Query: DNA sequence motifs for structure-specific recognition and separation of carbon nano- tubes

Candidate papers:

abstract: Single walled carbon nanotubes (SWNTs) are a family of molecules that have the same cylindrical shape but different chiralities. Many fundamental studies and technological applications of SWNTs require a population of tubes with identical chirality that current syntheses cannot provide. The SWNT sorting problem that is, separation of a synthetic mixture of tubes into individual single chirality components has attracted considerable attention in recent years. Intense efforts so far have focused largely on, and resulted in solutions for, a weaker version of the sorting problem: metal/semiconductor separation. A systematic and general method to purify each and every single chirality species of the same electronic type from the synthetic mixture of SWNTs is highly desirable, but the task has proven to be insurmountable to date. Here we report such a method, which allows purification of all 12 major single chirality semiconducting species from a synthetic mixture, with sufficient yield for both fundamental studies and application development. We have designed an effective search of a DNA library of ~1060 in size, and have identified more than 20 short DNA sequences, each of which recognizes and enables chromatographic purification of a particular nanotube species from the synthetic mixture. Recognition sequences exhibit a periodic purine pyrimidines pattern, which can undergo hydrogen bonding to form a two dimensional sheet, and fold selectively on nanotubes into a well ordered three dimensional barrel. We propose that the ordered two dimensional sheet and three dimensional barrel provide the structural basis for the observed DNA recognition of SWNTs.
author_names: Xiaomin X Tu

Suresh Manohar

Anand Jagota

Ming Zheng
title: DNA sequence motifs for structure specific recognition and separation of carbon nanotubes
venue: Nature
year: 2009

abstract: Carbon nanotubes are man made one dimensional carbon crystals with different diameters and chiralities. Owing to their superb mechanical and electrical properties, many potential applications have been proposed for them. However, polydispersity and poor solubility in both aqueous and non aqueous solution impose a considerable challenge for their separation and assembly, which is required for many applications. Here we report our finding of DNA assisted dispersion and separation of carbon nanotubes. Bundled single walled carbon nanotubes are effectively dispersed in water by their sonication in the presence of single stranded DNA (ssDNA) Optical absorption and fluorescence spectroscopy and atomic force microscopy measurements provide evidence for individually dispersed carbon nanotubes. Molecular modelling suggests that ssDNA can bind to carbon nanotubes through p stacking, resulting in helical wrapping to the surface. The binding free energy of ssDNA to carbon nanotubes rivals that of two nanotubes for each other. We also demonstrate that DNA coated carbon nanotubes can be separated into fractions with different electronic structures by ion exchange chromatography. This finding links one of the central molecules in biology to a technologically very important nanomaterial, and opens the door to carbon nanotube based applications in biotechnology.
author_names: Ming Zheng

Anand Jagota

Ellen D Semke

Bruce A Diner

Robert S McLean

Steven R Lustig

Raymond E Richardson

Nancy G Tassi
title: DNA assisted dispersion and separation of carbon nanotubes
venue: Nature materials
year: 2003

abstract: For a successful analysis of the relation between amino acid sequence and protein structure, an unambiguous and physically meaningful definition of secondary structure is essential. We have developed a set of simple and physically motivated criteria for secondary structure, programmed as a pattern recognition process of hydrogen bonded and geometrical features extracted from x ray coordinates. Cooperative secondary structure is recognized as repeats of the elementary hydrogen bonding patterns "turn" and "bridge." Repeating turns are "helices," repeating bridges are "ladders," connected ladders are "sheets." Geometric structure is defined in terms of the concepts torsion and curvature of differential geometry. Local chain "chirality" is the torsional handedness of four consecutive Ca positions and is positive for right handed helices and negative for ideal twisted b sheets. Curved pieces are defined as "bends." Solvent "exposure" is given as the number of water molecules in possible contact with a residue. The end result is a compilation of the primary structure, including SS bonds, secondary structure, and solvent exposure of 62 different globular proteins. The presentation is in linear form: strip graphs for an overall view and strip tables for the details of each of 10.925 residues. The dictionary is also available in computer readable form for protein structure prediction work.
author_names: Wolfgang Kabsch

Christian A Sander
title: Dictionary of protein secondary structure: Pattern recognition of hydrogen bonded and geometrical features
venue: Biopolymers
year: 1983

abstract: Publisher Summary This chapter discusses the specific synthesis of deoxyribonucleic acid (DNA) in vitro through the medium of a polymerase catalyzed chain reaction. A method whereby a nucleic acid sequence can be exponentially amplified in vitro is described in the chapter. The same method can be used to alter the amplified sequence or to append new sequence information to it. It is necessary that the ends of the sequence be known in sufficient detail that oligonucleotides can be synthesized, which will hybridize to them and that a small amount of the sequence be available to initiate the reaction. The oligonucleotides are complementary to different strands of the desired sequence and at relative positions along the sequence such that the DNA polymerase extension product of the one, when denatured, can serve as a template for the other and vice versa. Oligonucleotides were synthesized using an automated DNA synthesis machine (Biosearch, Inc. San Rafael, California) using phosphoramidite chemistry. "Mispriming" can be usefully employed to make intentional in vitro mutations or to add sequence information to one or both ends of a given sequence. The chapter explores the possibility of utilizing a heat stable DNA polymerase so as to avoid the need for addition of new enzyme after each cycle of thermal denaturation
author_names: Kary Banks Mullis

Fred Faloona
title: Specific synthesis of DNA in vitro via a polymerase catalyzed chain reaction.
venue: Methods in enzymology
year: 1987

abstract: The specific bonding of DNA base pairs provides the chemical foundation for genetics. This powerful molecular recognition system can be used in nanotechnology to direct the assembly of highly structured materials with specific nanoscale features, as well as in DNA computation to process complex information. The exploitation of DNA for material purposes presents a new chapter in the history of the molecule.
author_names: Nadrian C Seeman
title: DNA in a material world
venue: Nature
year: 2003

abstract: The discovery of specific restriction endonucleases (Smith and Wilcox 1970) made possible the isolation of discrete molecular fragments of naturally occurring DNA for the first time. This capability was crucial to the development of molecular cloning (Cohen et al. 1973) and the combination of molecular cloning and endonuclease restriction allowed the synthesis and isolation of any naturally occurring DNA sequence that could be cloned into a useful vector and, on the basis of flanking restriction sites, excised from it. The availability of a large variety of restriction enzymes (Roberts 1985) has significantly extended the utility of these methods. The de novo organic synthesis of oligonucleotides and the development of methods for their assembly into long double stranded DNA molecules (Davies and Gassen 1983) have removed, at least theoretically, the minor limitations imposed by the availability of natural sequences with fortuitously unique flanking restriction sites. However, de novo synthesis, even with automated equipment, is not easy; it is often fraught with peril due to the inevitable indelicacy of chemical reagents (Urdea et al. 1985; Watt et al. 1985; Mullenbach et al. 1986) and it is not capable of producing, intentionally, a sequence that is not yet fully known. We have been exploring an alternative method for the synthesis of specific DNA sequences (Fig. 1) It involves the reciprocal interaction of two oligonucleotides and the DNA polymerase extension products whose synthesis they prime, when they are hybridized to different strands of a DNA template in a relative orientation such that their extension products overlap. The method consists of repetitive cycles of denaturation, hybridization, and polymerase extension and seems not a little boring until the realization occurs that this procedure is catalyzing a doubling with each cycle in the amount of the fragment defined by the positions of the 5' ends of the two primers on the template DNA, that this fragment is therefore increasing in concentration exponentially, and that the process can be continued for many cycles and is inherently very specific. The original template DNA molecule could have been a relatively small amount of the sequence to be synthesized (in a pure form and as a discrete molecule) or it could have been the same sequence embedded in a much larger molecule in a complex mixture as in the case of a fragment of a single copy gene in whole human DNA. It could also have been a single stranded DNA molecule or, with a minor modification in the technique, it could have been an RNA molecule. In any case, the product of the reaction will be a discrete double stranded DNA molecule with termini corresponding to the 5' ends of the oligonucleotides employed. We have called this process polymerase chain reaction or (inevitably) PCR. Several embodiments have been devised that enable one not only to extract a specific sequence from a complex template and amplify it, but also to increase the inherent specificity of this process by using nested primer sets, or to append sequence information to one or both ends of the sequence as it is being amplified, or to construct a sequence entirely from synthetic fragments.
author_names: Kary Banks Mullis

Fred Faloona

Stephen Joel Scharf

Randall Keichi Saiki

G Horn

Henry A Erlich
title: Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction.
venue: Cold Spring Harbor symposia on quantitative biology
year: 1986

abstract: The DNA single walled carbon nanotube (SWCNT) hybrid molecule has attracted significant attention recently for its ability to disperse and sort SWCNTs according to their chirality. Key for utilizing their unique properties is an understanding of the structure of DNA adsorbed on the SWCNT surface, which we study here using molecular simulations. Using replica exchange molecular dynamics (REMD) we explore equilibrium structures formed by single strands of 12 mer oligonucleotides, of varying sequence, adsorbed on a (6,5) SWCNT. We find a consistent motif in which the DNA strand forms a right handed helical wrap around the SWCNT, stabilized by "stitches" (hydrogen bonding between distant bases) to itself. Variability among equilibrium populations of DNA self stitched structures was observed and shown to be directly influenced by DNA sequence and composition. Competition between conformational entropy and hydrogen bonding between bases is predicted to be responsible for the formation of random versus stitched configurations.
author_names: Daniel Roxbury

Anand Jagota

Jeetain Mittal
title: Sequence specific self stitching motif of short single stranded DNA on a single walled carbon nanotube.
venue: Journal of the American Chemical Society
year: 2011

abstract: ABSTRACT Cultured isolates of the marine cyanobacteria Prochlorococcus and Synechococcus vary widely in their pigment compositions and growth responses to light and nutrients, yet show greater than 96% identity in their 16S ribosomal DNA (rDNA) sequences. In order to better define the genetic variation that accompanies their physiological diversity, sequences for the 16S 23S rDNA internal transcribed spacer (ITS) region were determined in 32 Prochlorococcus isolates and 25 Synechococcus isolates from around the globe. Each strain examined yielded one ITS sequence that contained two tRNA genes. Dramatic variations in the length and G+C content of the spacer were observed among the strains, particularly among Prochlorococcus strains. Secondary structure models of the ITS were predicted in order to facilitate alignment of the sequences for phylogenetic analyses. The previously observed division of Prochlorococcus into two ecotypes (called high and low B/A after their differences in chlorophyll content) were supported, as was the subdivision of the high B/A ecotype into four genetically distinct clades. ITS based phylogenies partitioned marine cluster A Synechococcus into six clades, three of which can be associated with a particular phenotype (motility, chromatic adaptation, and lack of phycourobilin) The pattern of sequence divergence within and between clades is suggestive of a mode of evolution driven by adaptive sweeps and implies that each clade represents an ecologically distinct population. Furthermore, many of the clades consist of strains isolated from disparate regions of the world's oceans, implying that they are geographically widely distributed. These results provide further evidence that natural populations of Prochlorococcus and Synechococcus consist of multiple coexisting ecotypes, genetically closely related but physiologically distinct, which may vary in relative abundance with changing environmental conditions.
author_names: Gabrielle Rocap

Daniel L Distel

John B Waterbury

Sallie W Chisholm
title: Resolution of Prochlorococcus and Synechococcus Ecotypes by Using 16S 23S Ribosomal DNA Internal Transcribed Spacer Sequences
venue: Applied and Environmental Microbiology
year: 2002

abstract: Molecular self assembly presents a 'bottom up' approach to the fabrication of objects specified with nanometre precision. DNA molecular structures and intermolecular interactions are particularly amenable to the design and synthesis of complex molecular objects. We report the design and observation of two dimensional crystalline forms of DNA that self assemble from synthetic DNA double crossover molecules. Intermolecular interactions between the structural units are programmed by the design of 'sticky ends' that associate according to Watson Crick complementarity, enabling us to create specific periodic patterns on the nanometre scale. The patterned crystals have been visualized by atomic force microscopy.
author_names: Erik Winfree

Furong Liu

Lisa A Wenzler

Nadrian C Seeman
title: Design and self assembly of two dimensional DNA crystals
venue: Nature
year: 1998

abstract: The armchair carbon nanotube is an ideal system to study fundamental physics in one dimensional metals and potentially a superb material for applications such as electrical power transmission. Synthesis and purification efforts to date have failed to produce a homogeneous population of such a material. Here we report evolutionary strategies to find DNA sequences for the recognition and subsequent purification of (6,6) and (7,7) armchair species from synthetic mixtures. The new sequences were derived by single point scanning mutation and sequence motif variation of previously identified ones for semiconducting tubes. Optical absorption spectroscopy of the purified armchair tubes revealed well resolved first and second order electronic transitions accompanied by prominent sideband features that have neither been predicted nor observed previously. Resonance Raman spectroscopy showed a single Lorentzian peak for the in plane carbon carbon stretching mode (G band) of the armchair tubes, repudiating the common practice of using such a line shape to infer the absence of metallic species. Our work demonstrates the exquisite sensitivity of DNA to nanotube metallicity and makes the long anticipated pure armchair tubes available as seeds for their mass amplification.
author_names: Xiaomin X Tu

Angela R Hight Walker

Constantine Y Khripin

Ming Zheng
title: Evolution of DNA sequences toward recognition of metallic armchair carbon nanotubes.
venue: Journal of the American Chemical Society
year: 2011