scholarly journals Conservation of genetic information: a code for site-specific DNA recognition.

1993 ◽  
Vol 90 (12) ◽  
pp. 5534-5538 ◽  
Author(s):  
L. F. Harris ◽  
M. R. Sullivan ◽  
D. F. Hickok
Keyword(s):  
Genetic Information ◽  
Dna Recognition ◽  
Site Specific

scholarly journals Distinct Roles for Interfacial Hydration in Site-Specific DNA Recognition by ETS-Family Transcription Factors

2017 ◽  
Vol 121 (13) ◽  
pp. 2748-2758 ◽  
Author(s):  
Suela Xhani ◽  
Shingo Esaki ◽  
Kenneth Huang ◽  
Noa Erlitzki ◽  
Gregory M. K. Poon
Keyword(s):  
Transcription Factors ◽  
Dna Recognition ◽  
Site Specific ◽  
Ets Family

Energetics of Site-Specific DNA Recognition by Integrase Tn916

2005 ◽  
pp. 187-202
Author(s):  
Stoyan Milev ◽  
Hans Rudolf Bosshard ◽  
Ilian Jelesarov
Keyword(s):  
Dna Recognition ◽  
Site Specific

The Bacteriophage P1 Site-specific Recombinase Cin: Recombination Events and DNA Recognition Sequences

1984 ◽  
Vol 49 (0) ◽  
pp. 769-777 ◽  
Author(s):  
S. Iida ◽  
H. Huber ◽  
R. Hiestand-Nauer ◽  
J. Meyer ◽  
T.A. Bickle ◽  
...  
Keyword(s):  
Dna Recognition ◽  
Site Specific ◽  
Bacteriophage P1

Differentiation Induction In Acute Myeloid Leukemia Using Site-Specific DNA-Targeting

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 3940-3940
Author(s):  
Rahul Palchaudhuri ◽  
Kwan-Keat Ang ◽  
Borja Saez ◽  
David B. Sykes ◽  
Gregory L. Verdine ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Cell Differentiation ◽  
Calcium Binding ◽  
Fusion Proteins ◽  
Myeloid Leukemia ◽  
Dna Recognition ◽  
Control Group ◽  
Site Specific ◽  
Dna Targeting ◽  
Acute Myeloid

Abstract Hoxa9 and Meis1 are overexpressed in >70% of acute myeloid leukemia (AML) and associated with poor prognosis and survival. Hoxa9 and Meis1 interact with DNA and PBX to achieve transcription of differentiation-blocking genes. We tested transcriptional repression at Hoxa9-PBX-Meis1 genomic binding sites to induce differentiation in a model of human AML We designed a DNA-recognition strategy based on the known structure of the Hoxa9-PBX-DNA complex by fusing the DNA binding helices of Hoxa9 and PBX to create concise homeodomain fusion proteins that target the Hoxa9-PBX DNA recognition sequence. To confer transcription-repressing properties to the proteins, we attached a transcriptional repressor (sin3 interacting) domain and ectopically expressed this protein in Hoxa9-Meis1 immortalized murine progenitors. Introduction of this transcription repressor protein significantly enabled cell differentiation versus control (51.2% Mac-1high Gr-1high cells versus 11.3% for control). Multiple gene transcripts indicative of differentiation, such as GCSFR, myeloperoxidase, neutrophil elastase, and the calcium binding protein, S100A8, were also elevated in repressor-expressing cells. Furthermore, direct transcriptional targets of Hoxa9 (e.g. SOX2, CD34, FOXP1, FLT3R, DNAJC10) were down regulated in repressor-expressing cells. Importantly, a mutant repressor lacking the DNA-interacting amino acids did not affect transcription of Hoxa9 targets, demonstrating on-target specificity. Repressor-expressing cells also exhibited lower surface expression of c-Kit and Flt3 receptors and when transplanted into mice resulted in a significant increase in disease latency with a 94 day median latency versus 62 day latency for the control group (p value = 0.002). Our results demonstrate that site-specific DNA-targeting using homeodomain fusion proteins can enable AML cell differentiation and significantly increase disease latency. Disclosures: Scadden: Fate Therapeutics: Consultancy, Equity Ownership.

scholarly journals Recent Advances in Novel DNA Guiding Nanofabrication and Nanotechnology

2018 ◽  
Vol 4 (1) ◽  
pp. 32-52 ◽  
Author(s):  
Zhiguang Suo ◽  
Jingqi Chen ◽  
Ziheng Hu ◽  
Yihao Liu ◽  
Feifei Xing ◽  
...  
Keyword(s):  
Dna Recognition ◽  
Genetic Material ◽  
Dna Nanotechnology ◽  
Structural Features ◽  
Dna Origami ◽  
Site Specific ◽  
Metal Organic ◽  
Nanomaterials Synthesis ◽  
Promising Development ◽  
3D Topology

Abstract DNA as life’s genetic material has been widely investigated around the world. In recent years, with the fiery researches on nanomaterials, it also plays an important role in the development of material science due to its extraordinary molecular recognition capability and prominent structural features. In this mini review, we mainly overview the recent progresses of DNA guiding self-assembled nanostructures and nanofabrication. Typical DNA tile-based assembly and DNA origami nanotechnologies are presented, utilizing the recent 3D topology methods to fabricate multidimensional structures with unique properties. Then the site-specific nanomaterials synthesis and nano-DNA recognition on different DNA scaffolds/templates are demonstrated with excellent addressability, biocompatibility and structural programmability. Various nanomaterials, such as metals, carbon family materials, quantum dots, metal-organic frameworks, and DNA-based liquid crystals are briefly summarized. Finally, the present limitation and future promising development directions are discussed in conclusion and perspective. We wish this review would provide useful information toward the broader scientific interests in DNA nanotechnology.

Site-specific recombination by mutants of Tn21 resolvase with DNA recognition functions from Tn3 resolvase

1990 ◽  
Vol 216 (3) ◽  
pp. 633-643 ◽  
Author(s):  
Alison J. Ackroyd ◽  
Pilar Avila ◽  
Christian N. Parker ◽  
Stephen E. Halford
Keyword(s):  
Dna Recognition ◽  
Site Specific ◽  
Site Specific Recombination

scholarly journals DNA Recognition, Strand Selectivity, and Cleavage Mode during Integrase Family Site-specific Recombination

2000 ◽  
Vol 275 (29) ◽  
pp. 22255-22267 ◽  
Author(s):  
Gena Tribble ◽  
Yong-Tae Ahn ◽  
Jehee Lee ◽  
Thomas Dandekar ◽  
Makkuni Jayaram
Keyword(s):  
Dna Recognition ◽  
Site Specific ◽  
Site Specific Recombination

Interplay between Site-Specific Mutations and Cyclic Nucleotides in Modulating DNA Recognition byEscherichia coliCyclic AMP Receptor Protein†,‡

Biochemistry ◽  
2004 ◽  
Vol 43 (28) ◽  
pp. 8901-8910 ◽  
Author(s):  
Jiayin Dai ◽  
Shwu-Hwa Lin ◽  
Carly Kemmis ◽  
Anita J. Chin ◽  
J. Ching Lee
Keyword(s):  
Cyclic Nucleotides ◽  
Dna Recognition ◽  
Receptor Protein ◽  
Site Specific

Concerted DNA recognition and novel site-specific alkylation by duocarmycin A with distamycin A

Biochemistry ◽  
1993 ◽  
Vol 32 (4) ◽  
pp. 1059-1066 ◽  
Author(s):  
Koji Yamamoto ◽  
Hiroshi Sugiyama ◽  
Shosuke Kawanishi
Keyword(s):  
Dna Recognition ◽  
Site Specific ◽  
Distamycin A

scholarly journals Detection of preQ0 deazaguanine modifications in bacteriophage CAjan DNA using Nanopore sequencing reveals same hypermodification at two distinct DNA motifs

2020 ◽  
Vol 48 (18) ◽  
pp. 10383-10396
Author(s):  
Witold Kot ◽  
Nikoline S Olsen ◽  
Tue K Nielsen ◽  
Geoffrey Hutinet ◽  
Valérie de Crécy-Lagard ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Dna Recognition ◽  
Nanopore Sequencing ◽  
Site Specific ◽  
Dna Motifs ◽  
Gene Coding ◽  
Binding Surface ◽  
General Mode ◽  
Restriction Modification ◽  
Insight Into

Abstract In the constant evolutionary battle against mobile genetic elements (MGEs), bacteria have developed several defense mechanisms, some of which target the incoming, foreign nucleic acids e.g. restriction-modification (R-M) or CRISPR-Cas systems. Some of these MGEs, including bacteriophages, have in turn evolved different strategies to evade these hurdles. It was recently shown that the siphophage CAjan and 180 other viruses use 7-deazaguanine modifications in their DNA to evade bacterial R-M systems. Among others, phage CAjan genome contains a gene coding for a DNA-modifying homolog of a tRNA-deazapurine modification enzyme, together with four 7-cyano-7-deazaguanine synthesis genes. Using the CRISPR-Cas9 genome editing tool combined with the Nanopore Sequencing (ONT) we showed that the 7-deazaguanine modification in the CAjan genome is dependent on phage-encoded genes. The modification is also site-specific and is found mainly in two separate DNA sequence contexts: GA and GGC. Homology modeling of the modifying enzyme DpdA provides insight into its probable DNA binding surface and general mode of DNA recognition.

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