The Art of Designing DNA Nanostructures with CAD Software

Since the arrival of DNA nanotechnology nearly 40 years ago, the field has progressed from its beginnings of envisioning rather simple DNA structures having a branched, multi-strand architecture into creating beautifully complex structures comprising hundreds or even thousands of unique strands, with the possibility to exactly control the positions down to the molecular level. While the earliest construction methodologies, such as simple Holliday junctions or tiles, could reasonably be designed on pen and paper in a short amount of time, the advent of complex techniques, such as DNA origami or DNA bricks, require software to reduce the time required and propensity for human error within the design process. Where available, readily accessible design software catalyzes our ability to bring techniques to researchers in diverse fields and it has helped to speed the penetration of methods, such as DNA origami, into a wide range of applications from biomedicine to photonics. Here, we review the historical and current state of CAD software to enable a variety of methods that are fundamental to using structural DNA technology. Beginning with the first tools for predicting sequence-based secondary structure of nucleotides, we trace the development and significance of different software packages to the current state-of-the-art, with a particular focus on programs that are open source

Responsive Hydrogels for Label-Free Signal Transduction within Biosensors

Hydrogels have found wide application in biosensors due to their versatile nature. This family of materials is applied in biosensing either to increase the loading capacity compared to two-dimensional surfaces, or to support biospecific hydrogel swelling occurring subsequent to specific recognition of an analyte. This review focuses on various principles underpinning the design of biospecific hydrogels acting through various molecular mechanisms in transducing the recognition event of label-free analytes. Towards this end, we describe several promising hydrogel systems that when combined with the appropriate readout platform and quantitative approach could lead to future real-life applications

Nucleic acid nanostructures for biomedical applications

We review the current developments of DNA-based nanostructures for drug delivery, immunotherapy, diagnostics and molecular biology. DNA is a powerful building block, which by the nature of predictable base pairing, allows the creation of molecular scaffolds, cages and multifunctional carriers with nanoscale dimensions. These engineered constructs have unsurpassed structural qualities such as full control over size, shape and dispersity. Site-specific surface modification enables the presentation of biomolecules at defined distances and stochiometries, which allows tailored cell targeting and substance delivery on demand. As the first successful in vivo applications of DNA nanostructures have recently been demonstrated, we now expect a burst of biomedical studies involving this rapidly progressing technology

Application of exercise transcutaneous oxygen pressure measurements for detection of proximal lower extremity arterial disease: A case report.

International audienceProximal claudication is secondary to ischemia caused by peripheral artery disease (PAD), whereas proximal pseudo-claudication is secondary to other disease processes such as hip arthritis, spinal stenosis, neuropathy, and so forth. The differentiation between the two can be challenging. Exercise transcutaneous oxygen pressure measurement (exercise-TcPO2) allows noninvasive detection of flow-reducing lesions in the proximal arteries and tributaries of the lower extremity arterial tree. We present the first case report in the United States using an exercise-TcPO2 algorithm. A 71-year-old diabetic patient with proximal left-sided and right-calf claudication with indeterminate ankle-brachial indices underwent an exercise-TcPO2 study before and after endovascular intervention. Four TcPO2 probes were placed: one at chest level (reference probe), one on each buttock, and one on the symptomatic calf. The Delta from Resting Oxygen Pressure (DROP) index was calculated at each probe site using a previously validated protocol. Proximal left- and right-calf ischemia were confirmed by the initial exercise-TcPO2, and, after endovascular treatment of the left iliac artery lesion, improvements in proximal exercise-TcPO2 values were found. These data suggest that exercise-TcPO2 can be useful in PAD evaluation in patients with non-compressible arteries and/or proximal claudication

Discrepancies in Prevalence of Peripheral Arterial Disease between Lower Extremities at Rest and Postexercise

International audienceBackground  Lower extremity peripheral arterial disease (PAD) is a common medical condition causing substantial morbidity. Limited data exist on whether discrepancies in PAD prevalence exist between the lower extremities using resting ankle-brachial indices (ABIs) and postexercise pressures. Objective  We predicted the prevalence of PAD between the lower extremities. Methods and Results  Consecutive patients who had undergone a noninvasive arterial lower extremity study at Mayo Clinic, Rochester, MN, between January 1996 and December 2012 with suspected PAD were retrospectively reviewed. We identified 12,312 consecutive patients who underwent an arterial lower extremity and an exercise treadmill study. Prevalence of PAD was assessed at rest and after exercise using two criteria: a resting ABI ≤ 0.90 and a postexercise pressure decrease of > 30 mm Hg. Mean age was 67 ± 12 years and there were 4,780 (39%) women studied. At rest, we found a higher prevalence of PAD on the left extremity (27.4%) compared with the right (24.6%) ( p   30 mm Hg, our results suggest that there is a significantly higher prevalence of PAD in the left lower extremity at rest, in contrast to a greater prevalence of abnormal postexercise testing in the right lower extremity. The reason(s) of these discrepancies remain to be studied

Research Article A Structurally Variable Hinged Tetrahedron Framework from

License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Nanometer-sized polyhedral wire-frame objects hold a wide range of potential applications both as structural scaffoldsaswellas a basis for synthetic nanocontainers. The utilization of DNA as basic building blocks for such structures allows the exploitation of bottom-up self-assembly in order to achieve molecular programmability through the pairing of complementary bases. In this work, we report on a hollow but rigid tetrahedron framework of 75 nm strut length constructed with the DNA origami method. Flexible hinges at each of their four joints provide a means for structural variability of the object. Through the opening of gaps along the struts, four variants can be created as confirmed by both gel electrophoresis and direct imaging techniques. The intrinsic site addressability provided by this technique allows the unique targeted attachment of dye and/or linker molecules at any point on the structure’s surface, which we prove through the superresolution fluorescence microscopy technique DNA PAINT. 1

The Art of Designing DNA Nanostructures with CAD Software

Since the arrival of DNA nanotechnology nearly 40 years ago, the field has progressed from its beginnings of envisioning rather simple DNA structures having a branched, multi-strand architecture into creating beautifully complex structures comprising hundreds or even thousands of unique strands, with the possibility to exactly control the positions down to the molecular level. While the earliest construction methodologies, such as simple Holliday junctions or tiles, could reasonably be designed on pen and paper in a short amount of time, the advent of complex techniques, such as DNA origami or DNA bricks, require software to reduce the time required and propensity for human error within the design process. Where available, readily accessible design software catalyzes our ability to bring techniques to researchers in diverse fields and it has helped to speed the penetration of methods, such as DNA origami, into a wide range of applications from biomedicine to photonics. Here, we review the historical and current state of CAD software to enable a variety of methods that are fundamental to using structural DNA technology. Beginning with the first tools for predicting sequence-based secondary structure of nucleotides, we trace the development and significance of different software packages to the current state-of-the-art, with a particular focus on programs that are open source

The Art of Designing DNA Nanostructures with CAD Software.

Since the arrival of DNA nanotechnology nearly 40 years ago, the field has progressed from its beginnings of envisioning rather simple DNA structures having a branched, multi-strand architecture into creating beautifully complex structures comprising hundreds or even thousands of unique strands, with the possibility to exactly control the positions down to the molecular level. While the earliest construction methodologies, such as simple Holliday junctions or tiles, could reasonably be designed on pen and paper in a short amount of time, the advent of complex techniques, such as DNA origami or DNA bricks, require software to reduce the time required and propensity for human error within the design process. Where available, readily accessible design software catalyzes our ability to bring techniques to researchers in diverse fields and it has helped to speed the penetration of methods, such as DNA origami, into a wide range of applications from biomedicine to photonics. Here, we review the historical and current state of CAD software to enable a variety of methods that are fundamental to using structural DNA technology. Beginning with the first tools for predicting sequence-based secondary structure of nucleotides, we trace the development and significance of different software packages to the current state-of-the-art, with a particular focus on programs that are open source