DNA studies using atomic force microscopy: capabilities for measurement of short DNA fragments

Pang, Dalong; Thierry, Alain R.; Dritschilo, Anatoly

doi:10.3389/fmolb.2015.00001

Cited by 48 publications

(39 citation statements)

References 73 publications

(91 reference statements)

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“…In addition, a closer look at these circular templates showed that the sizes of the circular structures were around 10–15 nm in diameter. This result is in good agreement with a theoretical value of 20–30 nm, considering that the padlock probe is a linear ssDNA of 79 nt (Pang, Thierry, & Dritschilo, ). Significantly, although AFM has previously been used to probe RCA products (Mizuta et al, ), an “rolling” RCA product has been successfully imaged by AFM (shown in Figure e) for the first time.…”

Section: Resultssupporting

confidence: 91%

Rolling circle amplification and its application in microfluidic systems for Escherichia coli O157:H7 detections

Jiang

Qiu

et al. 2019

Journal of Food Safety

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Rolling circle amplification (RCA) has been widely used to enhance detection signals as its long single‐stranded RCA products can provide multiple binding sites for signal probes for sensitive detections. In the current study, we employ atomic force microscopy (AFM) to monitor the RCA products during the course of the RCA process over time. Subsequently, the results of the RCA obtained from the AFM study are combined with those from the conventional electrophoresis method to optimize RCA reactions for rapid and sensitive detection. We show that there appears to be an inhomogeneous RCA initiation phase in early to mid‐stage of the RCA reaction where some chains grow faster while others grow slower or remain dormant, an observation that has not been reported in the literature. Furthermore, we demonstrate that the RCA can significantly enhance detection signals by up to 100‐fold. We also show that the Escherichia coli O157:H7 detection with the RCA can be carried out in different food matrices with excellent detection sensitivities and specificities. In conclusion, these results suggest that a microfluidic device in combination with RCA signal enhancement is a simple and robust approach to sensitive whole‐cell detection in food samples. Practical applications The current research has exciting potentials for applications in sensitive detections of food samples for food safety inspections.

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Section: Resultssupporting

confidence: 91%

Rolling circle amplification and its application in microfluidic systems for Escherichia coli O157:H7 detections

Jiang

Qiu

et al. 2019

Journal of Food Safety

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“…The heights of single‐ and double‐stranded DNA chains measured by means of AFM are 0.3 and 0.7 nm, respectively, whereas here we observe hybrid multiplexes . Structures showing heights remarkably greater than that of normal DNA duplex and genomic DNA have been observed, especially for the sample with X 16 as a template . Because the generation of an amorphous 3D structure is associated with a highly diverse DNA library as a precursor, we called them high‐entropy structures, in contrast to self‐assembled DNA nanostructures with defined interaction networks, such as that in DNA origami …”

Section: Figurementioning

confidence: 69%

Using a PCR‐Based Method To Analyze and Model Large, Heterogeneous Populations of DNA

et al. 2020

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The study of populations of large size and high diversity is limited by the capability of collecting data. Moreover, for a pool of individuals, each associated with a unique characteristic feature, as the pool size grows, the possible interactions increase exponentially and quickly go beyond the limit of computation and experimental studies. Herein, the design of DNA libraries with various diversity is reported. By using a facile analytical method based on real‐time PCR, the diversity of a pool of DNA can be evaluated to allow extraordinarily high heterogenicity (e.g., >1 trillion). It is demonstrated that these DNA libraries can be used to model heterogeneous populations; these libraries exhibit functions such as self‐protection, suitability for biased expansion, and the possibility to evolve into amorphous structures. The method has shown the remarkable power of parallel computing with DNA, since it can resemble an analogue computer and be applied in selection‐based biotechnology methods, such as DNA‐encoded chemical libraries. As a chemical approach to solve problems traditionally for genetic and statistical analysis, the method provides a quick and cost‐efficient evaluation of library diversity for intermediate steps through a selection process.

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“…Phosphate interactions in the RNA and DNA structures were analyzed using DSSR, a new component of the 3DNA suite of software programs. 71–74 By a phosphate interaction, we mean an electrostatic interaction in which phosphate group accepts a hydrogen bond from a nucleotide. This effect has been observed in several RNA crystal structures in the RCSB database, 75 as shown in a meta-study across several such structures by Zirbel et al, 2009.…”

Section: Methodsmentioning

confidence: 99%

All-Atom MD Predicts Magnesium-Induced Hairpin in Chemically Perturbed RNA Analog of F10 Therapeutic

2017

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Given their increasingly frequent usage, understanding the chemical and structural properties which allow therapeutic nucleic acids to promote the death of cancer cells is critical for medical advancement. One molecule of interest is a 10-mer of FdUMP (5-fluoro-2′-deoxyuridine-5′-O-monophosphate) also called F10. To investigate causes of structural stability, we have computationally restored the 2′ oxygen on each ribose sugar of the phosphodiester backbone, creating FUMP[10]. Microsecond time-scale, all-atom, simulations of FUMP[10] in the presence of 150 mM MgCl2 predict that the strand has a 45% probability of folding into a stable hairpin-like secondary structure. Analysis of 16 μs of data reveals phosphate interactions as likely contributors to the stability of this folded state. Comparison with polydT and polyU simulations predicts that FUMP[10]’s lowest order structures last for one to 2 orders of magnitude longer than similar nucleic acid strands. Here we provide a brief structural and conformational analysis of the predicted structures of FUMP[10], and suggest insights into its stability via comparison to F10, polydT, and polyU.

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DNA studies using atomic force microscopy: capabilities for measurement of short DNA fragments

Cited by 48 publications

References 73 publications

Rolling circle amplification and its application in microfluidic systems for Escherichia coli O157:H7 detections

Rolling circle amplification and its application in microfluidic systems for Escherichia coli O157:H7 detections

Using a PCR‐Based Method To Analyze and Model Large, Heterogeneous Populations of DNA

All-Atom MD Predicts Magnesium-Induced Hairpin in Chemically Perturbed RNA Analog of F10 Therapeutic

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