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1. Sequencing by avidity enables high accuracy with low reagent consumption

Author

Arslan, Sinan, Garcia, Francisco J., Guo, Minghao, Kellinger, Matthew W., Kruglyak, Semyon, LeVieux, Jake A., Mah, Adeline H., Wang, Haosen, Zhao, Junhua, Zhou, Chunhong, Altomare, Andrew, Bailey, John, Byrne, Matthew B., Chang, Chiting, Chen, Steve X., Cho, Byungrae, Dennler, Claudia N., Dien, Vivian T., Fuller, Derek, Kelley, Ryan, Khandan, Omid, Klein, Michael G., Kim, Michael, Lajoie, Bryan R., Lin, Bill, Liu, Yu, Lopez, Tyler, Mains, Peter T., Price, Andrew D., Robertson, Samantha R., Taylor-Weiner, Hermes, Tippana, Ramreddy, Tomaney, Austin B., Zhang, Su, Abtahi, Minna, Ambroso, Mark R., Bajari, Rosita, Bellizzi, Ava M., Benitez, Chris B., Berard, Daniel R., Berti, Lorenzo, Blease, Kelly N., Blum, Angela P., Boddicker, Andrew M., Bondar, Leo, Brown, Chris, Bui, Chris A., Calleja-Aguirre, Juan, Cappa, Kevin, Chan, Joshua, Chang, Victor W., Charov, Katherine, Chen, Xiyi, Constandse, Rodger M., Damron, Weston, Dawood, Mariam, DeBuono, Nicole, Dimalanta, John D., Edoli, Laure, Elango, Keerthana, Faustino, Nikka, Feng, Chao, Ferrari, Matthew, Frankie, Keith, Fries, Adam, Galloway, Anne, Gavrila, Vlad, Gemmen, Gregory J., Ghadiali, James, Ghorbani, Arash, Goddard, Logan A., Guetter, Adriana Roginski, Hendricks, Garren L., Hentschel, Jendrik, Honigfort, Daniel J., Hsieh, Yun-Ting, Hwang Fu, Yu-Hsien, Im, Scott K., Jin, Chaoyi, Kabu, Shradha, Kincade, Daniel E., Levy, Shawn, Li, Yu, Liang, Vincent K., Light, William H., Lipsher, Jonathan B., Liu, Tsung-li, Long, Grace, Ma, Rui, Mailloux, John M., Mandla, Kyle A., Martinez, Anyssa R., Mass, Max, McKean, Daniel T., Meron, Michael, Miller, Edmund A., Moh, Celyne S., Moore, Rachel K., Moreno, Juan, Neysmith, Jordan M., Niman, Cassandra S., Nunez, Jesus M., Ojeda, Micah T., Ortiz, Sara Espinosa, Owens, Jenna, Piland, Geoffrey, Proctor, Daniel J., Purba, Josua B., Ray, Michael, Rong, Daisong, Saade, Virginia M., Saha, Sanchari, Tomas, Gustav Santo, Scheidler, Nicholas, Sirajudeen, Luqmanal H., Snow, Samantha, Stengel, Gudrun, Stinson, Ryan, Stone, Michael J., Sundseth, Keoni J., Thai, Eileen, Thompson, Connor J., Tjioe, Marco, Trejo, Christy L., Trieger, Greg, Truong, Diane Ni, Tse, Ben, Voiles, Benjamin, Vuong, Henry, Wong, Jennifer C., Wu, Chiung-Ting, Yu, Hua, Yu, Yingxian, Yu, Ming, Zhang, Xi, Zhao, Da, Zheng, Genhua, He, Molly, and Previte, Michael

Published
2024
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2. Sequencing by avidity enables high accuracy with low reagent consumption

Author

Arslan, Sinan, primary, Garcia, Francisco J., additional, Guo, Minghao, additional, Kellinger, Matthew W., additional, Kruglyak, Semyon, additional, LeVieux, Jake A., additional, Mah, Adeline H., additional, Wang, Haosen, additional, Zhao, Junhua, additional, Zhou, Chunhong, additional, Altomare, Andrew, additional, Bailey, John, additional, Byrne, Matthew B., additional, Chang, Chiting, additional, Chen, Steve X., additional, Cho, Byungrae, additional, Dennler, Claudia N., additional, Dien, Vivian T., additional, Fuller, Derek, additional, Kelley, Ryan, additional, Khandan, Omid, additional, Klein, Michael G., additional, Kim, Michael, additional, Lajoie, Bryan R., additional, Lin, Bill, additional, Liu, Yu, additional, Lopez, Tyler, additional, Mains, Peter T., additional, Price, Andrew D., additional, Robertson, Samantha R., additional, Taylor-Weiner, Hermes, additional, Tippana, Ramreddy, additional, Tomaney, Austin B., additional, Zhang, Su, additional, Abtahi, Minna, additional, Ambroso, Mark R., additional, Bajari, Rosita, additional, Bellizzi, Ava M., additional, Benitez, Chris B., additional, Berard, Daniel R., additional, Berti, Lorenzo, additional, Blease, Kelly N., additional, Blum, Angela P., additional, Boddicker, Andrew M., additional, Bondar, Leo, additional, Brown, Chris, additional, Bui, Chris A., additional, Calleja-Aguirre, Juan, additional, Cappa, Kevin, additional, Chan, Joshua, additional, Chang, Victor W., additional, Charov, Katherine, additional, Chen, Xiyi, additional, Constandse, Rodger M., additional, Damron, Weston, additional, Dawood, Mariam, additional, DeBuono, Nicole, additional, Dimalanta, John D., additional, Edoli, Laure, additional, Elango, Keerthana, additional, Faustino, Nikka, additional, Feng, Chao, additional, Ferrari, Matthew, additional, Frankie, Keith, additional, Fries, Adam, additional, Galloway, Anne, additional, Gavrila, Vlad, additional, Gemmen, Gregory J., additional, Ghadiali, James, additional, Ghorbani, Arash, additional, Goddard, Logan A., additional, Guetter, Adriana Roginski, additional, Hendricks, Garren L., additional, Hentschel, Jendrik, additional, Honigfort, Daniel J., additional, Hsieh, Yun-Ting, additional, Hwang Fu, Yu-Hsien, additional, Im, Scott K., additional, Jin, Chaoyi, additional, Kabu, Shradha, additional, Kincade, Daniel E., additional, Levy, Shawn, additional, Li, Yu, additional, Liang, Vincent K., additional, Light, William H., additional, Lipsher, Jonathan B., additional, Liu, Tsung-li, additional, Long, Grace, additional, Ma, Rui, additional, Mailloux, John M., additional, Mandla, Kyle A., additional, Martinez, Anyssa R., additional, Mass, Max, additional, McKean, Daniel T., additional, Meron, Michael, additional, Miller, Edmund A., additional, Moh, Celyne S., additional, Moore, Rachel K., additional, Moreno, Juan, additional, Neysmith, Jordan M., additional, Niman, Cassandra S., additional, Nunez, Jesus M., additional, Ojeda, Micah T., additional, Ortiz, Sara Espinosa, additional, Owens, Jenna, additional, Piland, Geoffrey, additional, Proctor, Daniel J., additional, Purba, Josua B., additional, Ray, Michael, additional, Rong, Daisong, additional, Saade, Virginia M., additional, Saha, Sanchari, additional, Tomas, Gustav Santo, additional, Scheidler, Nicholas, additional, Sirajudeen, Luqmanal H., additional, Snow, Samantha, additional, Stengel, Gudrun, additional, Stinson, Ryan, additional, Stone, Michael J., additional, Sundseth, Keoni J., additional, Thai, Eileen, additional, Thompson, Connor J., additional, Tjioe, Marco, additional, Trejo, Christy L., additional, Trieger, Greg, additional, Truong, Diane Ni, additional, Tse, Ben, additional, Voiles, Benjamin, additional, Vuong, Henry, additional, Wong, Jennifer C., additional, Wu, Chiung-Ting, additional, Yu, Hua, additional, Yu, Yingxian, additional, Yu, Ming, additional, Zhang, Xi, additional, Zhao, Da, additional, Zheng, Genhua, additional, He, Molly, additional, and Previte, Michael, additional

Published
2023
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5. Lipid membranes carrying lipophilic cholesterol-based oligonucleotides-characterization and application on layer-by-layer coated particles

Author

Bunge, Andreas, Loew, Martin, Pescador, Paula, Arbuzova, Anna, Brodersen, Nicolai, Jing Kang, Dahne, Lars, Liebscher, Jrgen, Herrmann, Andreas, Stengel, Gudrun, and Huster, Daniel

Subjects
Cholesterol -- Chemical properties, Lipid membranes -- Composition, Oligonucleotides -- Chemical properties, Chemicals, plastics and rubber industries
Published
2009

6. Effect of transition metal ions on the fluorescence and Taqcatalyzed PCR of tricyclic cytidine analogues

Author

Stengel, Gudrun, Purse, Byron, and Kuchta, Robert D.

Subjects
Ions, Phenothiazines, Oxazines, Biocatalysis, Transition Elements, Humans, Taq Polymerase, DNA, Polymerase Chain Reaction, Sensitivity and Specificity, Article, Fluorescence
Abstract

The cytosine analogs 1,3-diaza-2-oxophenothiazine (tC) and 1,3-diaza-2-oxophenoxazine (tCo) stand out among fluorescent bases due to their unquenched fluorescence emission in double-stranded DNA. Recently, we reported a method for the generation of densely tCo-labeled DNA by polymerase chain reaction (PCR) that relied on the use of the extremely thermostable Deep Vent polymerase. We have now developed a protocol that employs the more commonly used Taq polymerase. Supplementing the PCR with Mn(2+) or Co(2+) ions dramatically increased the amount of tCo triphosphate (dtCoTP) incorporated and, thus, enhanced the brightness of the PCR products. The resulting PCR products could be easily detected in gels based on their intrinsic fluorescence. The Mn(2+) ions modulate the PCR by improving the bypass of template tCo and the overall catalytic efficiency. In contrast to the lower fidelity during tCo bypass, Mn(2+) improved the ability of Taq polymerase to distinguish between dtCoTP and dTTP when copying a template dA. Interestingly, Mn(2+) ions hardly affect the fluorescence emission of tC(o), whereas the coordination of Co(2+) ions with the phosphate groups of DNA and nucleotides statically quenches tC(o) fluorescence with small reciprocal Stern-Vollmer constants of 10-300μM.

Published
2011

7. High Density Labeling of PCR Products with the Fluorescent Analogue tCo

Author

Stengel, Gudrun, Urban, Milan, Purse, Byron W., and Kuchta, Robert D.

Subjects
Oxazines, DNA, DNA-Directed DNA Polymerase, Base Pairing, Polymerase Chain Reaction, Article, Fluorescent Dyes
Abstract

Fluorescent DNA of high molecular weight is an important tool for studying the physical properties of DNA and DNA-protein interactions, and it plays a key role in modern biotechnology for DNA sequencing and detection. While several DNA polymerases can incorporate large numbers of dye-linked nucleotides into primed DNA templates, the amplification of the resulting densely labeled DNA strands by polymerase chain reaction (PCR) is problematic. Here, we report a method for high density labeling of DNA in PCR reactions employing the 5'-triphosphate of 1,3-diaza-2-oxo-phenoxazine (tCo) and Deep Vent DNA polymerase. tCo is a fluorescent cytosine analogue that absorbs and emits light at 365 and 460 nm, respectively. We obtained PCR products that were fluorescent enough to directly visualize them in a gel by excitation with long UV light, thus eliminating the need for staining with ethidium bromide. Reactions with Taq polymerase failed to produce PCR products in the presence of only small amounts of dtCoTP. A comparative kinetic study of Taq and Deep Vent polymerase revealed that Taq polymerase, although it inserts dtCoTP with high efficiency opposite G, is prone to forming mutagenic tCo-A base pairs and does not efficiently extend base pairs containing tCo. These kinetics features explain the poor outcome of the PCR reactions with Taq polymerase. Since tCo substitutes structurally for cytosine, the presented labeling method is believed to be less invasive than labeling with dye-linked nucleotides and, therefore, produces DNA that is ideally suited for biophysical studies.

Published
2009

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