandem repeats. The synthesis method is based on self-assembly of short (6-15 bases) half-complementary 5'-end phosphorylated single-stranded oligonucleotides into long ds polymer molecules and covalent association of the oligonucleotide fragments in the polymer by DNA ligase to yield complete non-nicked ds DNA. The method is very flexible in regard to the sequence of the oligonucleotides and their length. Human telomeric DNA comprising thousands of base pairs as well as methylated, mismatched, and fluorescent dye-modified uniform dsDNA molecules can be synthesized. We have demonstrated by high resolution frequency-modulation atomic force microscopy that the structure of DNA containing mismatches is strongly different from that of the non-mismatched one. The DNA molecules comprising groups capable of anchoring metal particles and other redox active elements along the whole length of the nucleic acid polymer should find use as wires or transistors in future nanoelectronic applications.
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Affiliation(s)
- Liat Katrivas
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and the Center of Nanoscience and Nanotechnology , Tel Aviv University , Ramat Aviv , Tel Aviv 69978 , Israel
| | - Benjamin Kempinski
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and the Center of Nanoscience and Nanotechnology , Tel Aviv University , Ramat Aviv , Tel Aviv 69978 , Israel
| | - Kfir Kuchuk
- Department of Physics and the Russell Berrie Nanotechnology Institute , Technion - Israel Institute of Technology , Haifa , 3200003 , Israel
| | - Uri Sivan
- Department of Physics and the Russell Berrie Nanotechnology Institute , Technion - Israel Institute of Technology , Haifa , 3200003 , Israel
| | - Alexander Kotlyar
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and the Center of Nanoscience and Nanotechnology , Tel Aviv University , Ramat Aviv , Tel Aviv 69978 , Israel
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8
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Fardian-Melamed N, Eidelshtein G, Rotem D, Kotlyar A, Porath D. Scanning Tunneling Microscopy and Spectroscopy of Novel Silver-Containing DNA Molecules. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1902816. [PMID: 31265189 DOI: 10.1002/adma.201902816] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/11/2019] [Indexed: 06/09/2023]
Abstract
The quest for a suitable molecule to pave the way to molecular nanoelectronics has been met with obstacles for over a decade. Candidate molecules such as carbon nanotubes lack the appealing trait of self-assembly, while DNA seems to lack the desirable feature of conductivity. Silver-containing poly(dG)-poly(dC) DNA (E-DNA) molecules have recently been reported as promising candidates for molecular electronics, owing to the selectivity of their metallization, their thin and uniform structure, their resistance to deformation, and their maximum possible high conductivity. Ultrahigh vacuum (UHV) scanning tunneling microscopy (STM) of E-DNA presents an elaborate high-resolution morphology characterization of these unique molecules, along with a detailed depiction of their electronic level structure. The energy levels found for E-DNA indicate a novel truly hybrid metal-molecule structure, potentially more conductive than other DNA-based alternatives.
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Affiliation(s)
- Natalie Fardian-Melamed
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Gennady Eidelshtein
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv, 69978, Israel
| | - Dvir Rotem
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Alexander Kotlyar
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv, 69978, Israel
- Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv, 69978, Israel
| | - Danny Porath
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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9
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Abstract
Here we describe novel enzymatic procedures for the production of long (from tens of nanometers to microns) double-stranded poly(dG)-poly(dC), triple-helical poly(dG)-poly(dG)-poly(dC), and quadruple-helical G4 DNA. All these molecules are uniform in size and possess improved mechanical and electrical properties with respect to a canonical random sequence double-stranded DNA. They can potentially be used as elements in nanoelectronic devices and circuits.
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10
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Abstract
DNA has played an early and powerful role in the development of bottom-up nanotechnologies, not least because of DNA's precise, predictable, and controllable properties of assembly on the nanometer scale. Watson-Crick complementarity has been used to build complex 2D and 3D architectures and design a number of nanometer-scale systems for molecular computing, transport, motors, and biosensing applications. Most of such devices are built with classical B-DNA helices and involve classical A-T/U and G-C base pairs. However, in addition to the above components underlying the iconic double helix, a number of alternative pairing schemes of nucleobases are known. This review focuses on two of these noncanonical classes of DNA helices: G-quadruplexes and the i-motif. The unique properties of these two classes of DNA helix have been utilized toward some remarkable constructions and applications: G-wires; nanostructures such as DNA origami; reconfigurable structures and nanodevices; the formation and utilization of hemin-utilizing DNAzymes, capable of generating varied outputs from biosensing nanostructures; composite nanostructures made up of DNA as well as inorganic materials; and the construction of nanocarriers that show promise for the therapeutics of diseases.
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Affiliation(s)
- Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering , Nanjing University , Nanjing 210023 , China.,ARNA Laboratory , Université de Bordeaux, Inserm U 1212, CNRS UMR5320, IECB , Pessac 33600 , France.,Institute of Biophysics of the CAS , v.v.i., Královopolská 135 , 612 65 Brno , Czech Republic
| | - Dipankar Sen
- Department of Molecular Biology & Biochemistry , Simon Fraser University , Burnaby , British Columbia V5A 1S6 , Canada.,Department of Chemistry , Simon Fraser University , Burnaby , British Columbia V5A 1S6 , Canada
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11
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Zhuravel R, Stern A, Fardian-Melamed N, Eidelshtein G, Katrivas L, Rotem D, Kotlyar AB, Porath D. Advances in Synthesis and Measurement of Charge Transport in DNA-Based Derivatives. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1706984. [PMID: 29984432 DOI: 10.1002/adma.201706984] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 03/28/2018] [Indexed: 06/08/2023]
Abstract
Charge transport through molecular structures is interesting both scientifically and technologically. To date, DNA is the only type of polymer that transports significant currents over distances of more than a few nanometers in individual molecules. For molecular electronics, DNA derivatives are by far more promising than native DNA due to their improved charge-transport properties. Here, the synthesis of several unique DNA derivatives along with electrical characterization and theoretical models is surveyed. The derivatives include double stranded poly(G)-poly(C) DNA molecules, four stranded G4-DNA, metal-DNA hybrid molecular wires, and other DNA molecules that are modified either at the bases or at the backbone. The electrical characteristics of these nanostructures, studied experimentally by electrostatic force microscopy, conductive atomic force microscopy, and scanning tunneling microscopy and spectroscopy, are reviewed.
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Affiliation(s)
- Roman Zhuravel
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Avigail Stern
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Natalie Fardian-Melamed
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Gennady Eidelshtein
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, and The Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv, 69978, Israel
| | - Liat Katrivas
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, and The Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv, 69978, Israel
| | - Dvir Rotem
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Alexander B Kotlyar
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, and The Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv, 69978, Israel
| | - Danny Porath
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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12
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Whitfield CJ, Little RC, Khan K, Ijiro K, Connolly BA, Tuite EM, Pike AR. Self-Priming Enzymatic Fabrication of Multiply Modified DNA. Chemistry 2018; 24:15267-15274. [PMID: 29931815 DOI: 10.1002/chem.201801976] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/19/2018] [Indexed: 12/15/2022]
Abstract
The self-priming synthesis of multiply modified DNA by the extension of repeating unit duplex "oligoseeds" provides a source of versatile DNA. Sterically-demanding nucleotides 5-Br-dUTP, 7-deaza-7-I-dATP, 6-S-dGTP, 5-I-dCTP as well as 5-(octadiynyl)-dCTP were incorporated into two extending oligoseeds; [GATC]5 /[GATC]5 and [A4 G]4 /[CT4 ]4 . The products contained modifications on one or both strands of DNA, demonstrating their recognition by the polymerase as both template (reading) and substrate (writing). Nucleobase modifications that lie in the major groove were reliably read and written by the polymerase during the extension reaction, even when bulky or in contiguous sequences. Repeat sequence DNA over 500 bp long, bearing four different modified units was produced by this method. The number, position and type of modification, as well as the overall length of the DNA can be controlled to yield designer DNA that offers sequence-determined sites for further chemical adaptations, targeted small molecule binding studies, or sensing and sequencing applications.
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Affiliation(s)
- Colette J Whitfield
- Chemistry-School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Rachel C Little
- Chemistry-School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Kasid Khan
- Chemistry-School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Kuniharu Ijiro
- Research Institute for Electronic Science, Hokkaido University, Sapporo, 001-0021, Japan
| | - Bernard A Connolly
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Eimer M Tuite
- Chemistry-School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Andrew R Pike
- Chemistry-School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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13
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14
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Eidelshtein G, Fattal M, Avishai G, Kempinski B, Giannini C, Kotlyar A. Preparation, Characterization and Manipulation of Conjugates between Gold Nanoparticles and DNA. NANOMATERIALS 2016; 6:nano6090167. [PMID: 28335294 PMCID: PMC5224630 DOI: 10.3390/nano6090167] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 08/24/2016] [Accepted: 08/26/2016] [Indexed: 02/05/2023]
Abstract
Here we described the preparation and characterization by atomic force microscopy of dumbbell-shaped conjugates between 450 bp double-stranded DNA polymer, poly(dG)-poly(dC), and 5 nm gold nanoparticles (GNPs). We have demonstrated that the size of the nanoparticles in the conjugates can be increased in a controlled fashion. Application of the conjugates for measuring the electrical conductivity of DNA is discussed.
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Affiliation(s)
- Gennady Eidelshtein
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and the Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel.
| | - Moran Fattal
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and the Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel.
| | - Gavriel Avishai
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and the Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel.
| | - Benjamin Kempinski
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and the Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel.
| | - Clelia Giannini
- Department of Chemistry, University of Milan, via Golgi 19, 20133 Milan, Italy.
| | - Alexander Kotlyar
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and the Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel.
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15
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Eidelshtein G, Fardian-Melamed N, Gutkin V, Basmanov D, Klinov D, Rotem D, Levi-Kalisman Y, Porath D, Kotlyar A. Synthesis and Properties of Novel Silver-Containing DNA Molecules. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:4839-4844. [PMID: 27116695 DOI: 10.1002/adma.201505049] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 01/23/2016] [Indexed: 06/05/2023]
Abstract
Migration of silver atoms from silver nano-particles selectively to a double-stranded poly(dG)-poly(dC) polymer leads to metallization of the DNA. As a result the DNA molecules become shorter and thicker (higher), as evident from the atomic force microscopy imaging analysis. The metalized molecules can be detected by transmission and scanning electron microscopy in contrast to the initial non-metalized ones.
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Affiliation(s)
- Gennady Eidelshtein
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and The Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv, 69978, Israel
| | - Natalie Fardian-Melamed
- Institute of Chemistry, The Hebrew University of Jerusalem, and The Center for Nanoscience and Nanotechnology of the Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Vitaly Gutkin
- Institute of Chemistry, The Hebrew University of Jerusalem, and The Center for Nanoscience and Nanotechnology of the Hebrew University of Jerusalem, Jerusalem, 91904, Israel
- The Center for Nanoscience and Nanotechnology of the Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Dmitry Basmanov
- Institute of Physical-Chemical Medicine, Malaya Pirogovskaya str. 1a, 119435, Moscow, Russia
| | - Dmitry Klinov
- Institute of Physical-Chemical Medicine, Malaya Pirogovskaya str. 1a, 119435, Moscow, Russia
- Russia and Moscow Institute of Physics and Technology (State University), 9 Institutskiy per. Dolgoprudny, 141700, Moscow Region, Russia
| | - Dvir Rotem
- Institute of Chemistry, The Hebrew University of Jerusalem, and The Center for Nanoscience and Nanotechnology of the Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Yael Levi-Kalisman
- Institute for Life SciencesThe Hebrew University of Jerusalem, and The Center for Nanoscience and Nanotechnology of the Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Danny Porath
- Institute of Chemistry, The Hebrew University of Jerusalem, and The Center for Nanoscience and Nanotechnology of the Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Alexander Kotlyar
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences and The Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv, 69978, Israel
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Eidelshtein G, Kotlyar A, Hashemi M, Gurevich L. Aligned deposition and electrical measurements on single DNA molecules. NANOTECHNOLOGY 2015; 26:475102. [PMID: 26538384 DOI: 10.1088/0957-4484/26/47/475102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A reliable method of deposition of aligned individual dsDNA molecules on mica, silicon, and micro/nanofabricated circuits is presented. Complexes of biotinylated double stranded poly(dG)-poly(dC) DNA with avidin were prepared and deposited on mica and silicon surfaces in the absence of Mg(2+) ions. Due to its positive charge, the avidin attached to one end of the DNA anchors the complex to negatively charged substrates. Subsequent drying with a directional gas flow yields DNA molecules perfectly aligned on the surface. In the avidin-DNA complex only the avidin moiety is strongly and irreversibly bound to the surface, while the DNA counterpart interacts with the substrates much more weakly and can be lifted from the surface and realigned in any direction. Using this technique, avidin-DNA complexes were deposited across platinum electrodes on a silicon substrate. Electrical measurements on the deposited DNA molecules revealed linear IV-characteristics and exponential dependence on relative humidity.
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Affiliation(s)
- Gennady Eidelshtein
- Department of Biochemistry and Molecular Biology, George S Wise Faculty of Life Sciences and The Center of Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
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Whitfield CJ, Turley AT, Tuite EM, Connolly BA, Pike AR. Enzymatic Method for the Synthesis of Long DNA Sequences with Multiple Repeat Units. Angew Chem Int Ed Engl 2015; 54:8971-4. [DOI: 10.1002/anie.201502971] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Indexed: 11/09/2022]
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18
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Whitfield CJ, Turley AT, Tuite EM, Connolly BA, Pike AR. Enzymatic Method for the Synthesis of Long DNA Sequences with Multiple Repeat Units. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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19
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Mitomo H, Watanabe Y, Matsuo Y, Niikura K, Ijiro K. Enzymatic synthesis of a DNA triblock copolymer that is composed of natural and unnatural nucleotides. Chem Asian J 2014; 10:455-60. [PMID: 25388958 DOI: 10.1002/asia.201403108] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Indexed: 12/23/2022]
Abstract
DNA molecules have come under the spotlight as potential templates for the fabrication of nanoscale products, such as molecular-scale electronic or photonic devices. Herein, we report an enhanced approach for the synthesis of oligoblock copolymer-type DNA by using the Klenow fragment exonuclease minus of E. coli DNA polymerase I (KF(-) ) in a multi-step reaction with natural and unnatural nucleotides. First, we confirmed the applicability of unnatural nucleotides with 7-deaza-nucleosides-which was expected because they were non-metalized nucleotides-on the unique polymerization process known as the "strand-slippage model". Because the length of the DNA sequence could be controlled by tuning the reaction time, analogous to a living polymerization reaction on this process, stepwise polymerization provided DNA block copolymers with natural and unnatural bases. AFM images showed that this DNA block copolymer could be metalized sequence-selectively. This approach could expand the utility of DNA as a template.
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Affiliation(s)
- Hideyuki Mitomo
- Research Institute for Electronic Science, Hokkaido University, Sapporo, Hokkaido, 001-0021 (Japan)
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20
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Zhou J, Rosu F, Amrane S, Korkut DN, Gabelica V, Mergny JL. Assembly of chemically modified G-rich sequences into tetramolecular DNA G-quadruplexes and higher order structures. Methods 2014; 67:159-68. [DOI: 10.1016/j.ymeth.2014.01.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/20/2013] [Accepted: 01/02/2014] [Indexed: 10/25/2022] Open
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21
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Induction of innate and adaptive immunity by delivery of poly dA:dT to dendritic cells. Nat Chem Biol 2013; 9:250-6. [PMID: 23416331 DOI: 10.1038/nchembio.1186] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 01/18/2013] [Indexed: 01/02/2023]
Abstract
Targeted delivery of antigens to dendritic cells (DCs) is a promising vaccination strategy. However, to ensure immunity, the approach depends on coadministration of an adjuvant. Here we ask whether targeting of both adjuvant and antigen to DCs is sufficient to induce immunity. Using a protein ligation method, we develop a general approach for linking the immune stimulant, poly dA:dT (pdA:dT), to a monoclonal antibody (mAb) specific for DEC205 (DEC). We show that DEC-specific mAbs deliver pdA:dT to DCs for the efficient production of type I interferon in human monocyte-derived DCs and in mice. Notably, adaptive T-cell immunity is elicited when mAbs specific for DEC-pdA:dT are used as the activation stimuli and are administered together with a DC-targeted antigen. Collectively, our studies indicate that DCs can integrate innate and adaptive immunity in vivo and suggest that dual delivery of antigen and adjuvant to DCs might be an efficient approach to vaccine development.
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MITOMO H, WATANABE Y, MATSUO Y, NIIKURA K, IJIRO K. Preparation of Triblock DNA as a Template for Fabrication of Nano-Gap Structures Using Sequence-Selective Metallization. KOBUNSHI RONBUNSHU 2013. [DOI: 10.1295/koron.70.337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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23
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Kato T, Liang X, Asanuma H. Model of elongation of short DNA sequence by thermophilic DNA polymerase under isothermal conditions. Biochemistry 2012; 51:7846-53. [PMID: 22992125 DOI: 10.1021/bi3010413] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Short DNA sequences, especially those that are repetitive or palindromic, can be used as the seeds for synthesis of long DNA by some DNA polymerases in an unusual manner. Although several elongation mechanisms have been proposed, there is no well-established model that explains highly efficient elongation under isothermal conditions. In the present study, we analyzed the elongation of nonrepetitive sequences with distinct hairpins at each end. These DNAs were elongated efficiently under isothermal conditions by thermophilic Vent (exo(-)) DNA polymerase, and the products were longer than 10 kb within 10 min of the reaction. A 20-nucleotide DNA with only one hairpin was also elongated. Sequence analysis revealed that the long products are mainly tandem repeats of the short seed sequences. The thermal melting temperatures of the products were much higher than the reaction temperature, indicating that most DNAs form duplexes during the reaction. Accordingly, a terminal hairpin formation and self-priming extension model was proposed in detail, and the efficient elongation was explained. Formation of the hairpin at the 5' end plays an important role during the elongation.
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Affiliation(s)
- Tomohiro Kato
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8603, Japan
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24
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Sequence-Specific Metallization of Single Divalent DNA-Nanoparticle Conjugates: A Potential Route to Single-Electron Devices. Chempluschem 2012. [DOI: 10.1002/cplu.201200096] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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25
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Borovok N, Gillon E, Kotlyar A. Synthesis and assembly of conjugates bearing specific numbers of DNA strands per gold nanoparticle. Bioconjug Chem 2012; 23:916-22. [PMID: 22515478 DOI: 10.1021/bc200485r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Here, we present a relatively simple, efficient, and high-yielding polymerase-based method for the synthesis of 15 nm gold nanoparticle conjugates bearing a specific number of 25 base oligonucleotide strands. We have shown that the conjugates bearing one or two oligonucleotide strands per particle, with the conjugates comprising a single complementary strand, self-assemble into nanoparticle dimers and trimers, respectively. Incubation of fully coated AuNPs, containing tens of oligonucleotide strands, with a conjugate bearing a single complementary strand leads to the formation of flower-shaped structures. The assembly of particles into nanoparticle structures shown here is a prerequisite for more complex controlled assembly of particles into three-dimensional macrostructures.
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Affiliation(s)
- Natalia Borovok
- Department of Biochemistry, George S. Wise Faculty of Life Sciences and ‡The Center of Nanoscience and Nanotechnology, Tel-Aviv University , Ramat Aviv 69978, Israel
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26
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27
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Zikich D, Liu K, Sagiv L, Porath D, Kotlyar A. I-motif nanospheres: unusual self-assembly of long cytosine strands. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2011; 7:1029-34. [PMID: 21381197 DOI: 10.1002/smll.201002213] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2010] [Revised: 01/14/2011] [Indexed: 05/25/2023]
Abstract
The synthesis and characterization of novel DNA structures based on tetraplex cytosine (C) arrangements, known as i-motifs or i-tetraplexes, is reported. Atomic force microscopy (AFM) investigation shows that long C-strands in mild acidic conditions form compact spherically shaped nanostructures. The DNA nanospheres are characterized by a typical uniform shape and narrow height distribution. Electrostatic force microscopy (EFM) measurements performed on the i-motif spheres clearly show their electrical polarizability. Further investigations by scanning tunneling microscopy (STM) at ultrahigh vacuum reveals that the structures exhibit an average voltage gap of 1.9 eV, which is narrower than the voltage gap previously measured for poly(dG)-poly(dC) molecules in similar conditions.
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Affiliation(s)
- Dragoslav Zikich
- Department of Biochemistry George S. Wise Faculty of Life Sciences, Tel Aviv University Ramat Aviv 69978, Israel
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28
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Abstract
Here we describe novel procedures for production of DNA-based nanowires. This include synthesis and characterization of the one-to-one double-helical complex of poly(dG)-poly(dC), triple-helical poly(dG)-poly(dG)-poly(dC) and G4-DNA, which is a quadruple-helical form of DNA. All these types of DNA-based molecules were synthesized enzymatically using Klenow exo(-) fragment of DNA Polymerase I. All the above types of nanowires are characterized by a narrow-size distribution of molecules. The contour length of the molecules can be varied from tens to hundreds of nanometers. These structures possess improved conductive and mechanical properties with respect to a canonical random-sequenced DNA and can possibly be used as wire-like conducting or semiconducting nanostructures in the field of nanoelectronics.
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Affiliation(s)
- Alexander Kotlyar
- Department of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel.
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Kovalska VB, Losytskyy MY, Yarmoluk SM, Lubitz I, Kotlyar AB. Mono and trimethine cyanines Cyan 40 and Cyan 2 as probes for highly selective fluorescent detection of non-canonical DNA structures. J Fluoresc 2010; 21:223-30. [PMID: 20809136 DOI: 10.1007/s10895-010-0709-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Accepted: 08/11/2010] [Indexed: 01/14/2023]
Abstract
Two of earlier reported dsDNA sensitive cyanine dyes-monomethine Cyan 40 and meso-substituted trimethine Cyan 2 were studied for their ability to interact with non-canonical DNA conformations. These dyes were characterized by spectral-luminescent methods in the presence of G-quadruplex, triplex and dsDNA motifs. We have demonstrated that Cyan 2 binds strongly and preferentially to triple- and quadruple-stranded DNA forms that results in a strong enhancement of the dye fluorescence, as compared to dsDNA, while Cyan 40 form fluorescent complexes preferentially only with the triplex form. Highly fluorescent complexes of Cyan 2 with DNA triplexes and G-quadruplexes and Cyan 40 with DNA triplexes are very stable and do not dissociate during gel electrophoresis, leading to preferential staining of the above DNA forms in gels. The data presented point to the intercalation mechanism of the Cyan 2 binding to G4-DNA, while the complexes of Cyan 40 and Cyan 2 with triplex DNA are believed to be formed via groove binding mode. The Cyan dyes can provide a highly sensitive method for detection and quantification of non-canonical structures in genome.
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Affiliation(s)
- Vladyslava B Kovalska
- Department of Combinatorial Chemistry, Institute of Molecular Biology and Genetics of the National Academy of Sciences of Ukraine, Kyiv, Ukraine.
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30
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Vayá I, Changenet-Barret P, Gustavsson T, Zikich D, Kotlyar AB, Markovitsi D. Long-lived fluorescence of homopolymeric guanine-cytosine DNA duplexes. Photochem Photobiol Sci 2010; 9:1193-5. [PMID: 20714677 DOI: 10.1039/c0pp00201a] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The fluorescence spectrum of the homopolymeric double helix poly(dG) x poly(dC) is dominated by emission decaying on the nanosecond time-scale, as previously reported for the alternating homologue poly(dGdC) x poly(dGdC). Thus, energy trapping over long periods of time is a common feature of GC duplexes which contrast with AT duplexes. The impact of such behaviour on DNA photodamage needs to be evaluated.
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Affiliation(s)
- Ignacio Vayá
- Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM-CNRS URA 2453, 91191, Gif-sur-Yvette, France
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31
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Lubitz I, Zikich D, Kotlyar A. Specific high-affinity binding of thiazole orange to triplex and G-quadruplex DNA. Biochemistry 2010; 49:3567-74. [PMID: 20329708 DOI: 10.1021/bi1000849] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Interaction of Thiazole Orange (TO) with double-, triple-, and quadruple-stranded forms of DNA was studied. We have demonstrated by UV-vis absorption, circular dichroism (CD), and fluorescence spectroscopy that TO binds with much higher affinity to triplex and G-quadruplex DNA structures compared to double-stranded (ds) DNA. Complexes of the dye with DNA triplexes and G-quadruplexes are very stable and do not dissociate during chromatography and gel electrophoresis. TO binding to either triple- or quadruple-stranded DNA structures results in a >1000-fold increase in dye fluorescence. The fluorescence titration data showed that TO to triad and tetrad ratios, in tight complexes with the triplex and the G-quadruplex, are equal to 0.5 and 1, respectively. Preferential binding of TO to triplexes and G-quadruplexes enables selective detection of only these DNA forms in gels in the absence of free TO in electrophoresis running buffer. We have also demonstrated that incubation of U2OS cells with submicromolar concentrations of TO results in preferential staining of certain areas in the nucleus in contrast to DAPI which binds to dsDNA and efficiently stains regions that are unstained with TO. We suggest that TO staining may be useful for the detection of noncanonical structural motifs in genomic DNA.
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Affiliation(s)
- Irit Lubitz
- Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Israel
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32
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Wang H, Lin J, Wang C, Zhang X, An H, Zhou X, Sun J, Hu J. Evaluation of the radial deformability of poly(dG)-poly(dC) DNA and G4-DNA using vibrating scanning polarization force microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:7523-7528. [PMID: 20095534 DOI: 10.1021/la904329q] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Poly(dG)-poly(dC) DNA and G4-DNA are two types of synthetic molecules that are regarded as promising candidates for molecular nanodevices. In this work, vibrating scanning polarization force microscopy (VSPFM) was employed to study the radial deformability of these two molecules coadsorbed on a Ni(2+)-modified mica surface. The values of the radial compressive elastic modulus of these two types of molecules were found to be similar (approximately 5-10 MPa) when the external loading force was between approximately 0.04 and approximately 0.12 nN. However, G4-DNA molecules possessed higher stiffness than poly(dG)-poly(dC) DNA (approximately 20-40 vs approximately 10-20 MPa) when the loading force was larger than approximately 0.12 nN. The results will aid us in understanding these molecule's mechanical performances.
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Affiliation(s)
- Huabin Wang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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33
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Zikich D, Borovok N, Molotsky T, Kotlyar A. Synthesis and AFM characterization of poly(dG)-poly(dC)-gold nanoparticle conjugates. Bioconjug Chem 2010; 21:544-7. [PMID: 20166677 DOI: 10.1021/bc900527a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the present work, we have synthesized conjugates between the 5 nm gold nanoparticles (Au-NP) and 5' thiol-functionalized, 700 bp poly(dG)-poly(dC). We have completely separated and purified to homogeneity conjugates bearing different number of poly(dG)-poly(dC) molecules per Au-NP by electrophoresis and HPLC. The conjugates were directly visualized by atomic force microscopy. We have demonstrated that Au NP-bound poly(dG)-poly(dC) can be considerably extended by Klenow exo(-) polymerase in the presence of dCTP and dGTP.
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Affiliation(s)
- Dragoslav Zikich
- Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, The Center for Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, 69978
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Cavallari M, Garbesi A, Di Felice R. Porphyrin Intercalation in G4-DNA Quadruplexes by Molecular Dynamics Simulations. J Phys Chem B 2009; 113:13152-60. [DOI: 10.1021/jp9039226] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Manuela Cavallari
- INFM-CNR National Center on nanoStructures and bioSystems at Surfaces (S3), I-41100 Modena, Italy
| | - Anna Garbesi
- INFM-CNR National Center on nanoStructures and bioSystems at Surfaces (S3), I-41100 Modena, Italy
| | - Rosa Di Felice
- INFM-CNR National Center on nanoStructures and bioSystems at Surfaces (S3), I-41100 Modena, Italy
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35
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Borovok N, Iram N, Zikich D, Ghabboun J, Livshits GI, Porath D, Kotlyar AB. Assembling of G-strands into novel tetra-molecular parallel G4-DNA nanostructures using avidin-biotin recognition. Nucleic Acids Res 2008; 36:5050-60. [PMID: 18663013 PMCID: PMC2528189 DOI: 10.1093/nar/gkn459] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We describe a method for the preparation of novel long (hundreds of nanometers), uniform, inter-molecular G4-DNA molecules composed of four parallel G-strands. The only long continuous G4-DNA reported so far are intra-molecular structures made of a single G-strand. To enable a tetra-molecular assembly of the G-strands we developed a novel approach based on avidin–biotin biological recognition. The steps of the G4-DNA production include: (i) Enzymatic synthesis of long poly(dG)-poly(dC) molecules with biotinylated poly(dG)-strand; (ii) Formation of a complex between avidin-tetramer and four biotinylated poly(dG)-poly(dC) molecules; (iii) Separation of the poly(dC) strands from the poly(dG)-strands, which are connected to the avidin; (iv) Assembly of the four G-strands attached to the avidin into tetra-molecular G4-DNA. The average contour length of the formed structures, as measured by AFM, is equal to that of the initial poly(dG)-poly(dC) molecules, suggesting a tetra-molecular mechanism of the G-strands assembly. The height of tetra-molecular G4-nanostructures is larger than that of mono-molecular G4-DNA molecules having similar contour length. The CD spectra of the tetra- and mono-molecular G4-DNA are markedly different, suggesting different structural organization of these two types of molecules. The tetra-molecular G4-DNA nanostructures showed clear electrical polarizability. This suggests that they may be useful for molecular electronics.
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Affiliation(s)
- Natalia Borovok
- Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978
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36
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Shapir E, Sagiv L, Borovok N, Molotski T, Kotlyar AB, Porath D. High-Resolution STM Imaging of Novel Single G4-DNA Molecules. J Phys Chem B 2008; 112:9267-9. [DOI: 10.1021/jp803478f] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Errez Shapir
- Physical Chemistry Department, The Hebrew University, Jerusalem 91904, Israel, and Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Israel
| | - Lior Sagiv
- Physical Chemistry Department, The Hebrew University, Jerusalem 91904, Israel, and Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Israel
| | - Natalia Borovok
- Physical Chemistry Department, The Hebrew University, Jerusalem 91904, Israel, and Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Israel
| | - Tatiana Molotski
- Physical Chemistry Department, The Hebrew University, Jerusalem 91904, Israel, and Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Israel
| | - Alexander B. Kotlyar
- Physical Chemistry Department, The Hebrew University, Jerusalem 91904, Israel, and Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Israel
| | - Danny Porath
- Physical Chemistry Department, The Hebrew University, Jerusalem 91904, Israel, and Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Israel
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Tanaka A, Matsuo Y, Hashimoto Y, Ijiro K. Sequence-specifically platinum metal deposition on enzymatically synthesized DNA block copolymer. Chem Commun (Camb) 2008:4270-2. [DOI: 10.1039/b805989f] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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Shapir E, Cohen H, Calzolari A, Cavazzoni C, Ryndyk DA, Cuniberti G, Kotlyar A, Di Felice R, Porath D. Electronic structure of single DNA molecules resolved by transverse scanning tunnelling spectroscopy. NATURE MATERIALS 2008; 7:68-74. [PMID: 18037894 DOI: 10.1038/nmat2060] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2007] [Accepted: 10/15/2007] [Indexed: 05/25/2023]
Abstract
Attempts to resolve the energy-level structure of single DNA molecules by scanning tunnelling spectroscopy span over the past two decades, owing to the unique ability of this technique to probe the local density of states of objects deposited on a surface. Nevertheless, success was hindered by extreme technical difficulties in stable deposition and reproducibility. Here, by using scanning tunnelling spectroscopy at cryogenic temperature, we disclose the energy spectrum of poly(G)-poly(C) DNA molecules deposited on gold. The tunnelling current-voltage (I-V) characteristics and their derivative (dI/dV-V) curves at 78 K exhibit a clear gap and a peak structure around the gap. Limited fluctuations in the I-V curves are observed and statistically characterized. By means of ab initio density functional theory calculations, the character of the observed peaks is generally assigned to groups of orbitals originating from the different molecular components, namely the nucleobases, the backbone and the counterions.
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Affiliation(s)
- Errez Shapir
- Physical Chemistry Department and Center for Nanoscience and Nanotechnology, The Hebrew University, Jerusalem 91904, Israel
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Klinov D, Atlasov K, Kotlyar A, Dwir B, Kapon E. DNA nanopositioning and alignment by electron-beam-induced surface chemical patterning. NANO LETTERS 2007; 7:3583-3587. [PMID: 18044947 DOI: 10.1021/nl072177y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Nanopositioning and alignment of arrays of DNA molecules on a surface by combination of high-resolution prepatterning and standard macroscopic deposition is presented. Direct electron beam exposure of a graphite substrate activated by amino groups neutralizes locally the surface charge, preventing the DNA adhesion during the consequent deposition. Because of the high resolution of the electron beam writing process, precise active patches can be created directly on the functionalized surface. Narrow (50 nm) stripe patterns produce both positioning and alignment acting as electrostatic traps for the DNA molecules. The approach is demonstrated using triple- and double-stranded DNA of medium length (350 nm). High yield of alignment and regular arrangement of the deposited molecules are achieved in a simple way within large areas.
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Affiliation(s)
- Dmitry Klinov
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Laboratory of Physics of Nanostructures CH-1015, Lausanne, Switzerland
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Borovok N, Molotsky T, Ghabboun J, Cohen H, Porath D, Kotlyar A. Poly(dG)-poly(dC) DNA appears shorter than poly(dA)-poly(dT) and possibly adopts an A-related conformation on a mica surface under ambient conditions. FEBS Lett 2007; 581:5843-6. [PMID: 18053809 DOI: 10.1016/j.febslet.2007.11.058] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2007] [Revised: 10/10/2007] [Accepted: 11/14/2007] [Indexed: 10/22/2022]
Abstract
Three types of DNA: approximately 2700 bp polydeoxyguanylic olydeoxycytidylic acid [poly(dG)-poly(dC)], approximately 2700 bp polydeoxyadenylic polydeoxythymidylic acid [poly(dA)-poly(dT)] and 2686 bp linear plasmid pUC19 were deposited on a mica surface and imaged by atomic force microscopy. Contour length measurements show that the average length of poly(dG)-poly(dC) is approximately 30% shorter than that of poly(dA)-poly(dT) and the plasmid. This led us to suggest that individual poly(dG)-poly(dC) molecules are immobilized on mica under ambient conditions in a form which is likely related to the A-form of DNA in contrast to poly(dA)-poly(dT) and random sequence DNA which are immobilized in a form that is related to the DNA B-form.
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Affiliation(s)
- Natalia Borovok
- Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
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Efficient procedure of preparation and properties of long uniform G4-DNA nanowires. Anal Biochem 2007; 374:71-8. [PMID: 17996714 DOI: 10.1016/j.ab.2007.10.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2007] [Revised: 10/08/2007] [Accepted: 10/13/2007] [Indexed: 10/22/2022]
Abstract
Here we describe a novel and efficient procedure for preparation of long uniform G4-DNA wires. The procedure includes (i) enzymatic synthesis of double-stranded DNA molecules consisting of long (up to 10,000 bases), continuous G strands and chains of complementary (dC)20-oligonucleotides, poly(dG)-n(dC)20; (ii) size exclusion HPLC separation of the G strands from the (dC)20 oligonucleotides in 0.1M NaOH; and (iii) folding of the purified G strands into G4-DNA structures by lowering the pH to 7.0. We show by atomic force microscopy (AFM) that the preparation procedure yielded G4-DNA wires with a uniform morphology and a narrow length distribution. The correlation between the total amount of nucleotides in the G strands and the contour length of the G4-DNA molecules estimated by AFM suggests monomolecular folding of the G strands into quadruplex structures. The folding takes place either in the presence or in the absence of stabilizing ions (K+ or Na+). The addition of these cations leads to a dramatic change in the circular dichroism spectrum of the G4-DNA.
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Platzer M, Hiller M, Szafranski K, Jahn N, Hampe J, Schreiber S, Backofen R, Huse K. Sequencing errors or SNPs at splice-acceptor guanines in dbSNP? Nat Biotechnol 2006; 24:1068-70. [PMID: 16964207 DOI: 10.1038/nbt0906-1068b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Tanaka A, Matsuo Y, Ijiro K. Immobilizing and stretching of poly(dG)–poly(dC) synthesized by Klenow fragment exo− on substrates by LB method. Colloids Surf A Physicochem Eng Asp 2006. [DOI: 10.1016/j.colsurfa.2005.11.055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Kotlyar A, Borovok N, Molotsky T, Klinov D, Dwir B, Kapon E. Synthesis of novel poly(dG)-poly(dG)-poly(dC) triplex structure by Klenow exo- fragment of DNA polymerase I. Nucleic Acids Res 2005; 33:6515-21. [PMID: 16314313 PMCID: PMC1292991 DOI: 10.1093/nar/gki963] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The extension of the G-strand of long (700 bp) poly(dG)-poly(dC) by the Klenow exo(-) fragment of DNA polymerase I yields a complete triplex structure of the H-DNA type. High-performance liquid chromatography analysis demonstrates that the length of the G-strand is doubled during the polymerase synthesis. Fluorescence resonance energy transfer analysis shows that the 5' ends of the G- and the C-strands, labeled with fluorescein and TAMRA, respectively, are positioned close to each other in the product of the synthesis. Atomic force microscopy morphology imaging shows that the synthesized structures lack single-stranded fragments and have approximately the same length as the parent 700 bp poly(dG)-poly(dC). CD spectrum of the polymer has a large negative peak at 278 nm, which is characteristic of the poly(dG)-poly(dG)-poly(dC) triplex. The polymer is resistant to DNase and interacts much more weakly with ethidium bromide as compared with the double-stranded DNA.
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Affiliation(s)
- Alexander Kotlyar
- Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978 Israel.
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Hartig JS, Kool ET. Efficient isothermal expansion of human telomeric and minisatellite repeats by Thermococcus litoralis DNA polymerase. Nucleic Acids Res 2005; 33:4922-7. [PMID: 16284196 PMCID: PMC1199558 DOI: 10.1093/nar/gki803] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Repeating DNA sequences, such as telomeres, centromeres, and micro- and mini-satellites, comprise 50% of the genome and play important roles in regulatory and pathogenic mechanisms. In order to study structures and functions of such repeating sequences, it is important to have simple and efficient methods for making them in vitro. Here, we describe the efficient and convenient expansion of repetitive telomeric and minisatellite DNA sequences starting from small synthetic templates to final product lengths of several hundreds to thousands of nucleotides by the thermostable DNA polymerase from Thermococcus litoralis (Vent DNA polymerase). This enzyme was so far unknown to catalyze repeat expansion. Either single-stranded or double-stranded DNAs could be produced, depending on nucleotides present. Compared to earlier results obtained with other enzymes, the expansion reaction is highly efficient both in its yield and product length, and proceeds without thermal cycling. Moreover, the products are characterized by a narrow length distribution.
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Affiliation(s)
| | - Eric T. Kool
- To whom correspondence should be addressed. Tel: +1 650 724 4741; Fax: +1 650 725 0259;
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