While molecular diagnostics generally require heating
elements
that supply high temperatures such as 95 °C in polymerase chain
reaction and 60–69 °C in loop-mediated isothermal amplification,
the recently developed CRISPR-based SHERLOCK (specific high-sensitivity
enzymatic reporter unlocking) platform can operate at 37 °C or
a similar ambient temperature. This unique advantage may be translated
into highly energy-efficient or equipment-free molecular diagnostic
systems with unrestricted deployability. SHERLOCK is characterized
by ultra-high sensitivity when performed in a traditional two-step
format. For RNA sensing, the first step combines reverse transcription
with recombinase polymerase amplification, while the second step consists
of T7 transcription and CRISPR-Cas13a detection. The sensitivity drops
dramatically, however, when all these components are combined into
a single reaction mixture, and it largely remains an unmet need in
the field to establish a high-performance one-pot SHERLOCK assay.
An underlying challenge, conceivably, is the extremely complex nature
of a one-pot formulation, crowding a large number of reaction types
using at least eight enzymes/proteins. Although previous work has
made substantial improvements by serving individual enzymes/reactions
with accommodating conditions, we reason that the interactions among
different enzymatic reactions could be another layer of complicating
factors. In this study, we seek optimization strategies by which inter-enzymatic
interference may be eliminated or reduced and cooperation created
or enhanced. Several such strategies are identified for SARS-CoV-2
detection, each leading to a significantly improved reaction profile
with faster and stronger signal amplification. Designed based on common
molecular biology principles, these strategies are expected to be
customizable and generalizable with various buffer conditions or pathogen
types, thus holding broad applicability for integration into future
development of one-pot diagnostics in the form of a highly coordinated
multi-enzyme reaction system.