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Biology subjects

Cuthbert, A.

Publications and source records attributed to Cuthbert, A..

2 recordsLinked to original sources

Information and genetic counselling for psychiatric risks in children with rare disorders

BackgroundThe diagnosis of developmental disorders is being transformed by advances in whole genome technologies. However, continuing uncertainties about the individual risks and potential severity of psychiatric impacts attributed to causal genomic variants limits the availability of comprehensive family-oriented information. In addition, there is insufficient evidence about how the parents of children with developmental disorders comprehend the facts and implications of their diagnosis through genetic counselling, nor how they gather developmental and mental health information to guide their understanding. MethodsParents of children (aged 0-17 years) referred to paediatric genetics services completed an anonymous online 46-item survey about: (i) the experience of attending services to receive their childs genetic diagnosis, and (ii) the availability, quality and helpfulness of information about psychiatric and neurodevelopmental conditions associated with genomic disorders. FindingsTwo-hundred and eighty-six families (199 UK and 87 USA) completed the survey. One-in-three UK and one-in-five US respondents were dissatisfied with how their childs genetic diagnosis was communicated. Satisfaction was predicted by face-to-face communication (odds ratio 2{middle dot}91 [95% CI 1{middle dot}43-5{middle dot}94]; p=0{middle dot}003); results being presented by genetics specialists (2{middle dot}97 [1{middle dot}41-6{middle dot}26]; p=0{middle dot}004); receiving clear explanations (5{middle dot}14 [2{middle dot}58- 10{middle dot}26]; p<0{middle dot}001); receiving support (2{middle dot}99 [1{middle dot}21-7{middle dot}36], p=0{middle dot}017); and male gender of the tested child (2{middle dot}56 [1{middle dot}28-5{middle dot}14]; p=0{middle dot}008). Compared to health-related information on developmental delay or intellectual disability, parents were more likely to obtain information about psychiatric manifestations from non-professional lay sources than from clinical specialists (p<0{middle dot}001). This was particularly evident for families in the UK compared to the USA (p<0{middle dot}001). Parents considered information from rare disorder support groups to be more helpful than from genetics specialists (odds ratio 11{middle dot}0 [95% CI 5{middle dot}08-86{middle dot}75]; p<0{middle dot}001), or paediatricians (11{middle dot}0 [1{middle dot}42-85{middle dot}20]; p=0{middle dot}006), or internet sites (15{middle dot}5 [3{middle dot}71-64{middle dot}77]; p<0{middle dot}001), which in turn proved more helpful than information provided by geneticists (2{middle dot}5 [1{middle dot}44-4{middle dot}31]; p=0{middle dot}001). InterpretationPsychiatric comorbidity is a common feature of rare genomic disorders, but the paucity of suitable information available from clinical specialists suggests families are not optimally informed about these challenges. Wider implementation of genomic testing in general medicine should include adequate training in genetic counselling to ensure best practice in communicating and explaining complex test results supported by comprehensive, family-oriented information. FundingThe Waterloo Foundation: Changing Minds Programme (506296); The Medical Research Council (MRC) Research Grant: Intellectual Disability and Mental Health: Assessing Genomic Impact on Neurodevelopment (MR/N022572/1).

genetics↗

Substrate conformational dynamics drive structure-specific recognition of gapped DNA by DNA polymerase

DNA-binding proteins utilise different recognition mechanisms to locate their DNA targets. Some proteins recognise specific nucleotide sequences, while many DNA repair proteins interact with specific (often bent) DNA structures. While sequence-specific DNA binding mechanisms have been studied extensively, structure-specific mechanisms remain unclear. Here, we study structure-specific DNA recognition by examining the structure and dynamics of DNA polymerase I (Pol) substrates both alone and in Pol-DNA complexes. Using a rigid-body docking approach based on a network of 73 distance restraints collected using single-molecule FRET, we determined a novel solution structure of the singlenucleotide-gapped DNA-Pol binary complex. The structure was highly consistent with previous crystal structures with regards to the downstream primer-template DNA substrate; further, our structure showed a previously unobserved sharp bend (~120{degrees}) in the DNA substrate; we also showed that this pronounced bending of the substrate is present in living bacteria. All-atom molecular dynamics simulations and single-molecule quenching assays revealed that 4-5 nt of downstream gap-proximal DNA are unwound in the binary complex. Coarsegrained simulations on free gapped substrates reproduced our experimental FRET values with remarkable accuracy (<{Delta}FRET> = -0.0025 across 34 independent distances) and revealed that the one-nucleotide-gapped DNA frequently adopted highly bent conformations similar to those in the Pol-bound state ({Delta}G < 4 kT); such conformations were much less accessible to nicked (> 7 kT) or duplex (>> 10 kT) DNA. Our results suggest a mechanism by which Pol and other structure-specific DNA-binding proteins locate their DNA targets through sensing of the conformational dynamics of DNA substrates.\n\nSignificance StatementMost genetic processes, including DNA replication, repair and transcription, rely on DNA-binding proteins locating specific sites on DNA; some sites contain a specific sequence, whereas others present a specific structure. While sequence-specific recognition has a clear physical basis, structure-specific recognition mechanisms remain obscure. Here, we use single-molecule FRET and computer simulations to show that the conformational dynamics of an important repair intermediate (1nt-gapped DNA) act as central recognition signals for structure-specific binding by DNA polymerase I (Pol). Our conclusion is strongly supported by a novel solution structure of the Pol-DNA complex wherein the gapped-DNA is significantly bent. Our iterative approach combining precise single-molecule measurements with molecular modelling is general and can elucidate the structure and dynamics for many large biomachines.

biophysics↗