Ana Rita Santos

Class 2017
PhD GrantPD/BD/135138/2017 | COVID/BD/151841/2021phdARS

 

PhD thesis

Biomanufacturing of DNA-origami nanostructures for bio-imaging

 

Supervisor

• Miguel F. Prazeres, Professor @ IST/ULisboa, PT

• Pedro Paulo, Research Scientist @ IST/ULisboa, PT

Collaborators

• Hendrik Ditz, Professor @ TUMünchen, Munique, D

 

Proposal summary

DNA nanostructures assembled from large (~500-50000 bp) single stranded DNA scaffolds and short staple strands via DNA origami techniques are finding application as components of nanomachines, nanorobots and biosensors. Currently, scaffolds are obtained by asymmetric PCR or from the DNA of phages like M13, and purified using a range of lab-based, cumbersome techniques that are neither scalable nor compatible with drug delivery and biosensing applications. The goals of this project are (i) to develop scalable processes for the biomanufacturing of scaffolds and DNA-origami nanostructures, and (ii) to study the possibility of using fluorescently labelled DNA nanostructures in bio-imaging applications. Scaffolds will be purified from PCR mixtures or from the M13 DNA using scalable operations like precipitation and chromatography. Nanostructures will be assembled from these scaffolds and purified further. The obtained nanostructures are labeled with fluorophores and studied by FRET and confocal fluorescence lifetime microscopy techniques.

 

PUBLICATIONS

Papers

Silva-Santos AR, Oliveira-Silva R, Rosa SS, Paulo PMR, Prazeres DMF, Affinity-Based Magnetic Particles for the Purification of Single-Stranded DNA Scaffolds for Biomanufacturing DNA-Origami Nanostructures, ACS Applied Nano Materials, 4 (12) 14169–14177, 2021

Silva-Santos AR, Alves CPA, Monteiro M, Azevedo AM, Prazeres DMF, Multimodal chromatography of supercoiled minicircles: A closer look into DNA-ligand interactions, Separation and Purification Technology, 212, 161-170, 2019.

 

Pre-prints:

Ana Rita Silva-Santos, Pedro Paulo, Miguel Prazeres. Scalable purification of single stranded DNA scaffolds for biomanufacturing DNA-origami nanostructures: exploring anion-exchange and multimodal chromatography. Authorea. March 31, 2022. (10.22541/au.164870304.41072457/v1)

 

Book chapters:

Wagner A, Silva-Santos AR, Rosa SS, Gierak S, Azevedo AM, Prazeres DMF, Primary Purification of Plasmid DNA Using Differential Isopropanol Precipitation, DNA Vaccines, 2021, 151-165, Humana, New York, NY

Silva-Santos AR, Rosa SS, Prazeres DMF, Azevedo AM, Purification of Plasmid DNA by Multimodal Chromatography, DNA Vaccines, 2021, 193-205, Humana, New York, NY

 

Oral Communications

Silva-Santos AR, Prazeres DMF, DNA-origami nanostructures: exploring chromatography for the purification of single stranded DNA scaffolds. 40th ISPPP – International Symposium on the Separation of Proteins, Peptides and Nucleotides, November 2021, Porto, Portugal

Silva-Santos AR, Oliveira-Silva R, Paulo PMR, Prazeres DMF, Magnetic particles as affinity-based ligands: purification of single stranded DNA scaffolds for biomanufacturing DNA-origami nanostructures, 6th ECAB – European Congress of Applied Biotechnology, September 2021, virtual event

Silva-Santos AR, Prazeres DMF, Chromatographic isolation of single stranded DNA scaffolds for biomanufacturing scale-up of DNA-origami nanostructures, 6th ECAB – European Congress of Applied Biotechnology, September 2021, virtual event

Silva-Santos AR, Oliveira-Silva R, Paulo PMR, Prazeres DMF, Magnetic particles as affinity-based ligands: purification of single stranded DNA scaffolds for biomanufacturing DNA-origami nanostructures, Affinity 2021, June 2021, virtual event

Silva-Santos AR, Oliveira-Silva R, Paulo PMR, Prazeres DMF, Magnetic particles as affinity-based ligands for the purification of single stranded DNA scaffolds for biomanufacturing DNA-origami nanostructures, 13thESBES – European Symposium on Biochemical Engineering Sciences 2021, May 2021, virtual event

Silva-Santos AR, Prazeres DMF, Chromatographic isolation of single stranded DNA scaffolds for biomanufacturing of DNA-origami nanostructures, 15th SBCN – International Symposium on Biochromatography and Nanoseparations, May 2021, virtual event (Bronze VIJI award)

Silva-Santos AR, Prazeres DMF, “Chromatographic purification of single stranded DNA scaffolds for biomanufacturing DNA-origami nanostructures”, MicroBiotec2019, December 5-7, 2019, Coimbra, Portugal

Capela EV, Silva-Santos AR, Campos-Pinto I, Rodríguez MA, Gavara PR, Fernandez-Lahore M, Aires-Barros MR, Azevedo AM, “LYTAG-driven purification strategies as a key to integrate and intensify the downstream processing of monoclonal antibodies”, MicroBiotec2017, December 7-8, 2017, Porto, Portugal

 

Poster Communications

Silva-Santos AR, Oliveira-Silva R, Paulo PMR, Prazeres DMF, Single-step purification of ssDNA scaffolds using affinity magnetic beads for DNA-origami biomanufacturing, 40th ISPPP – International Symposium on the Separation of Proteins, Peptides and Nucleotides, November 2021, Porto, Portugal (Best Poster Prize)

Silva-Santos AR, Prazeres DMF, Chromatographic purification of single stranded DNA scaffolds for DNA-origami nanostructures biomanufacturing, 13th ESBES – European Symposium on Biochemical Engineering Sciences 2021, May 2021, virtual event

Silva-Santos AR, Prazeres DMF, “Biomanufacturing of DNA-origami nanostructures for bio-imaging”, PhD open days 2018Instituto Superior Técnico, Lisboa, Portugal

A.Rita Silva-Santos, Cláudia P.A. Alves, Michaela Simčíková, Gabriel Monteiro, Ana M Azevedo, Duarte Miguel F. Prazeres, “Multimodal chromatography of supercoiled minicircles: a closer look into DNA-ligand interactions, 12th ESBES – European Symposium on Biochemical Engineering Sciences, September 2018, Lisboa, Portugal

Silva-Santos AR, Alves CPA, Šimčiková M, Monteiro G, Azevedo AM, Prazeres DMF, “Multimodal chromatography: a closer look to supercoiled minicircle DNA interactions”, MicroBiotec2017 December 7-8, 2017, Porto, Portugal

 

DOCTORAL PROGRAM (36 ECTS)

Curricular units:

• General Doctoral Training (6 ECTS)

• Advanced Experimental Techniques and methodologies (6 ECTS)

• Bioentrepreneurship (6 ECTS)

  • Outreach and Teaching Skills (6 ECTS)

  • Nanobiotechnology (6 ECTS)

  • Advanced Topics in Bioengineering and Biosciences (6 ECTS)


Advanced courses:

• ABC2 – Anything but conventional chromatography workshop, Lisbon, Portugal, November 22-24, 2017

• BIOPRO World Talent Campus, organized by DTU and sponsored by NovoNordisk Foundation, Copenhagen, Denmark, August, 2018

• Cell Culture-based Viral Vaccines course – 3rd edition, organized by the European Society for Animal Cell Technology in Llafranc, Girona, Spain, September, 2018

• Drug Development course – 3rd edition, organized by the European Society for Animal Cell Technology in Llafranc, Girona, Spain, September, 2018