Zunyi Yang's Publications
Aptamers against Cells Overexpressing Glypican 3 from Expanded
Genetic Systems Combined with Cell Engineering and Laboratory
Zhang, L, Yang, Z, Trinh, TL, Teng, I-T, Wang, S, Bradley, KM, Hoshika, S, Wu, Q, Cansiz, S, Rowold, DJ, McLendon, C, Kim, M-S, Wu, Y, Cui, C, Liu, Y, Hou, W, Stewart, K, Wan, S, Liu, C, Benner, SA, Tan, W
Angew. Chem. Int. Ed.
55 (2016) doi: 10.1002/anie.201605058
Laboratory in vitro evolution (LIVE) might deliver
DNA aptamers that bind proteins expressed on the surface of
cells. In this work, we used cell engineering to place glypican 3
(GPC3), a possible marker for liver cancer theranostics, on the
surface of a liver cell line. Libraries were then built from a sixletter
genetic alphabet containing the standard nucleobases and
two added nucleobases (2-amino-8H-imidazo[1,2-a]-
[1,3,5]triazin-4-one and 6-amino-5-nitropyridin-2-one),
Watson-Crick complements from an artificially expanded
genetic information system (AEGIS). With counterselection
against non-engineered cells, eight AEGIS-containing aptamers
were recovered. Five bound selectively to GPC3-overexpressing
cells. This selectionâ€“counterselection scheme had
acceptable statistics, notwithstanding the possibility that cells
engineered to overexpress GPC3 might also express different
off-target proteins. This is the first example of such a combination.
A norovirus detection architecture based on isothermal amplification and expanded genetic systems
Ozlem Yaren, Kevin M. Bradley, Patricia Moussatche, Shuichi Hoshika, Zunyi Yang,Shu Zhu, Stephanie M. Karst, Steven A. Benner
J Virol Methods
(237) , Elsevier 64-71 (2016) doi: 10.1016/j.jviromet.2016.08.012
Noroviruses are the major cause of global viral gastroenteritis with short incubation times and small inoculums required for infection. This creates a need for a rapid molecular test for norovirus for early diagnosis, in the hope of preventing the spread of the disease. Non-chemists generally use off-the shelf reagents and natural DNA to create such tests, suffering from background noise that comes from adventitious DNA and RNA (collectively xNA) that is abundant in real biological samples, especially feces, a common location for norovirus. Here, we create an assay that combines artificially expanded genetic information systems (AEGIS, which adds nucleotides to the four in standard xNA, pairing orthogonally to A:T and G:C) with loop-mediated isothermal amplification (LAMP) to amplify norovirus RNA at constant temperatures, without the power or instrument requirements of PCR cycling. This assay was then validated using feces contaminated with murine norovirus (MNV). Treating stool samples with ammonia extracts the MNV RNA, which is then amplified in an AEGIS-RT-LAMP where AEGIS segments are incorporated both into an internal LAMP primer and into a molecular beacon stem, the second lowering background signaling noise. This is coupled with RNase H nicking during sample amplification, allowing detection of as few as 10 copies of noroviral RNA in a stool sample, generating a fluorescent signal visible to human eye, all in a closed reaction vessel.
Evolution of functional six-nucleotide DNA
Zhang, L., Yang, Z., Sefah, K., Bradley, K. M., Hoshika, S., Kim, M-J,. Kim, H-J., Zhu., Jimenez, E., Cansiz, S., Teng, I-T., Champanhac, C, McLendon, C., Liu, C., Zhang, W., Gerloff, D. L., Huang, Z., Tan, W., Benner, S. A.
J. Am. Chem. Soc.
(2015) DOI: 10.1021/jacs.5b02251
Axiomatically, the density of information
stored in DNA, with just four nucleotides (GACT), is
higher than in a binary code, but less than it might be if
synthetic biologists succeed in adding independently
replicating nucleotides to genetic systems. Such addition
could also add additional functional groups, not found in
natural DNA but useful for molecular performance. Here,
we consider two new nucleotides (Z and P, 6-amino-5-
[1,2-a]-1,3,5-triazin-4(8H)-one). These are designed to
pair via strict Watson?Crick geometry. These were added
to a laboratory in vitro evolution (LIVE) experiment; the
GACTZP library was challenged to deliver molecules that
bind selectively to liver cancer cells, but not to
untransformed liver cells. Unlike in classical in vitro
selection systems, low levels of mutation allow this system
to evolve to create binding molecules not necessarily
present in the original library. Over a dozen binding
species were recovered. The best had Z and/or P in their
sequences. Several had multiple, nearby, and adjacent Zs
and Ps. Only the weaker binders contained no Z or P at all.
This suggests that this system explored much of the
sequence space available to this genetic system and that
GACTZP libraries are richer reservoirs of functionality
than standard libraries.
Detecting respiratory viral RNA using expanded genetic alphabets and
Lyudmyla G. Glushakova, Nidhi Sharma, Shuichi Hoshika, Andrea C. Bradley, Kevin M. Bradley, Zunyi Yang, Steven A. Benner
, Elsevier (2015) Nov 15;489:62-72. doi: 10.1016/j.ab.2015.08.015
Nucleic acid (NA)-targeted tests detect and quantify viral DNA and RNA (collectively xNA) to support
epidemiological surveillance and, in individual patients, to guide therapy. They commonly use polymerase
chain reaction (PCR) and reverse transcription PCR. Although these all have rapid turnaround,
they are expensive to run. Multiplexing would allow their cost to be spread over multiple targets, but
often only with lower sensitivity and accuracy, noise, false positives, and false negatives; these arise by
interactions between the multiple nucleic acid primers and probes in a multiplexed kit. Here we offer a
multiplexed assay for a panel of respiratory viruses that mitigates these problems by combining several
nucleic acid analogs from the emerging field of synthetic biology: (i) self-avoiding molecular recognition
systems (SAMRSs), which facilitate multiplexing, and (ii) artificially expanded genetic information systems
(AEGISs), which enable low-noise PCR. These are supplemented by "transliteration" technology,
which converts standard nucleotides in a target to AEGIS nucleotides in a product, improving hybridization. The combination supports a multiplexed Luminex-based respiratory panel that potentially differentiates influenza viruses A and B, respiratory syncytial virus, severe acute respiratory syndrome
coronavirus (SARS), and Middle East respiratory syndrome (MERS) coronavirus, detecting as few as 10
MERS virions in a 20-ml sample.
High-throughput multiplexed xMAP Luminex array panel for
detection of twenty two medically important mosquito-borne
arboviruses based on innovations in synthetic biology
Lyudmyla G. Glushakova, Andrea Bradley, Kevin M. Bradley, Barry W. Alto, Shuichi Hoshika, Daniel Hutter, Nidhi Sharma, Zunyi Yang, Myong-Jung Kim, Steven A. Benner
J Virol Methods
214 , Elsevier 60-74 (2015) doi: 10.1016/j.jviromet.2015.01.003
Mosquito-borne arboviruses are emerging world-wide as important human and animal pathogens. This
makes assays for their accurate and rapid identification essential for public health, epidemiological, ecological
studies. Over the past decade, many mono- and multiplexed assays targeting arboviruses nucleic
acids have been reported. None has become established for the routine identification of multiple viruses
in a "single tube" setting. With increasing multiplexing, the detection of viral RNAs is complicated by
noise, false positives and negatives. In this study, an assay was developed that avoids these problems
by combining two new kinds of nucleic acids emerging from the field of synthetic biology. The first is a
"self-avoiding molecular recognition system" (SAMRS), which enables high levels of multiplexing. The
second is an "artificially expanded genetic information system" (AEGIS), which enables clean PCR amplification
in nested PCR formats. A conversion technology was used to place AEGIS component into amplicon,
improving their efficiency of hybridization on Luminex beads. When Luminex "liquid microarrays" are
exploited for downstream detection, this combination supports single-tube PCR amplification assays that
can identify 22 mosquito-borne RNA viruses from the genera Flavivirus, Alphavirus, Orthobunyavirus. The
assay differentiates between closely-related viruses, as dengue, West Nile, Japanese encephalitis, and the
California serological group. The performance and the sensitivity of the assay were evaluated with dengue
viruses and infected mosquitoes; as few as 6-10 dengue virions can be detected in a single mosquito.
A Crystal Structure of a Functional RNA Molecule Containing an
Artificial Nucleobase Pair
Armando R. Hernandez, Yaming Shao, Shuichi Hoshika, Zunyi Yang, Sandip A. Shelke, Julien Herrou, Hyo-Joong Kim, Myong-Jung Kim, Joseph A. Piccirilli, and Steven A. Benner
Angew. Chem. Int. Ed.
54 9853-9856 (2015) doi: 10.1002/anie.201504731
As one of its goals, synthetic biology seeks to
increase the number of building blocks in nucleic acids. While
efforts towards this goal are well advanced for DNA, they have
hardly begun for RNA. Herein, we present a crystal structure
for an RNA riboswitch where a stem C:G pair has been
replaced by a pair between two components of an artificially
expanded genetic-information system (AEGIS), Z and P, (6-
amino-5-nitro-2(1H)-pyridone and 2-aminoimidazo[
1,2-a]-1,3,5-triazin-4-(8H)-one). The structure
shows that the Z:P pair does not greatly change
the conformation of the RNAmolecule nor the details
of its interaction with a hypoxanthine ligand. This was
confirmed in solution by in-line probing, which also
measured a 3.7 nm affinity of the riboswitch for
guanine. These data show that the Z:P pair mimics the
natural Watson-Crick geometry in RNA in the first
example of a crystal structure of an RNA molecule
that contains an orthogonal added nucleobase pair.
Helicase Dependent Isothermal Amplification of DNA and RNA using Self-Avoiding Molecular Recognition Systems
Zunyi Yang, Chris McLendon, Daniel Hutter, Kevin M. Bradley, Shuichi Hoshika, Carole Frye, and Steven A. Benner
(2015) June 15; 16(9): 1365-1370. doi:10.1002/cbic.201500135.
Assays that target DNA or RNA (xNA) are highly sensitive, as small amounts of xNA can be amplified by PCR. Unfortunately, PCR is inconvenient in low resource environments, requiring equipment and power that may not be available in these environments. However, isothermal procedures that avoid thermal cycling are often confounded by primer dimers, off-target priming, and other artifacts. Here, we show how a "self avoiding molecular recognition system" (SAMRS) eliminates these artifacts to give clean amplicons in a helicase-dependent isothermal amplification (SAMRS-HDA). We also show that incorporating SAMRS into the 3'-ends of primers facilitates the design and screening of primers for HDA assays. Finally, we show that SAMRS-HDA can be twofold multiplexed, something difficult to achieve with HDA using standard primers. This shows that SAMRS-HDA is a more versatile approach than standard HDA with a broader applicability for xNA-targeted diagnostics and research.
Conversion strategy using an expanded genetic alphabet to assay nucleic acids
Yang, Z., Durante, M., Glushakova, L., Sharma, N., Leal, N., Bradley, K., Chen, F., Benner, S. A.
Methods to detect DNA and RNA (collectively
xNA) are easily plagued by noise, false positives, and false
negatives, especially with increasing levels of multiplexing in
complex assay mixtures. Here, we describe assay architectures
that mitigate these problems by converting standard xNA
analyte sequences into sequences that incorporate nonstandard
nucleotides (Z and P). Z and P are extra DNA building blocks
that form tight nonstandard base pairs without cross-binding
to natural oligonucleotides containing G, A, C, and T
(GACT). The resulting improvements are assessed in an
assay that inverts the standard Luminex xTAG architecture,
placing a biotin on a primer (rather than on a triphosphate).
This primer is extended on the target to create a standard
GACT extension product that is captured by a CTGA oligonucleotide attached to a Luminex bead. By using conversion, a
polymerase incorporates dZTP opposite template dG in the absence of dCTP. This creates a Z-containing extension product that
is captured by a bead-bound oligonucleotide containing P, which binds selectively to Z. The assay with conversion produces
higher signals than the assay without conversion, possibly because the Z/P pair is stronger than the C/G pair. These architectures
improve the ability of the Luminex instruments to detect xNA analytes, producing higher signals without the possibility of
competition from any natural oligonucleotides, even in complex biological samples.
Recognition of an expanded genetic alphabet by type-II restriction endonucleases and their application to analyze polymerase fidelity.
Chen, F; Yang, ZY; Yan, M; Alvarado, JB; Wang, G; Benner, SA
Nucl. Acids Res.
39 (9) 3949-3961 (2011)
To explore the possibility of using restriction enzymes in a synthetic biology based on artificially expanded genetic information systems (AEGIS), 24 type-II restriction endonucleases (REases) were challenged to digest DNA duplexes containing recognition sites where individual Cs and Gs were replaced by the AEGIS nucleotides Z and P [respectively, 6-amino-5-nitro-3-(1'-?-d-2'-deoxyribofuranosyl)-2(1H)-pyridone and 2-amino-8-(1'-?-d-2'-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one]. These AEGIS nucleotides implement complementary hydrogen bond donor-donor-acceptor and acceptor-acceptor-donor patterns. Results allowed us to classify type-II REases into five groups based on their performance, and to infer some specifics of their interactions with functional groups in the major and minor grooves of the target DNA. For three enzymes among these 24 where crystal structures are available (BcnI, EcoO109I and NotI), these interactions were modeled. Further, we applied a type-II REase to quantitate the fidelity polymerases challenged to maintain in a DNA duplex C:G, T:A and Z:P pairs through repetitive PCR cycles. This work thus adds tools that are able to manipulate this expanded genetic alphabet in vitro, provides some structural insights into the working of restriction enzymes, and offers some preliminary data needed to take the next step in synthetic biology to use an artificial genetic system inside of living bacterial cells.
Amplification, Mutation, and Sequencing of a Six-Letter Synthetic
Yang, Z; Chen, F; Alvarado, JB; Benner, SA
J. Am. Chem. Soc.
133 (38) 15105-15112 (2011) dx.doi.org/10.1021/ja204910n
The next goals in the development of a synthetic biology that uses
artificial genetic systems will require chemistry-biology combinations that
allow the amplification of DNA containing any number of sequential and
nonsequential nonstandard nucleotides. This amplification must ensure that the
nonstandard nucleotides are not unidirectionally lost during PCR amplification
(unidirectional loss would cause the artificial system to revert to an all-natural
genetic system). Further, technology is needed to sequence artificial genetic
DNA molecules. The work reported here meets all three of these goals for a sixletter
artificially expanded genetic information system (AEGIS) that comprises
four standard nucleotides (G, A, C, and T) and two additional nonstandard
nucleotides (Z and P). We report polymerases and PCR conditions that amplify
a wide range of GACTZP DNA sequences having multiple consecutive
unnatural synthetic genetic components with low (0.2% per theoretical cycle)
levels of mutation. We demonstrate that residual mutation processes both introduce and remove unnatural nucleotides, allowing the
artificial genetic system to evolve as such, rather than revert to a wholly natural system. We then show that mechanisms for these
residual mutation processes can be exploited in a strategy to sequence "six-letter" GACTZP DNA. These are all not yet reported for
any other synthetic genetic system.
Synthetic Biology for Improved Personalized Medicine
Benner, SA; Hoshika, S; Sukeda, M; Hutter, D; Leal, NA; Yang, ZY; Chen, F
Nucleic Acids Symp. Ser.
52 (1) 243-244 (2008) doi: 10.1093/nass/nrn123
Tools to re-sequence the genomes of individual patients having well described medical histories is the first step required to connect genetic information to diagnosis, prognosis, and treatment. There is little doubt that in the future, genomics will influence the choice of therapies for individual patients based on their specific genetic inheritance, as well as the genetic defects that led to disease. Cost is the principle obstacle preventing the realization of this vision. Unless the interesting parts of a patient genome can be resequenced for less than $10,000 (as opposed to $100,000 or more), it will be difficult to start the discovery process that will enable this vision. While instrumentation and biology are important to reducing costs, the key element to cost-effective personalized genomic sequencing will be new chemical reagents that deliver capabilities that are not available from standard DNA. Scientists at the Foundation for Applied Molecular Evolution and the Westheimer Institute have developed several of these, which will be the topic of this talk.
Nucleoside alpha-thiotriphosphates, polymerases and the exonuclease III analysis of oligonucleotides containing phosphorothioate linkages
Yang, ZY; Sismour, AM; Benner, SA
Nucl. Acids Res.
35 (9) 3118-3127 (2007)
The use of DNA polymerases to incorporate phosphorothioate linkages into DNA, and the use of exonuclease III to determine where those linkages have been incorporated, are re- examined in this work. The results presented here show that exonuclease III degrades single- stranded DNA as a substrate and digests through phosphorothioate linkages having one absolute stereochemistry, assigned ( assuming inversion in the polymerase reaction) as S, but not the other absolute stereochemistry. This contrasts with a general view in the literature that exonuclease III favors double-stranded nucleic acid as a substrate and stops completely at phosphorothioate linkages. Furthermore, not all DNA polymerases appear to accept exclusively the ( R) stereoisomer of nucleoside alpha- thiotriphosphates [ and not the ( S) diastereomer], a conclusion inferred two decades ago by examination of five Family- A polymerases and a reverse transcriptase. This suggests that caution is appropriate when extrapolating the detailed behavior of one polymerase from the behaviors of other polymerases. Furthermore, these results provide constraints on how exonuclease III - thiotriphosphate - polymerase combinations can be used to analyze the behavior of the components of a synthetic biology.
Enzymatic incorporation of a third nucleobase pair
Yang, ZY; Sismour, AM; Sheng, PP; Puskar, NL; Benner, SA
Nucl. Acids Res.
35 (13) 4238-4249 (2007)
DNA polymerases are identified that copy a nonstandard nucleotide pair joined by a hydrogen bonding pattern different from the patterns joining the dA:T and dG:dC pairs. 6-Amino-5-nitro3-(l'-p-D-2'-deoxyribofuranosyl)-2(1H)-pyridone (dZ) implements the non-standard 'small' donordonor-acceptor (pyDDA) hydrogen bonding pattern. 2-Amino-8-(1-beta-D-2'-deoxyribofuranosyl)imidazo[1,2-a]-1,3,5-triazin-4 (8H)-one [dP) implements the 'large' acceptor-acceptor-donor (puAAD) pattern. These nucleobases were designed to present electron density to the minor groove, density hypothesized to help determine specificity for polymerases. Consistent with this hypothesis, both dZTP and dPTP are accepted by many polymerases from both Families A and B. Further, the dZ:dP pair participates in PCR reactions catalyzed by Taq, Vent (exo(-)) and Deep Vent (exo-) polymerases, with 94.4%, 97.5% and 97.5%, respectively, retention per round. The dZ:dP pair appears to be lost principally via transition to a dC:dG pair. This is consistent with a mechanistic hypothesis that deprotonated dZ (presenting a pyDAA pattern) complements dG (presenting a puADD pattern), while protonated dC (presenting a pyDDA pattern) complements dP (presenting a puAAD pattern). This hypothesis, grounded in the Watson-Crick model for nucleobase pairing, was confirmed by studies of the pH-dependence of mismatching. The dZ:dP pair and these polymerases, should be useful in dynamic architectures for sequencing, molecular-, systems- and synthetic-biology.
Artificially expanded genetic information system: a new base pair with an alternative hydrogen bonding pattern
Yang, ZY; Hutter, D; Sheng, PP; Sismour, AM; Benner, SA
Nucl. Acids Res.
34 (21) 6095-6101 (2006)
To support efforts to develop a 'synthetic biology' based on an artificially expanded genetic information system (AEGIS), we have developed a route to two components of a non-standard nucleobase pair, the pyrimidine analog 6-amino-5-nitro-3-(1'-beta-D-2'-deoxyribofuranosyl)-2(1H)-pyridone (dZ) and its Watson-Crick complement, the purine analog 2-amino-8-(1'-beta-D-2'-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin -4(8H)-one (dP). These implement the pyDDA:puAAD hydrogen bonding pattern (where 'py' indicates a pyrimidine analog and 'pu' indicates a purine analog, while A and D indicate the hydrogen bonding patterns of acceptor and donor groups presented to the complementary nucleobases, from the major to the minor groove). Also described is the synthesis of the triphosphates and protected phosphoramidites of these two nucleosides. We also describe the use of the protected phosphoramidites to synthesize DNA oligonucleotides containing these AEGIS components, verify the absence of epimerization of dZ in those oligonucleotides, and report some hybridization properties of the dZ:dP nucleobase pair, which is rather strong, and the ability of each to effectively discriminate against mismatches in short duplex DNA.
One-pot glycosylation (OPG) for the chemical synthesis of oligosaccharides
Yu, B; Yang, ZY; Cao, HZ
Curr. Org. Chem.
9 (2) 179-194 (2005)
This review provides a comprehensive survey of the "one pot glycosylation" (OPG) strategy for the chemical synthesis of oligosaccharides, covering literatures from the first example reported by Kahne and Raghavan in 1993 through May 2003. The essence of the OPG is to distinguish the reactivity difference of a pair of the glycosylation donors or acceptors so as to carry out two glycosylation steps sequentially without purification of the first-step coupling product. Accordingly, the literature reports are grouped based on the major stereoelectronic factors causing the reactivity differences, those include the "armed-disarmed effect", "orthogonality of leaving groups", "distinguishable acceptors", and "the hybrid". "The hybrid" OPG procedure takes advantage of a combination of the reactivity disparity of a set of the armed-disarmed donors, orthogonal leaving groups, as well as acceptors so as to proceed three or more steps of glycosylation sequentially in one pot. Relevant conception and exploitation of the reactivity differences of the donors and acceptors in the synthesis of oligosaccharides, which finally evolve the OPG or advance parallelly, are briefly described at the beginning.
1 -> 2 Migration and concurrent glycosidation of phenyl 1-thio-alpha-mannopyranosides via 2,3-O-cyclic dioxonium intermediates
Yang, ZY; Cao, HZ; Hu, J; Shan, RL; Yu, B
59 (2) 249-254 (2003)
Treatment of phenyl 2,3-O-cyclic ketene acetal- and 2,3-O-thionocarbonyl-1-thio-mannopyranosides with TMSOTf and MeOTf, respectively, gave the corresponding 2,3-O-cyclic dioxonium intermediates, which proceeded via 1-->2 migration and concurrent glycosidation in the presence of alcohols to provide the corresponding 2-S-phenyl glycosides stereoselectively. While the former donors were too labile, the latter donors have proved superior for the present purpose. The X-ray crystallographic structures of phenyl 4-O-methyl-2,3-O-thiocarbonyl-1-thio-alpha-L-rhamnopyranoside (1), a typical donor for the present reaction, and its anomeric azide analogue (6), which could not undergo the present reaction under similar conditions, are provided. (C) 2002 Elsevier Science Ltd. All rights reserved.