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DNA sequence design using templates

Masanori Arita, Satoshi Kobayashi
2002 New generation computing  
Sequence design is a crucial problem in information-based biotechnology such as DNA-based computation.  ...  We introduce a simple strategy named template method that systematically generates a set of sequences of length l such that any of its member will have approximately l/3 mismatches with other sequences  ...  Hereafter, the word 'sequence' is used for DNA sequences to be designed (i.e. 4-alphabet words), whereas 'string' is for templates or binary codewords. The length of a string is denoted |x|.  ... 
doi:10.1007/bf03037360 fatcat:gtq2gxlulvdlpkcimv5svekbku

Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies

S. A. F. T. van Hijum, A. L. Zomer, O. P. Kuipers, J. Kok
2005 Nucleic Acids Research  
Primer design takes into account that, in many cases, contig ends contain unreliable DNA sequences and repetitive sequences.  ...  Moreover, when using multiple fragments of a template genome, primers for multiplex PCR strategies can also be designed.  ...  Primer design for multiplex PCR purposes In the case that multiple DNA sequences are used as template, multiplex PCR primers are designed to close gaps between contigs that are mapped onto the edges of  ... 
doi:10.1093/nar/gki356 pmid:15980536 pmcid:PMC1160117 fatcat:pul5iqku5rcgtjoqiplwvd57ky

Methodological improvements of pyrosequencing technology

Baback Gharizadeh, Michael Akhras, Nader Nourizad, Mehran Ghaderi, Kenji Yasuda, Pål Nyrén, Nader Pourmand
2006 Journal of Biotechnology  
Pyrosequencing technology is a rather novel DNA sequencing method based on the sequencing-bysynthesis principle.  ...  This bioluminometric, real-time DNA sequencing technique employs a cascade of four enzymatic reactions producing sequence peak signals.  ...  BG02-short can be used for short and rapid sequence results. BG03-long is designed for use with relatively longer sequences.  ... 
doi:10.1016/j.jbiotec.2006.01.025 pmid:16530870 pmcid:PMC2933062 fatcat:bghxh5vqrnd3ja6klcnlfwqszy

Easy quantification of template-directed CRISPR/Cas9 editing [article]

Eva Karina Brinkman, Arne Nedergaard Kousholt, Tim Harmsen, Christ Leemans, Tao Chen, Jos Jonkers, Bas van Steensel
2017 biorxiv/medrxiv   pre-print
Here, we adapted the widely used TIDE method for quantification of templated editing events, including point mutations.  ...  Template-directed CRISPR/Cas9 editing is a powerful tool for introducing subtle mutations in genomes.  ...  As input a sgRNA sequence string and three sequences are required: (1) wild-type control, (2) reference file with designed mutations in the used donor template and (3) composite test sample.  ... 
doi:10.1101/218156 fatcat:3xil6pg6rzci5hvwkzy2qmgory

DNAjig: A New Approach for Building DNA Nanostructures

Md. Muksitul Haque, Ananth Kalyanaraman, Amit Dhingra, Nehal Abu-Lail, Kaori Graybeal
2009 2009 IEEE International Conference on Bioinformatics and Biomedicine  
In this paper, we propose a new design methodology called DNAjig to build DNA nanostructures.  ...  DNA self-assembly is an emerging technique in DNA nanotechnology that holds promise for high impact applications such as in the synthesis of DNA-based nanodevices in medicine, robotics and electronics.  ...  ACKNOWLEDGMENTS We are grateful to Paul Rothemund for helping us in the understanding of DNA self-assembly and origami technique via constructive discussions and email exchanges.  ... 
doi:10.1109/bibm.2009.71 dblp:conf/bibm/HaqueKDAG09 fatcat:ialfsqd2bfb6blsc23k3tu7o2q

Barcoding blood meals: New vertebrate-specific primer sets for assigning taxonomic identities to host DNA from mosquito blood meals

Lawrence E. Reeves, Jennifer L. Gillett-Kaufman, Akito Y. Kawahara, Phillip E. Kaufman, Fabiano Oliveira
2018 PLoS Neglected Tropical Diseases  
Modern blood meal analyses rely on polymerase chain reaction (PCR), DNA sequencing, and bioinformatic comparisons of blood meal DNA sequences to reference databases.  ...  Here, we present new primer sets designed to amplify fragments of the DNA barcoding region of the vertebrate COI gene, while avoiding co-amplification of mosquito templates, without multiplexed or nested  ...  suggestions in primer design.  ... 
doi:10.1371/journal.pntd.0006767 pmid:30161128 fatcat:d4bv2obcgnhvxne3zpjt26qi5y

Primer Design Using Polymerase Chain Reaction for SNPs Analysis in SLC22A1 rs622342 Encoding OCT1 as Metformin Main Transporter

Rochmy Istikharah, Vitarani Dwi Ananda Ningrum, Maylinda Gemantari
2018 Journal of Pharmacy and Nutrition Science  
Sensitivity test was performed on PCR condition using a variety of volumes and DNA template qualities undergoing multiple freeze-thaw cycles.  ...  Such PCR condition could amplify DNA with 0.2 µL of template volume and 7 freeze-thaw cycles.  ...  Primer Design and Analysis Sequence of DNA template, which encodes OCT1, with 285bp of length containing rs622342 from NCBI website (http://www.ncbi.nlm.nih.gov/snp) was used to design specific primers  ... 
doi:10.6000/1927-5951.2018.08.02.4 fatcat:dn3i3waljnga3dmlhh32cr43ce

An Integrated System for DNA Sequencing by Synthesis Using Novel Nucleotide Analogues

Jia Guo, Lin Yu, Nicholas J. Turro, Jingyue Ju
2010 Accounts of Chemical Research  
The sequence of a DNA template immobilized on a surface via click chemistry is unambiguously identified with this chip-SBS system.  ...  It has been established that millions of DNA templates can be immobilized on a chip surface through a variety of approaches.  ...  We then performed SBS using four CF-NRTs to identify the sequence of a DNA template immobilized on a chip via click chemistry.  ... 
doi:10.1021/ar900255c pmid:20121268 pmcid:PMC2857541 fatcat:cadfkgyqyff7veicpcsfebmmsu

Efficient CRISPR/Cas9-Mediated Genome Editing Using a Chimeric Single-Guide RNA Molecule

Haroon Butt, Ayman Eid, Zahir Ali, Mohamed A. M. Atia, Morad M. Mokhtar, Norhan Hassan, Ciaran M. Lee, Gang Bao, Magdy M. Mahfouz
2017 Frontiers in Plant Science  
We used chimeric single-guide RNA (cgRNA) molecules carrying both sequences for target site specificity (to generate the double-strand breaks) and repair template sequences (to direct HDR), flanked by  ...  Gene editing was more efficient in rice protoplasts using repair templates complementary to the non-target DNA strand, rather than the target strand.  ...  RESULTS Design and Construction of Chimeric gRNA Repair-Templates for Genome Editing To investigate whether a cgRNA can be used as a template for DNA repair in plant cells, we designed several modalities  ... 
doi:10.3389/fpls.2017.01441 pmid:28883826 pmcid:PMC5573723 fatcat:kzprysee2jfjbfdny37konsu4q

DNA polymerase preference determines PCR priming efficiency

Wenjing Pan, Miranda Byrne-Steele, Chunlin Wang, Stanley Lu, Scott Clemmons, Robert J Zahorchak, Jian Han
2014 BMC Biotechnology  
The DNA polymerase preference for certain sequence motifs was verified by amplification from single-primer templates.  ...  Results: Here, high throughput sequencing was used to systematically demonstrate and characterize DNA polymerase priming bias.  ...  The identified bias patterns were used to guide primer design.  ... 
doi:10.1186/1472-6750-14-10 pmid:24479830 pmcid:PMC3937175 fatcat:yobshi6b5bfypl4c3v6vgtarha

Four PCR primers necessary for the detection of periplasmic nitrate reductase genes in all groups of Proteobacteria and in environmental DNA

Tobias Klatte, Laura Evans, Rebekah N. Whitehead, Jeffrey A. Cole
2011 Biochemical Society Transactions  
Using an iterative approach, we report the first successful design of three forward oligonucleotide primers and one reverse primer that, in three separate PCRs, can amplify napA DNA from all five groups  ...  All 140 napA sequences currently listed in the NCBI (National Center for Biotechnology Information) database are predicted to be amplified by one or more of these primer pairs.  ...  Amplification of napA sequences using community DNA as a template We recently described the use of community DNA from the faeces of patients suffering from the gastric diseases ulcerative colitis, irritable  ... 
doi:10.1042/bst0390321 pmid:21265796 pmcid:PMC3064403 fatcat:yqp576vykffntohl4pml6pq4em

Connecting DNA Origami Structures into a Designed and Functionalized Network

George Amoako
2019 Journal of Materials Science Research  
These approaches were used to design DNA origami structures and to functionalize them with gold nanoparticles after designing attachment sites on the DNA origami structures.  ...  Finally, use was made of the specific affinity interaction between biotin and streptavidin to connect the DNA origami templated AuNP helices to the cross-like structure.  ...  The sequences from the designed connection sites were extended with biotin. The AuNP helices were formed using a DNA origami nanotube as the template.  ... 
doi:10.5539/jmsr.v8n4p14 fatcat:iiixp4xjerf2hciu3mewowjerm

Optimizing sgRNA length to improve target specificity and efficiency for the GGTA1 gene using the CRISPR/Cas9 gene editing system

Anders W. Matson, Nora Hosny, Zachary A. Swanson, Bernhard J. Hering, Christopher Burlak, Alfred S. Lewin
2019 PLoS ONE  
The sgRNA was tested against synthetic double stranded DNA templates replicating both the native GGTA1 DNA template and the two most likely off-target binding sites in the porcine genome.  ...  Extension of sgRNA length, responsible for recognition of the target DNA sequence for Cas9 cleavage, resulted in improved specificity for the GGTA1 gene and less off-target DNA cleavage.  ...  Masato Yamamoto for permitting us to use their equipment. Finally, thank you to Dr. Amar Singh and Dr.  ... 
doi:10.1371/journal.pone.0226107 pmid:31821359 pmcid:PMC6903732 fatcat:viikcv2sazczdmt4wrfw7imcae

Combining CRISPR/Cas9 and rAAV Templates for Efficient Gene Editing

Manuel Kaulich, Steven F. Dowdy
2015 Nucleic Acid Therapeutics  
The ease-of-use of the CRISPR/Cas9 system to introduce genomic DNA breaks at specific sites in vivo has led to its rapid and wide adoption.  ...  However, in the presence of a homologous DNA template, homology-directed repair occurs with variable efficiencies.  ...  In addition to the design of guide RNA and FIG. 4. HDR template design strategies.  ... 
doi:10.1089/nat.2015.0545 pmid:26540648 pmcid:PMC4657517 fatcat:a7tujuvdrzd3pkvk3ukkyamgxm

Page 43 of Infertility and Reproductive Medicine Clinics of North America Vol. 5, Issue 1 [page]

1994 Infertility and Reproductive Medicine Clinics of North America  
Next, one of a variety of commercially available dideoxy sequencing kits designed for use with ssDNA templates can be used.  ...  Cycle Sequencing of DNA Many of the problems encountered in sequencing ds PCR templates are addressed by the cycle sequencing method.* % 72 ** The cycle sequencing procedure is designed to specifically  ... 
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