DNA-Mimicking Metal-Organic Frameworks with Accessible Adenine Faces for Complementary Base Pairing

Area of Science:

• Biomaterials Science
• Nanotechnology
• Biochemistry

Background:

• Biologically derived metal-organic frameworks (Bio-MOFs) offer potential in advanced biomedical applications, including targeted gene delivery.
• Developing biocompatible materials with controlled porous structures is crucial for effective genetic material encapsulation and release.

Purpose of the Study:

• To synthesize and characterize novel Bio-MOFs (KBM-1 and KBM-2) using adenine and unnatural amino acids for ssDNA loading and delivery.
• To investigate the role of base pairing interactions in ssDNA loading efficiency within the Bio-MOF frameworks.
• To evaluate the protective capabilities and cellular delivery of ssDNA by the synthesized Bio-MOFs.

Main Methods:

• Coordination of adenine and unnatural amino acids with Zn²⁺ to form KBM-1 and KBM-2 frameworks.
• Assessment of ssDNA loading efficiency using varying DNA sequences and competitive binding assays with thymine.
• Utilizing self-consistent charge density functional tight-binding (SCC-DFTB) for theoretical analysis of host-guest interactions.
• Testing ssDNA protection against enzymatic degradation and pH-dependent release.
• In vitro evaluation of Bio-MOF mediated gene delivery to the cell nucleus.

Main Results:

• KBM-1 and KBM-2 exhibited defined porous channels and accessible adenine sites for hydrogen bonding.
• ssDNA loading efficiencies of 13% (KBM-1) and 41% (KBM-2) were achieved.
• Thymine competed with ssDNA for adenine sites, reducing loading by over 50%, indicating base-pairing mediated loading.
• KBM-2 showed higher efficiency for thymine-rich ssDNA, confirming the role of Thy-Ade pairing.
• Theoretical calculations confirmed hydrogen bonding and van der Waals interactions at the host-guest interface.
• KBM-1 and KBM-2 protected ssDNA from degradation and facilitated release at acidic pH.
• Efficient delivery of active genetic cargo to the cell nucleus was demonstrated.

Conclusions:

• Novel Bio-MOFs (KBM-1, KBM-2) demonstrate efficient ssDNA loading and protective capabilities.
• Adenine-thymine base pairing plays a significant role in promoting ssDNA loading within these frameworks.
• These biocompatible Bio-MOFs show great potential for sensing, stabilizing, and delivering genetic materials, particularly for gene therapy applications.