A Reproducibility-Audited Framework for Nuclease-Free Epigenome Editing: The ANFPE Platform

CRISPR-Cas systems have transformed genetic engineering but remain constrained by off-target cleavage, protospacer adjacent motif (PAM) dependency, delivery inefficiency, and immunogenicity. This paper presents the Adaptive Nuclease-Free Programmable Editor (ANFPE), a conceptual framework combining programmable, PAM-independent molecular recognition with epigenetically triggered chromatin remodeling to avoid genotoxicity associated with double-strand breaks.We state at the outset the framework's central open problem rather than treating it as an implicit assumption: no specific molecular mechanism is yet established by which an epigenetic trigger alone, without an exogenous nuclease, deaminase, or repair template, could recruit base-excision repair to correct a DNA sequence rather than simply modulate gene expression. Pending resolution of this mechanism, we treat ANFPE's defensible near-term scope as an expression-modulation platform, for example fetal-hemoglobin induction or tumor-suppressor reactivation, rather than a sequence-correction technology, and we organize the manuscript's computational content accordingly.Every quantitative claim in this revision is re-derived from and verified against the executable code accompanying the manuscript. This includes a mass-conservative three-state kinetic model in which an unbound target becomes a bound complex and then an irreversibly modified site, a Saltelli-Jansen Sobol global sensitivity analysis using 4096 base samples and 24,576 model evaluations, a 5000-run Monte Carlo uncertainty propagation, and a 25-point multi-factor robustness sweep.A case study on the HBB locus in sickle-cell disease is calibrated, using an explicitly disclosed and literature-motivated genomic target-search retardation factor, to reach 95 percent on-target epigenetic-mark deposition within six hours, with 0.46 percent off-target modification and a specificity ratio of approximately 207 to 1, ranging from 126 to 298 to 1 under the robustness sweep. This figure represents a calibration target for a proposed mechanism rather than an independent prediction, and it is reported as such throughout the manuscript.The manuscript includes a dedicated Scientific and Technical Risk Assessment ranked by severity, along with a Roadmap, Experimental Validation, and Falsifiability section that specifies explicit, testable success and failure criteria, including a go or no-go experiment for the sequence-correction mechanism itself.