Year: 2019
Type: article
Abstract: Label-free in situ X-ray scattering from protein spherical nucleic acids (Pro-SNAs, consisting of protein cores densely functionalized with covalently bound DNA) was used to elucidate the enzymatic reaction pathway for the DNase I-induced degradation of DNA. Time-course small-angle X-ray scattering (SAXS) and gel electrophoresis reveal a two-state system with time-dependent populations of intact and fully degraded DNA in the Pro-SNAs. SAXS shows that in the fully degraded state, the DNA strands forming the outer shell of the Pro-SNA were completely digested. SAXS analysis of reactions with different Pro-SNA concentrations reveals a reaction pathway characterized by a slow, rate determining DNase I-Pro-SNA association, followed by rapid DNA hydrolysis. Molecular dynamics (MD) simulations provide the distributions of monovalent and divalent ions around the Pro-SNA, relevant to the activity of DNase I. Taken together, in situ SAXS in conjunction with MD simulations yield key mechanistic and structural insights into the interaction of DNA with DNase I. The approach presented here should prove invaluable in probing other enzyme-catalyzed reactions on the nanoscale.
Source: ACS Nano
Institution: Northwestern University
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
Funders: National Science Foundation, U.S. Department of Energy, DuPont, Northwestern University, Sherman Fairchild Foundation, Office of Science, Materials Research Science and Engineering Center, Harvard University, National Defense Science and Engineering Graduate, Office of Naval Research, Division of Materials Research, Basic Energy Sciences, Argonne National Laboratory
Awards: G102163711, G1066689932, G107546177, G1169090945, G1286251239, G1313983767, G1657001476, G1664757510, ELECTROLYTE-MEDIATED ASSEMBLY OF LIKE-CHARGED COLLOIDS, G2287611682, G262962599, G3075337988, G3454132534, G3589692066, G3954585026, G426311843, G4285583887, G4289625387, MRSEC: Center for Multifunctional Materials, G4912152698, G498139845, G506652095, G513797252, G5218300437, G5387317844, G6848031779, G6918803902, G7583137537, G8876996369, G969889393, G993121649, G993149817
OpenAlex ID: W2972860168