![156131-Thumbnail Image.png](https://d1rbsgppyrdqq4.cloudfront.net/s3fs-public/styles/width_400/public/2021-08/156131-Thumbnail%20Image.png?versionId=3xInxMfVXoTm2mU7OB7KNAUQ6jis_eqL&X-Amz-Content-Sha256=UNSIGNED-PAYLOAD&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIASBVQ3ZQ42ZLA5CUJ/20240617/us-west-2/s3/aws4_request&X-Amz-Date=20240617T110123Z&X-Amz-SignedHeaders=host&X-Amz-Expires=120&X-Amz-Signature=07ebaa72c114989f3f92af6d89ff2749e5754a982da5ad51b1520e30ff0d08b6&itok=Ptn01L0R)
Several strategies were investigated to address the three previously mentioned limitations. The first attempt was to study the effect length and conformation of polyethylene glycol (PEG) on DN stability. DNs were also coated with PEG-lipid and human serum albumin (HSA) and their stealth efficiencies were compared. The findings reveal that both PEGylation and albumin coating enhance low salt stability, increase resistance towards nuclease action and reduce uptake of DNs by macrophages. Any protective coating around a DN increases its hydrodynamic radius, which is a crucial parameter influencing their clearance. Keeping this in mind, intrinsically stable DNs that can survive low salt concentration without any polymer coating were built. Several DNA compaction agents and DNA binders were screened to stabilize DNs in low magnesium conditions. Among them arginine, lysine, bis-lysine and hexamine cobalt showed the potential to enhance DN stability.
This thesis also presents a sensitive assay, the Proximity Ligation Assay (PLA), for the estimation of DN stability with time. It requires very simple modifications on the DNs and it can yield precise results from a very small amount of sample. The applicability of PLA was successfully tested on several DNs ranging from a simple wireframe tetrahedron to a 3D origami and the protocol to collect in vivo samples, isolate the DNs and measure their stability was developed.
![161707-Thumbnail Image.png](https://d1rbsgppyrdqq4.cloudfront.net/s3fs-public/styles/width_400/public/2021-11/161707-Thumbnail%20Image.png?versionId=bSSShTcNhB2F9gs2s9e7aFQdw0JSp_KF&X-Amz-Content-Sha256=UNSIGNED-PAYLOAD&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIASBVQ3ZQ42ZLA5CUJ/20240617/us-west-2/s3/aws4_request&X-Amz-Date=20240617T105707Z&X-Amz-SignedHeaders=host&X-Amz-Expires=120&X-Amz-Signature=9be7a3fcc6a07b5ab89a32ebe8731fde07c2ebb5a5487056b1e0c55a14b10d0d&itok=pQ4ADanT)
![158847-Thumbnail Image.png](https://d1rbsgppyrdqq4.cloudfront.net/s3fs-public/styles/width_400/public/2021-09/158847-Thumbnail%20Image.png?versionId=m.N33Pq4MPGwHXuVAzR96wCSRD9bAHIm&X-Amz-Content-Sha256=UNSIGNED-PAYLOAD&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIASBVQ3ZQ42ZLA5CUJ/20240616/us-west-2/s3/aws4_request&X-Amz-Date=20240616T210735Z&X-Amz-SignedHeaders=host&X-Amz-Expires=120&X-Amz-Signature=47155c1510d6d537b0f4112347b2b0493aaac92f6bd7b5817162708fb95b5d60&itok=mZV8eIMA)
![158875-Thumbnail Image.png](https://d1rbsgppyrdqq4.cloudfront.net/s3fs-public/styles/width_400/public/2021-09/158875-Thumbnail%20Image.png?versionId=6LQWyKS2vPj.NxQySWlpc8pHr72kqF2b&X-Amz-Content-Sha256=UNSIGNED-PAYLOAD&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIASBVQ3ZQ42ZLA5CUJ/20240616/us-west-2/s3/aws4_request&X-Amz-Date=20240616T180337Z&X-Amz-SignedHeaders=host&X-Amz-Expires=120&X-Amz-Signature=c8fd7cb4d4600be3182b170f9cc893d98b94ab649d4336a27a2e28b0b0c9a32a&itok=KOjvfK4j)
![161916-Thumbnail Image.png](https://d1rbsgppyrdqq4.cloudfront.net/s3fs-public/styles/width_400/public/2021-11/161916-Thumbnail%20Image.png?versionId=nHWAScIfIC3rTQR0bK77xR9glYO7cZ6T&X-Amz-Content-Sha256=UNSIGNED-PAYLOAD&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIASBVQ3ZQ42ZLA5CUJ/20240617/us-west-2/s3/aws4_request&X-Amz-Date=20240617T042505Z&X-Amz-SignedHeaders=host&X-Amz-Expires=120&X-Amz-Signature=8b98e17d4dbfe0b39f1d8aa1953a6fa18758ad9c5da77627b8ba41a3b7b77cae&itok=_1j9bU6J)
![161416-Thumbnail Image.png](https://d1rbsgppyrdqq4.cloudfront.net/s3fs-public/styles/width_400/public/2021-11/161416-Thumbnail%20Image.png?versionId=flb0.9GZn_k.EuU4wl.5r8oHyM2tJ2s4&X-Amz-Content-Sha256=UNSIGNED-PAYLOAD&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIASBVQ3ZQ42ZLA5CUJ/20240617/us-west-2/s3/aws4_request&X-Amz-Date=20240617T033542Z&X-Amz-SignedHeaders=host&X-Amz-Expires=120&X-Amz-Signature=b2df21aa6e48ac6919349524b6a3dc13d1b1426530efbdd209426cb17417a328&itok=o0Nlb1tG)
![129532-Thumbnail Image.png](https://d1rbsgppyrdqq4.cloudfront.net/s3fs-public/styles/width_400/public/2021-04/129532-Thumbnail%20Image.png?versionId=CIGKna3hun06aOZWd4_P3seyGyt0htLm&X-Amz-Content-Sha256=UNSIGNED-PAYLOAD&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIASBVQ3ZQ42ZLA5CUJ/20240615/us-west-2/s3/aws4_request&X-Amz-Date=20240615T195658Z&X-Amz-SignedHeaders=host&X-Amz-Expires=120&X-Amz-Signature=ac3588383420b5c287b7c5cb88d44f3dfb9bc4a36fa81af7c146277f57ae2807&itok=hCs1BMlD)
Swinging arms are a key functional component of multistep catalytic transformations in many naturally occurring multi-enzyme complexes. This arm is typically a prosthetic chemical group that is covalently attached to the enzyme complex via a flexible linker, allowing the direct transfer of substrate molecules between multiple active sites within the complex. Mimicking this method of substrate channelling outside the cellular environment requires precise control over the spatial parameters of the individual components within the assembled complex. DNA nanostructures can be used to organize functional molecules with nanoscale precision and can also provide nanomechanical control. Until now, protein–DNA assemblies have been used to organize cascades of enzymatic reactions by controlling the relative distance and orientation of enzymatic components or by facilitating the interface between enzymes/cofactors and electrode surfaces. Here, we show that a DNA nanostructure can be used to create a multi-enzyme complex in which an artificial swinging arm facilitates hydride transfer between two coupled dehydrogenases. By exploiting the programmability of DNA nanostructures, key parameters including position, stoichiometry and inter-enzyme distance can be manipulated for optimal activity.
A structurally and compositionally well-defined and spectrally tunable artificial light-harvesting system has been constructed in which multiple organic dyes attached to a three-arm-DNA nanostructure serve as an antenna conjugated to a photosynthetic reaction center isolated from Rhodobacter sphaeroides 2.4.1. The light energy absorbed by the dye molecules is transferred to the reaction center, where charge separation takes place. The average number of DNA three-arm junctions per reaction center was tuned from 0.75 to 2.35. This DNA-templated multichromophore system serves as a modular light-harvesting antenna that is capable of being optimized for its spectral properties, energy transfer efficiency, and photostability, allowing one to adjust both the size and spectrum of the resulting structures. This may serve as a useful test bed for developing nanostructured photonic systems.
![128194-Thumbnail Image.png](https://d1rbsgppyrdqq4.cloudfront.net/s3fs-public/styles/width_400/public/2021-04/128194-Thumbnail%20Image.png?versionId=eWc0R0E6CDYzBotGMB7wZ6lQsfpvB6jM&X-Amz-Content-Sha256=UNSIGNED-PAYLOAD&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIASBVQ3ZQ42ZLA5CUJ/20240615/us-west-2/s3/aws4_request&X-Amz-Date=20240615T172910Z&X-Amz-SignedHeaders=host&X-Amz-Expires=120&X-Amz-Signature=0e5ae0b03b4d7c8a77151ea0f9d95b04ecd42a2fb6a7a2a06e582599318c7c6b&itok=17NORzoy)
There is an increasing awareness that health care must move from post-symptomatic treatment to presymptomatic intervention. An ideal system would allow regular inexpensive monitoring of health status using circulating antibodies to report on health fluctuations. Recently, we demonstrated that peptide microarrays can do this through antibody signatures (immunosignatures). Unfortunately, printed microarrays are not scalable. Here we demonstrate a platform based on fabricating microarrays (~10 M peptides per slide, 330,000 peptides per assay) on silicon wafers using equipment common to semiconductor manufacturing. The potential of these microarrays for comprehensive health monitoring is verified through the simultaneous detection and classification of six different infectious diseases and six different cancers. Besides diagnostics, these high-density peptide chips have numerous other applications both in health care and elsewhere.
![128347-Thumbnail Image.png](https://d1rbsgppyrdqq4.cloudfront.net/s3fs-public/styles/width_400/public/2021-04/128347-Thumbnail%20Image.png?versionId=cGyVAMcEtvHPsW.8WR1Zg9dX_zpth8KK&X-Amz-Content-Sha256=UNSIGNED-PAYLOAD&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIASBVQ3ZQ42ZLA5CUJ/20240617/us-west-2/s3/aws4_request&X-Amz-Date=20240617T100207Z&X-Amz-SignedHeaders=host&X-Amz-Expires=120&X-Amz-Signature=ba93a3d2ca38f763fc6873e9d49a275dd9032216d9a403e0781247b2ccd859ae&itok=MJ3nKAVi)
Bismuth drugs, despite being clinically used for decades, surprisingly remain in use and effective for the treatment of Helicobacter pylori infection, even for resistant strains when co-administrated with antibiotics. However, the molecular mechanisms underlying the clinically sustained susceptibility of H. pylori to bismuth drugs remain elusive. Herein, we report that integration of in-house metalloproteomics and quantitative proteomics allows comprehensive uncovering of the bismuth-associated proteomes, including 63 bismuth-binding and 119 bismuth-regulated proteins from Helicobacter pylori, with over 60% being annotated with catalytic functions. Through bioinformatics analysis in combination with bioassays, we demonstrated that bismuth drugs disrupted multiple essential pathways in the pathogen, including ROS defence and pH buffering, by binding and functional perturbation of a number of key enzymes. Moreover, we discovered that HpDnaK may serve as a new target of bismuth drugs to inhibit bacterium-host cell adhesion. The integrative approach we report, herein, provides a novel strategy to unveil the molecular mechanisms of antimicrobial metals against pathogens in general. This study sheds light on the design of new types of antimicrobial agents with multiple targets to tackle the current crisis of antimicrobial resistance.