The natural four-letter genetic alphabet, comprised of just two base pairs (dA-dT and dG-dC), is conserved throughout all life, and its expansion by the development of a third, unnatural base pair has emerged as a central goal of chemical and synthetic biology. We recently developed a class of candidate unnatural base pairs, exemplified by the pair formed between d5SICS and dNaM. Here, we examine the PCR amplification of DNA containing one or more d5SICS-dNaM pairs in a wide variety of sequence contexts. Under standard conditions, we show that this DNA may be amplified with high efficiency and greater than 99.9% fidelity. To more rigorously explore potential sequence effects, we used deep sequencing to characterize a library of templates containing the unnatural base pair as a function of amplification. We found that the unnatural base pair is efficiently replicated with high fidelity in virtually all sequence contexts. The results show that, for PCR and PCR-based applications, d5SICS-dNaM is functionally equivalent to a natural base pair, and when combined with dA-dT and dG-dC, it provides a fully functional six-letter genetic alphabet.expanded genetic alphabet | hydrophobic | artificial DNA | unnatural nucleotides | bioinformatics E xpansion of the genetic alphabet to include an unnatural base pair has emerged as a central goal of chemical and synthetic biology. Success would represent a remarkable integration of orthogonal synthetic components into a fundamental biological system and build the foundation for a semisynthetic organism with increased potential for information storage and retrieval (1). Moreover, the constituent unnatural nucleotides could be used to site-specifically label DNA or RNA with different functionalities of interest (2-4) and potentially revolutionize the already ubiquitous in vitro applications of nucleic acids, such as aptamer and DNA/RNAzyme selections (5, 6), PCR-based diagnostics (7, 8), and DNA-based nanomaterials and devices (9).Although many candidate unnatural base pairs have been reported (10-21), only a few are actually replicable by DNA polymerases (10,11,13,16). Moreover, it is clear that most applications will require that the unnatural base pair not only be replicated with high efficiency and fidelity but also, that replication be at least approximately independent of sequence context. Sequence dependencies would cause biased amplification and effectively preclude many uses of the unnatural base pair. No candidate unnatural base pair has been shown to be replicated without sequence bias, and thus, none can yet claim functional equivalence to a natural base pair.In general, the most promising unnatural base pair candidates currently available have been developed by pursuing one of two different strategies. The first strategy, pioneered in the work by Benner and coworkers (22), relies on the use of nucleotide analogs bearing nucleobases that pair through complementary hydrogen bonding (H-bonding) patterns that are orthogonal to those patterns of the natural pairs. Early ef...
BackgroundWith the dramatically increasing contribution of Alzheimer’s Disease and other forms of dementia to the global burden of disease, countries are being urged to address this as a public health priority. This study investigated whether Australian adults recognise this as an important health issue, and hold beliefs and knowledge that are consistent with recommendations concerning dementia risk reduction. This research was undertaken to guide national brain health awareness and education strategies.MethodsA cross-sectional telephone survey was undertaken of 1,003 Australians aged 20–75 years. This measured the importance placed on dementia, beliefs and confidence related to risk reduction, knowledge of risk reduction methods, and the perceived age-relevance of these. In analysis the data were stratified by sex, age, educational attainment, household income, language preference and previous exposure to dementia. Multivariable logistic regression was undertaken to identify variables independently associated with beliefs and knowledge.ResultsPeople aged 60 years and over identified dementia as very important (17.2%) more often than those aged 40–59 years (5.1%) or 20–39 years (2.1%). While 41.5% of respondents believed the risk of dementia could be reduced, 26.9% were very confident that they could achieve this. Mental activity (57.1%) was identified as beneficial much more often than physical activity (31.3%), healthy eating (23.3%) and other cardiovascular health behaviours. Women, people of English-speaking origin, and those having contact with a person with dementia, showed better knowledge of several health behaviours.ConclusionsGrowing attention is being given to population risk reduction to combat the dramatic increase in the burden of disease due to dementia. In Australia many people do not yet hold beliefs and knowledge that support this, which highlights the need for concerted awareness raising that dementia is not an inevitable aspect of ageing, and for education about the role of vascular health in dementia risk reduction.
Issue addressed: Alzheimer's disease and dementia are recognised as critical public health priorities. This study investigated intentions and behaviours concerning brain health and dementia risk reduction among Australians. Methods: A cross-sectional survey of 1000 persons aged 20-75 years measured knowledge, beliefs, intentions and behaviours concerning brain health and dementia. The demographic, experiential and cognitive factors associated with intentions and actions were examined. Results: Around half of respondents were motivated to improve brain health. Behaviours most often reported were mental activity (19%), physical activity (9.6%) and dietary action (6.5%). Actions were most likely among women (OR 1.59, 95% CI 1.19-2.14), those aged 60 years and over (OR 3.07, 95% CI 2.01-2.58), with university education (OR 1.67, 95% CI 1.08-2.58) or with prior contact with a person with dementia (OR 1.99, 95% CI 1.12-3.56). Both intentions and actions were associated with moderate to high knowledge, and beliefs and confidence that favoured dementia risk reduction. Conclusions: A lower proportion of Australians reported taking action to improve brain health than who expressed intentions in this regard. Strategies are needed to improve knowledge about the range of behaviours that contribute to dementia risk reduction and to increase confidence that this outcome is personally achievable. So what?The burden of disease due to Alzheimer's disease and dementia is growing dramatically. It is essential to promote awareness that dementia is not an inevitable result of ageing and to increase understanding that action can be taken throughout the life course to promote brain health.
As part of an ongoing effort to expand the genetic alphabet for in vitro and eventually in vivo applications, we have synthesized a wide variety of predominantly hydrophobic unnatural base pairs exemplified by d5SICS-dMMO2 and d5SICS-dNaM. When incorporated into DNA, the latter is replicated and transcribed with greater efficiency and fidelity than the former, however previous optimization efforts identified the para and methoxy-distal meta positions of dMMO2 as particularly promising for further optimization. Here, we report the stepwise optimization of dMMO2 via the synthesis and evaluation of eighteen novel para-derivatized analogs of dMMO2, followed by further derivatization and evaluation of the most promising analogs with meta substituents. Subject to size constraints, we find that para substituents can optimize replication via both steric and electronic effects and that meta methoxy groups are unfavorable while fluoro substituents can be beneficial or deleterious depending on the para substituent. In addition, we find that improvements in the efficiency of unnatural triphosphate insertion translate most directly into higher fidelity replication. Importantly, we identify multiple, unique base pair derivatives that when incorporated into DNA are well replicated. The most promising, d5SICS-dFEMO, is replicated under some conditions with greater efficiency and fidelity than d5SICS-dNaM. These results clearly demonstrate the generality of hydrophobic forces for the control of base pairing within DNA, provide a wealth of new SAR data, and importantly identify multiple new candidates for eventual in vivo evaluation.
The discovery of the Cystic fibrosis (CF) gene in 1989 has paved the way for incredible progress in treating the disease such that the mean survival age of individuals living with CF is now ~58 years in Canada. Recent developments in gene targeting tools and new cell and animal models have re-ignited the search for a permanent genetic cure for all CF. In this review, we highlight some of the more recent gene therapy approaches as well as new models that will provide insight into personalized therapies for CF.
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