ChemInform Abstract: Synthetic DNA-Oligonucleotides: Synthesis, Modifications, Applications

ChemInform ◽  
2010 ◽  
Vol 26 (50) ◽  
pp. no-no
Author(s):  
S. DUES ◽  
E. GRIESS
Keyword(s):  
Synthetic Dna ◽  
Dna Oligonucleotides ◽  
Oligonucleotides Synthesis

scholarly journals Integration of diverse DNA substrates by a casposase can be targeted to R-loops in vitro by its fusion to Cas9

2021 ◽  
Vol 41 (1) ◽  
Author(s):  
Chun Hang Lau ◽  
Edward L. Bolt
Keyword(s):  
Protein Complexes ◽  
Dna Integration ◽  
Synthetic Dna ◽  
Methanosarcina Mazei ◽  
Dna Oligonucleotides ◽  
Double Stranded Dna ◽  
Dna Insertion ◽  
Dna Capture ◽  
Target Molecules

Abstract CRISPR systems build adaptive immunity against mobile genetic elements by DNA capture and integration catalysed by Cas1–Cas2 protein complexes. Recent studies suggested that CRISPR repeats and adaptation module originated from a novel type of DNA transposons called casposons. Casposons encode a Cas1 homologue called casposase that alone integrates into target molecules single and double-stranded DNA containing terminal inverted repeats (TIRs) from casposons. A recent study showed Methanosarcina mazei casposase is able to integrate random DNA oligonucleotides, followed up in this work using Acidoprofundum boonei casposase, from which we also observe promiscuous substrate integration. Here we first show that the substrate flexibility of Acidoprofundum boonei casposase extends to random integration of DNA without TIRs, including integration of a functional gene. We then used this to investigate targeting of the casposase-catalysed DNA integration reactions to specific DNA sites that would allow insertion of defined DNA payloads. Casposase–Cas9 fusions were engineered that were catalytically proficient in vitro and generated RNA-guided DNA integration products from short synthetic DNA or a gene, with or without TIRs. However, DNA integration could still occur unguided due to the competing background activity of the casposase moiety. Expression of Casposase-dCas9 in Escherichia coli cells effectively targeted chromosomal and plasmid lacZ revealed by reduced β-galactosidase activity but DNA integration was not detected. The promiscuous substrate integration properties of casposases make them potential DNA insertion tools. The Casposase–dCas9 fusion protein may serves as a prototype for development in genetic editing for DNA insertion that is independent of homology-directed DNA repair.

scholarly journals In vitrosite-directed mutagenesis with synthetic DNA oligonucleotides yields unexpected deletions and insertions at high frequency

1983 ◽  
Vol 11 (24) ◽  
pp. 8595-8608 ◽  
Author(s):  
K.A. Osinga ◽  
A.M. van der Bliek ◽  
G. Van der Horst ◽  
M.J.A.Groot Koerkamp ◽  
H.F. Tabak ◽  
...  
Keyword(s):  
High Frequency ◽  
Directed Mutagenesis ◽  
Synthetic Dna ◽  
Dna Oligonucleotides

Recognition and elongation of telomeres by telomerase

Genome ◽  
1989 ◽  
Vol 31 (2) ◽  
pp. 553-560 ◽  
Author(s):  
Elizabeth H. Blackburn ◽  
Carol W. Greider ◽  
Eric Henderson ◽  
Margaret S. Lee ◽  
Janis Shampay ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
De Novo ◽  
Telomeric Sequence ◽  
Telomeric Dna ◽  
Synthetic Dna ◽  
Dna Oligonucleotides ◽  
Protein Components ◽  
Dynamic Structures

Telomeres stabilize chromosomal ends and allow their complete replication in vivo. In diverse eukaryotes, the essential telomeric DNA sequence consists of variable numbers of tandem repeats of simple, G + C rich sequences, with a strong strand bias of G residues on the strand oriented 5′ to 3′ toward the chromosomal terminus. This strand forms a protruding 3′ overhang at the chromosomal terminus in three different eukaryotes analyzed. Analysis of yeast and protozoan telomeres showed that telomeres are dynamic structures in vivo, being acted on by shortening and lengthening activities. We previously identified and partially purified an enzymatic activity, telomere terminal transferase, or telomerase, from the ciliate Tetrahymena. Telomerase is a ribonucleoprotein enzyme with essential RNA and protein components. This activity adds repeats of the Tetrahymena telomeric sequence, TTGGGG, onto the 3′ end of a single-stranded DNA primer consisting of a few repeats of the G-rich strand of known telomeric, and telomere-like, sequences. The shortest oligonucleotide active as a primer was the decamer G4T2G4. Structural analysis of synthetic DNA oligonucleotides that are active as primers showed that they all formed discrete intramolecular foldback structures at temperatures below 40 °C. Addition of TTGGGG repeats occurs one nucleotide at a time by de novo synthesis, which is not templated by the DNA primer. Up to 8000 nucleotides of G4T2 repeats were added to the primer in vitro. We discuss the implications of this finding for regulation of telomerase in vivo and a model for telomere elongation by telomerase.Key words: chromosome telomeres, telomerase, oligonucleotide repeats.

Validating siRNA using a reporter made from synthetic DNA oligonucleotides

2004 ◽  
Vol 325 (1) ◽  
pp. 243-249 ◽  
Author(s):  
Quan Du ◽  
Håkan Thonberg ◽  
Hong-Yan Zhang ◽  
Claes Wahlestedt ◽  
Zicai Liang
Keyword(s):  
Synthetic Dna ◽  
Dna Oligonucleotides

scholarly journals Scaling up DNA data storage and random access retrieval

2017 ◽  
Author(s):  
Lee Organick ◽  
Siena Dumas Ang ◽  
Yuan-Jyue Chen ◽  
Randolph Lopez ◽  
Sergey Yekhanin ◽  
...  
Keyword(s):  
Data Storage ◽  
Dna Sequences ◽  
Large Scale ◽  
Random Access ◽  
Attractive Alternative ◽  
Data Types ◽  
High Definition ◽  
Synthetic Dna ◽  
Dna Oligonucleotides ◽  
Order Of Magnitude

Current storage technologies can no longer keep pace with exponentially growing amounts of data. 1 Synthetic DNA offers an attractive alternative due to its potential information density of ~ 1018 B/mm3, 107 times denser than magnetic tape, and potential durability of thousands of years.2 Recent advances in DNA data storage have highlighted technical challenges, in particular, coding and random access, but have stored only modest amounts of data in synthetic DNA. 3,4,5 This paper demonstrates an end-to-end approach toward the viability of DNA data storage with large-scale random access. We encoded and stored 35 distinct files, totaling 200MB of data, in more than 13 million DNA oligonucleotides (about 2 billion nucleotides in total) and fully recovered the data with no bit errors, representing an advance of almost an order of magnitude compared to prior work. 6 Our data curation focused on technologically advanced data types and historical relevance, including the Universal Declaration of Human Rights in over 100 languages,7 a high-definition music video of the band OK Go,8 and a CropTrust database of the seeds stored in the Svalbard Global Seed Vault.9 We developed a random access methodology based on selective amplification, for which we designed and validated a large library of primers, and successfully retrieved arbitrarily chosen items from a subset of our pool containing 10.3 million DNA sequences. Moreover, we developed a novel coding scheme that dramatically reduces the physical redundancy (sequencing read coverage) required for error-free decoding to a median of 5x, while maintaining levels of logical redundancy comparable to the best prior codes. We further stress-tested our coding approach by successfully decoding a file using the more error-prone nanopore-based sequencing. We provide a detailed analysis of errors in the process of writing, storing, and reading data from synthetic DNA at a large scale, which helps characterize DNA as a storage medium and justify our coding approach. Thus, we have demonstrated a significant improvement in data volume, random access, and encoding/decoding schemes that contribute to a whole-system vision for DNA data storage.

Selective Functionalization at N2-Position of Guanine in Oligonucleotides via Reductive Amination

2020 ◽  
Author(s):  
Bapurao Bhoge ◽  
Ishu Saraogi
Keyword(s):  
Organic Chemistry ◽  
Chemical Biology ◽  
Reductive Amination ◽  
The Other ◽  
Dna Oligomers ◽  
Site Specific ◽  
Wide Applicability ◽  
Dna Oligonucleotides ◽  
Selective Functionalization

Chemo- and site-specific modifications in oligonucleotides have wide applicability as mechanistic probes in chemical biology. Here we have employed a classical reaction in organic chemistry, reductive amination, to selectively functionalize the N<sup>2</sup>-amine of guanine/2’-deoxyguanine monophosphate. This method specifically modifies guanine in several tested DNA oligonucleotides, while leaving the other bases unaffected. Using this approach, we have successfully incorporated desired handles chemoselectively into DNA oligomers.

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