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Thomas CA, Craig JM, Hoshika S, Brinkerhoff H, Huang JR, Abell SJ, Kim HC, Franzi MC, Carrasco JD, Kim HJ, Smith DC, Gundlach JH, Benner SA, Laszlo AH. Assessing Readability of an 8-Letter Expanded Deoxyribonucleic Acid Alphabet with Nanopores. J Am Chem Soc 2023. [PMID: 37036666 DOI: 10.1021/jacs.3c00829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Chemists have now synthesized new kinds of DNA that add nucleotides to the four standard nucleotides (guanine, adenine, cytosine, and thymine) found in standard Terran DNA. Such "artificially expanded genetic information systems" are today used in molecular diagnostics; to support directed evolution to create medically useful receptors, ligands, and catalysts; and to explore issues related to the early evolution of life. Further applications are limited by the inability to directly sequence DNA containing nonstandard nucleotides. Nanopore sequencing is well-suited for this purpose, as it does not require enzymatic synthesis, amplification, or nucleotide modification. Here, we take the first steps to realize nanopore sequencing of an 8-letter "hachimoji" expanded DNA alphabet by assessing its nanopore signal range using the MspA (Mycobacterium smegmatis porin A) nanopore. We find that hachimoji DNA exhibits a broader signal range in nanopore sequencing than standard DNA alone and that hachimoji single-base substitutions are distinguishable with high confidence. Because nanopore sequencing relies on a molecular motor to control the motion of DNA, we then assessed the compatibility of the Hel308 motor enzyme with nonstandard nucleotides by tracking the translocation of single Hel308 molecules along hachimoji DNA, monitoring the enzyme kinetics and premature enzyme dissociation from the DNA. We find that Hel308 is compatible with hachimoji DNA but dissociates more frequently when walking over C-glycoside nucleosides, compared to N-glycosides. C-glycocide nucleosides passing a particular site within Hel308 induce a higher likelihood of dissociation. This highlights the need to optimize nanopore sequencing motors to handle different glycosidic bonds. It may also inform designs of future alternative DNA systems that can be sequenced with existing motors and pores.
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Affiliation(s)
- Christopher A Thomas
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Jonathan M Craig
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615, United States
| | - Henry Brinkerhoff
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Jesse R Huang
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Sarah J Abell
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Hwanhee C Kim
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Michaela C Franzi
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Jessica D Carrasco
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Hyo-Joong Kim
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615, United States
| | - Drew C Smith
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Jens H Gundlach
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, Florida 32615, United States
| | - Andrew H Laszlo
- Department of Physics, University of Washington, Seattle, Washington 98195, United States
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Marx SK, Mickolajczyk KJ, Craig JM, Thomas CA, Pfeffer AM, Abell SJ, Carrasco JD, Franzi MC, Huang JR, Kim HC, Brinkerhoff HD, Kapoor TM, Gundlach JH, Laszlo AH. Inhibition of the SARS-CoV-2 helicase at single-nucleotide resolution. bioRxiv 2022:2022.10.07.511351. [PMID: 36238723 PMCID: PMC9558434 DOI: 10.1101/2022.10.07.511351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The genome of SARS-CoV-2 encodes for a helicase called nsp13 that is essential for viral replication and highly conserved across related viruses, making it an attractive antiviral target. Here we use nanopore tweezers, a high-resolution single-molecule technique, to gain detailed insight into how nsp13 turns ATP-hydrolysis into directed motion along nucleic acid strands. We measured nsp13 both as it translocates along single-stranded DNA or unwinds short DNA duplexes. Our data confirm that nsp13 uses the inchworm mechanism to move along the DNA in single-nucleotide steps, translocating at ~1000 nt/s or unwinding at ~100 bp/s. Nanopore tweezers' high spatio-temporal resolution enables observation of the fundamental physical steps taken by nsp13 even as it translocates at speeds in excess of 1000 nucleotides per second enabling detailed kinetic analysis of nsp13 motion. As a proof-of-principle for inhibition studies, we observed nsp13's motion in the presence of the ATPase inhibitor ATPγS. Our data reveals that ATPγS interferes with nsp13's action by affecting several different kinetic processes. The dominant mechanism of inhibition differs depending on the application of assisting force. These advances demonstrate that nanopore tweezers are a powerful method for studying viral helicase mechanism and inhibition.
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Affiliation(s)
- Sinduja K Marx
- Department of Physics, University of Washington, Seattle, WA 98195
| | - Keith J Mickolajczyk
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, New York
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA
| | - Jonathan M Craig
- Department of Physics, University of Washington, Seattle, WA 98195
| | | | - Akira M Pfeffer
- Department of Physics, University of Washington, Seattle, WA 98195
| | - Sarah J Abell
- Department of Physics, University of Washington, Seattle, WA 98195
| | | | | | - Jesse R Huang
- Department of Physics, University of Washington, Seattle, WA 98195
| | - Hwanhee C Kim
- Department of Physics, University of Washington, Seattle, WA 98195
| | | | - Tarun M Kapoor
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, New York
| | - Jens H Gundlach
- Department of Physics, University of Washington, Seattle, WA 98195
| | - Andrew H Laszlo
- Department of Physics, University of Washington, Seattle, WA 98195
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Khosropour CM, Dombrowski JC, Vojtech L, Patton DL, Campbell LA, Barbee LA, Franzi MC, Hybiske K. Rectal Chlamydia trachomatis Infection: A Narrative Review of the State of the Science and Research Priorities. Sex Transm Dis 2021; 48:e223-e227. [PMID: 34475361 PMCID: PMC8595876 DOI: 10.1097/olq.0000000000001549] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
ABSTRACT Chlamydia trachomatis (CT) is the most commonly reported infection in the United States. Most chlamydial research to date has focused on urogenital infection, but a growing body of research has demonstrated that rectal chlamydia is a relatively common infection among clinic-attending men and women. We know that most rectal CT infections are asymptomatic, but the health implications of these infections, particularly for women, are unclear. In addition, there are key knowledge gaps related to the epidemiologic parameters of rectal chlamydia, the routes of acquisition, the duration of infection, and the clinical significance of a positive rectal CT test result. This lack of information has led to a blind spot in the potential role of rectal chlamydia in sustaining high levels of CT transmission in the United States. Furthermore, recent findings from animal models suggest that the immune response generated from gastrointestinal chlamydial infection can protect against urogenital infection; however, it remains to be determined whether rectal chlamydia similarly modulates anti-CT immunity in humans. This is a critical question in the context of ongoing efforts to develop a CT vaccine. In this narrative review, we summarize the state of the science for rectal chlamydia and discuss the key outstanding questions and research priorities in this neglected area of sexual health research.
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Affiliation(s)
| | - Julia C. Dombrowski
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
- Public Health – Seattle and King County HIV/STD Program, Seattle, WA, USA
| | - Lucia Vojtech
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, USA
| | - Dorothy L. Patton
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, USA
| | - Lee Ann Campbell
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Lindley A. Barbee
- Department of Medicine, University of Washington, Seattle, WA, USA
- Public Health – Seattle and King County HIV/STD Program, Seattle, WA, USA
| | | | - Kevin Hybiske
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
- Department of Microbiology, University of Washington, Seattle, WA, USA
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