scholarly journals Thermodynamically balanced inside-out (TBIO) PCR-based gene synthesis: a novel method of primer design for high-fidelity assembly of longer gene sequences

2003 ◽  
Vol 31 (22) ◽  
pp. 143e-143 ◽  
Author(s):  
X. Gao
Author(s):  
Wouter H. Vermeer ◽  
Justin D. Smith ◽  
Uri Wilensky ◽  
C. Hendricks Brown

AbstractPreventing adverse health outcomes is complex due to the multi-level contexts and social systems in which these phenomena occur. To capture both the systemic effects, local determinants, and individual-level risks and protective factors simultaneously, the prevention field has called for adoption of system science methods in general and agent-based models (ABMs) specifically. While these models can provide unique and timely insight into the potential of prevention strategies, an ABM’s ability to do so depends strongly on its accuracy in capturing the phenomenon. Furthermore, for ABMs to be useful, they need to be accepted by and available to decision-makers and other stakeholders. These two attributes of accuracy and acceptability are key components of open science. To ensure the creation of high-fidelity models and reliability in their outcomes and consequent model-based decision-making, we present a set of recommendations for adopting and using this novel method. We recommend ways to include stakeholders throughout the modeling process, as well as ways to conduct model verification, validation, and replication. Examples from HIV and overdose prevention work illustrate how these recommendations can be applied.


2010 ◽  
Vol 28 (12) ◽  
pp. 1295-1299 ◽  
Author(s):  
Sriram Kosuri ◽  
Nikolai Eroshenko ◽  
Emily M LeProust ◽  
Michael Super ◽  
Jeffrey Way ◽  
...  

2020 ◽  
Vol 48 (16) ◽  
pp. e95-e95 ◽  
Author(s):  
Angus M Sidore ◽  
Calin Plesa ◽  
Joyce A Samson ◽  
Nathan B Lubock ◽  
Sriram Kosuri

Abstract Multiplexed assays allow functional testing of large synthetic libraries of genetic elements, but are limited by the designability, length, fidelity and scale of the input DNA. Here, we improve DropSynth, a low-cost, multiplexed method that builds gene libraries by compartmentalizing and assembling microarray-derived oligonucleotides in vortexed emulsions. By optimizing enzyme choice, adding enzymatic error correction and increasing scale, we show that DropSynth can build thousands of gene-length fragments at >20% fidelity.


2001 ◽  
Vol 105 (1) ◽  
pp. 5-15 ◽  
Author(s):  
Arthur Schüβler ◽  
Hans Gehrig ◽  
Daniel Schwarzott ◽  
Chris Walker

2021 ◽  
pp. 114146
Author(s):  
Saygın Hüseyin Portakal ◽  
Beyza Kanat ◽  
Murat Sayan ◽  
Burak Berber ◽  
Osman Doluca

2019 ◽  
Author(s):  
Angus M. Sidore ◽  
Calin Plesa ◽  
Joyce A. Samson ◽  
Sriram Kosuri

AbstractMultiplexed assays allow functional testing of large synthetic libraries of genetic elements, but are limited by the designability, length, fidelity and scale of the input DNA. Here we improve DropSynth, a low-cost, multiplexed method which builds gene libraries by compartmentalizing and assembling microarray-derived oligos in vortexed emulsions. By optimizing enzyme choice, adding enzymatic error correction, and increasing scale, we show that DropSynth can build thousands of gene-length fragments at >20% fidelity.


Blood ◽  
2002 ◽  
Vol 100 (1) ◽  
pp. 299-305 ◽  
Author(s):  
Kevin E. Sanders ◽  
John Lo ◽  
Stephen G. Sligar

Abstract For many years, human hemoglobin (Hb) isolated from erythrocytes has been investigated as a potential oxygen delivery therapeutic. Advantages with respect to the need for blood typing were balanced with various undesirable properties of cell-free Hb, including cost, overall oxygen affinity, alterations in cooperativity, and ready dissociation into toxic dimeric species. The use of total gene synthesis has resulted in very high levels of functional human Hb expression inEscherichia coli, but there remains a desire for effecting the crosslinking of the hemoglobin tetramer and providing for ready means for increasing the globular molecular weight. In this communication, we report a novel method for linking alpha chains. By circularly permuting one alpha sequence, the second alpha chain in the Hb tetramer can be linked with glycine residues to form 2 bridges across the central cavity. The second alpha chain thus presents its amino and carboxyl termini on a solvent exposed surface, providing for additional polymerization of oxygen-carrying subunits or attachment of any other peptide-based therapeutic.


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