An on-demand four-way junction DNAzyme nanoswitch driven by inosine-based partial strand displacement

Mo, Alexander H.; Landon, Preston B.; Meckes, Brian; Yang, Max M.; Glinsky, Gennadi V.; Lal, Ratnesh

doi:10.1039/c3nr05365b

Cited by 13 publications

(11 citation statements)

References 25 publications

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“…Methylation-associated DNA editing (MADE) alters the conventional double helix by replacing Watson–Crick base pairs with less energetically efficient noncanonical base pairing, creating nucleotide mismatches and nucleotide evictions at selected sites (Lee J, Hwang M, Landon PB, Lal R, Glinsky GV, in preparation). Recent experiments have shown that structural changes of DNA sequences resembling MADE markedly enhance the responsiveness of DNA to invading DNA and noncoding RNA molecules (Lee J, Hwang M, Landon PB, Lal R, Glinsky GV, in preparation) and these properties of “edited” DNA double helix can be exploited to engineer next-generation nanosensors, DNAzymes, and DNA motors ( Glinsky 2013 ; Landon et al 2014 ; Mo et al 2014 ). Invading RNAs induce a thermodynamically stable partial strand displacement state (PSDS), which may persist indefinitely as triple-stranded complexes (TSC) comprising RNA/DNA hybrids and single-stranded DNA chains.…”

Section: Resultsmentioning

confidence: 99%

Transposable Elements and DNA Methylation Create in Embryonic Stem Cells Human-Specific Regulatory Sequences Associated with Distal Enhancers and Noncoding RNAs

Glinsky

2015

Genome Biology and Evolution

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144

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Despite significant progress in the structural and functional characterization of the human genome, understanding of the mechanisms underlying the genetic basis of human phenotypic uniqueness remains limited. Here, I report that transposable element-derived sequences, most notably LTR7/HERV-H, LTR5_Hs, and L1HS, harbor 99.8% of the candidate human-specific regulatory loci (HSRL) with putative transcription factor-binding sites in the genome of human embryonic stem cells (hESC). A total of 4,094 candidate HSRL display selective and site-specific binding of critical regulators (NANOG [Nanog homeobox], POU5F1 [POU class 5 homeobox 1], CCCTC-binding factor [CTCF], Lamin B1), and are preferentially located within the matrix of transcriptionally active DNA segments that are hypermethylated in hESC. hESC-specific NANOG-binding sites are enriched near the protein-coding genes regulating brain size, pluripotency long noncoding RNAs, hESC enhancers, and 5-hydroxymethylcytosine-harboring regions immediately adjacent to binding sites. Sequences of only 4.3% of hESC-specific NANOG-binding sites are present in Neanderthals’ genome, suggesting that a majority of these regulatory elements emerged in Modern Humans. Comparisons of estimated creation rates of novel TF-binding sites revealed that there was 49.7-fold acceleration of creation rates of NANOG-binding sites in genomes of Chimpanzees compared with the mouse genomes and further 5.7-fold acceleration in genomes of Modern Humans compared with the Chimpanzees genomes. Preliminary estimates suggest that emergence of one novel NANOG-binding site detectable in hESC required 466 years of evolution. Pathway analysis of coding genes that have hESC-specific NANOG-binding sites within gene bodies or near gene boundaries revealed their association with physiological development and functions of nervous and cardiovascular systems, embryonic development, behavior, as well as development of a diverse spectrum of pathological conditions such as cancer, diseases of cardiovascular and reproductive systems, metabolic diseases, multiple neurological and psychological disorders. A proximity placement model is proposed explaining how a 33–47% excess of NANOG, CTCF, and POU5F1 proteins immobilized on a DNA scaffold may play a functional role at distal regulatory elements.

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Section: Resultsmentioning

confidence: 99%

Transposable Elements and DNA Methylation Create in Embryonic Stem Cells Human-Specific Regulatory Sequences Associated with Distal Enhancers and Noncoding RNAs

Glinsky

2015

Genome Biology and Evolution

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144

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“…The newly introduced strand with higher affinity to one strand in the initial double helix displaces the other strand with lower affinity. Additionally, inosine or RNA can be used to control kinetics or Gibbs free energy of hybridization (19)(20)(21)(22). Strand displacement has been a core technique in DNA nanomanipulation for over 20 years and has been used in several mechanical nanomachines (23), logic gates (24), and sensors (19,25).…”

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confidence: 99%

Highly specific SNP detection using 2D graphene electronics and DNA strand displacement

Hwang

Landon

Lee

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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117

102

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Single-nucleotide polymorphisms (SNPs) in a gene sequence are markers for a variety of human diseases. Detection of SNPs with high specificity and sensitivity is essential for effective practical implementation of personalized medicine. Current DNA sequencing, including SNP detection, primarily uses enzyme-based methods or fluorophore-labeled assays that are time-consuming, need laboratory-scale settings, and are expensive. Previously reported electrical charge-based SNP detectors have insufficient specificity and accuracy, limiting their effectiveness. Here, we demonstrate the use of a DNA strand displacement-based probe on a graphene field effect transistor (FET) for high-specificity, single-nucleotide mismatch detection. The single mismatch was detected by measuring strand displacement-induced resistance (and hence current) change and Dirac point shift in a graphene FET. SNP detection in large double-helix DNA strands (e.g., 47 nt) minimize false-positive results. Our electrical sensor-based SNP detection technology, without labeling and without apparent cross-hybridization artifacts, would allow fast, sensitive, and portable SNP detection with single-nucleotide resolution. The technology will have a wide range of applications in digital and implantable biosensors and high-throughput DNA genotyping, with transformative implications for personalized medicine.NA sequencing has opened new windows of opportunities for diagnosis of genetic disease (1), biological informatics (2), forensics (3), and environmental monitoring (4). Discrimination of a single mismatch in a long DNA strand is of significant importance and is essential to detect single nucleotide polymorphism (SNP). SNP is a single-nucleotide mutation in a gene sequence and varies among paired chromosomes, between individuals, and across biological species. SNP mutations can have dramatic influence on the health. They are markers for variety of diseases, including various forms of cancer, genetic disorders (5-7), and are of critical importance for successful practical implementation of the concept of personalized medicine (8). Thus, the development of biosensors detecting SNP mutations with high sensitivity and specificity is essential for effective personalized medicine approaches.Current DNA sequencing, including SNP detection, is achieved primarily by enzyme-based methods, using DNA ligase (9), DNA polymerase (9), and nucleases (10). These methods generate highly accurate genotyping. However, the methods are expensive and time-consuming. One of the common enzyme-free methods to detect SNPs uses hybridization of the target DNA to a probe on a microarray and detects their binding events with fluorescence microscopy/spectroscopy. Hybridization-based methods for SNP detection have several disadvantages, including cross-hybridization between allele-specific probes (11). This limits the detection of a single mismatch in long probe-target hybridization as the longer probes have more frequent cross hybridization. For example, a single mismatch in the center o...

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“…Nanobowls can then be capped with a sphere made of biocompatible materials, including PLGA 29 , liposomes, 30 and chitosan 31 . For conditional and controlled release of the therapeutic from the bowl, such a cap could be released by specific interaction with DNA 32, 33 , enzymatic processes, or environmental triggers like temperature and pH. Existing delivery systems usually have pores or open surfaces that allow passive and/or continuous release of their loads (imaging contrast molecules or therapeutic agents).…”

Section: Resultsmentioning

confidence: 99%

Synthesis of nano-bowls with a Janus template

Landon

Emerson

et al. 2015

Nanoscale

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Colloidal particles with two or more different surface properties (Janus particles) are of interest in catalysis, biological imaging, and drug delivery. Eccentric nanoparticles are a type of Janus particle consisting of a shell that envelops the majority of a core particle, leaving a portion of the core surface exposed. Previous work to synthesize eccentric nanoparticles from silica and polystyrene have only used microemulsion techniques. In contrast we report the solgel synthesis of eccentric Janus nanoparticles composed of a silica shell around a carboxylate-modified polystyrene core (Janus templates). In addition, we have synthesized nano-bowl-like structures after the removal of the polystyrene core by organic solvent. These Janus templates and nanobowls can be used as a versatile platform for site-specific functionalization or controlled theranostic delivery.

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An on-demand four-way junction DNAzyme nanoswitch driven by inosine-based partial strand displacement

Cited by 13 publications

References 25 publications

Transposable Elements and DNA Methylation Create in Embryonic Stem Cells Human-Specific Regulatory Sequences Associated with Distal Enhancers and Noncoding RNAs

Transposable Elements and DNA Methylation Create in Embryonic Stem Cells Human-Specific Regulatory Sequences Associated with Distal Enhancers and Noncoding RNAs

Highly specific SNP detection using 2D graphene electronics and DNA strand displacement

Synthesis of nano-bowls with a Janus template

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