Genomic SELEX: A discovery tool for genomic aptamers

Zimmermann, Bob; Bilusic, Ivana; Lorenz, Christina; Schroeder, Renée

doi:10.1016/j.ymeth.2010.06.004

Cited by 58 publications

(41 citation statements)

References 42 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…3), the best binding site was, of course, likely to be present in this library. Additionally, because aptameric libraries are usually generated at random and aptamers may be shorter than a complete binding site, a problem that SELEX encounters is questionable physiologic relevance of a determined motif (43). Therefore, a maximally bound motif may not actually be present in any organism.…”

Section: Discussionmentioning

confidence: 99%

Determination of Target Sequence Bound by PapX, Repressor of Bacterial Motility, in flhD Promoter Using Systematic Evolution of Ligands by Exponential Enrichment (SELEX) and High Throughput Sequencing

Reiss

Mobley

2011

Journal of Biological Chemistry

View full text Add to dashboard Cite

Background: When P fimbrial adhesins are expressed in uropathogenic E. coli, PapX represses motility. Results: SELEX combined with high throughput sequencing, using PapX as bait, identified a novel binding site. Conclusion: PapX represses motility by binding a unique nucleotide sequence within the flhDC promoter. Significance: Combining SELEX and high throughput sequencing technology represents a powerful new method to identify bacterial transcription factor binding sites.

show abstract

Section: Discussionmentioning

confidence: 99%

Determination of Target Sequence Bound by PapX, Repressor of Bacterial Motility, in flhD Promoter Using Systematic Evolution of Ligands by Exponential Enrichment (SELEX) and High Throughput Sequencing

Reiss

Mobley

2011

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…HIV-1 drug-resistant, HIV-2); use of new in silico approaches such as SELEX (US FDA guidelines) [19,20], receptor dependent QSAR (RD-QSAR) too needs attention. Up gradations of the in vitro assay platforms with additional holistic assays that tap the accessory genes of HIV (rev, protease and tat), is the current necessity [21].…”

Section: Future Direction For Phytochemical Research and Perspectivesmentioning

confidence: 99%

Repurposing Phytochemicals as Anti-HIV Agents

Jadaun¹,

Khopkar²,

Kulkarni³

2016

J Antivir Antiretrovir

View full text Add to dashboard Cite

Phytochemicals play crucial role in inhibiting key enzymes involved in HIV-1 replication. Repurposing of phytochemical based anti-HIV drug discovery through cross screening approaches and modern techniques is essential to provide better leads. Anti-HIV leads translated through phytochemicals could overcome current challenges of HIV therapy. Considering the immense potential of phytochemicals, this article summarizes the present status of the research carried out on their anti-HIV activities, with its limitations and future directions to foster drug discovery.

show abstract

“…In SELEX, the protein of interest is used as a selection matrix to capture high-affinity ligands from a pool of random DNA molecules [38,39]. By the successive capture of POT1/DNA complexes, two classes of high-affinity POT1 ligands were identified from a pool of randomized ssDNA molecules by SELEX.…”

Section: Introductionmentioning

confidence: 99%

The OB-fold domain 1 of human POT1 recognizes both telomeric and non-telomeric DNA motifs

et al. 2015

View full text Add to dashboard Cite

The POT1 protein plays a critical role in telomere protection and telomerase regulation. POT1 binds single-stranded 5’-TTAGGGTTAG-3’ and forms a dimer with the TPP1 protein. The dimer is recruited to telomeres, either directly or as part of the Shelterin complex. Human POT1 contains two Oligonucleotide/Oligosaccharide Binding (OB) fold domains, OB1 and OB2, which make physical contact with the DNA. OB1 recognizes 5’-TTAGGG whereas OB2 binds to the downstream TTAG-3’. Studies of POT1 proteins from other species have shown that some of these proteins are able to recognize a broader variety of DNA ligands than expected. To explore this possibility in humans, we have used SELEX to reexamine the sequence-specificity of the protein. Using human POT1 as a selection matrix, high-affinity DNA ligands were selected from a pool of randomized single-stranded oligonucleotides. After six successive rounds of selection, two classes of high-affinity targets were obtained. The first class was composed of oligonucleotides containing a cognate POT1 binding sites (5’-TTAGGGTTAG-3’). The second and more abundant class was made of molecules that carried a novel non-telomeric consensus: 5’-TNCANNAGKKKTTAGG-3’ (where K=G/T and N=any base). Binding studies showed that these non-telomeric sites were made of an OB1-binding motif (TTAGG) and a non-telomeric motif (NT motif), with the two motifs recognized by distinct regions of the OB1 domain. POT1 interacted with these non-telomeric binding sites with high affinity and specificity, even when bound to its dimerization partner TPP1. This intrinsic ability of POT1 to recognize NT motifs raises the possibility that the protein may fulfill additional functions at certain non-telomeric locations of the genome, in perhaps gene transcription, replication, or repair.

show abstract

Genomic SELEX: A discovery tool for genomic aptamers

Cited by 58 publications

References 42 publications

Determination of Target Sequence Bound by PapX, Repressor of Bacterial Motility, in flhD Promoter Using Systematic Evolution of Ligands by Exponential Enrichment (SELEX) and High Throughput Sequencing

Determination of Target Sequence Bound by PapX, Repressor of Bacterial Motility, in flhD Promoter Using Systematic Evolution of Ligands by Exponential Enrichment (SELEX) and High Throughput Sequencing

Repurposing Phytochemicals as Anti-HIV Agents

The OB-fold domain 1 of human POT1 recognizes both telomeric and non-telomeric DNA motifs

Contact Info

Product

Resources

About