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Drozdzal P, Manszewski T, Gilski M, Brzezinski K, Jaskolski M. Right-handed Z-DNA at ultrahigh resolution: a tale of two hands and the power of the crystallographic method. Acta Crystallogr D Struct Biol 2023; 79:133-139. [PMID: 36762859 PMCID: PMC9912920 DOI: 10.1107/s2059798322011937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 12/16/2022] [Indexed: 01/21/2023] Open
Abstract
The self-complementary L-d(CGCGCG)2 purine/pyrimidine hexanucleotide was crystallized in complex with the polyamine cadaverine and potassium cations. Since the oligonucleotide contained the enantiomeric 2'-deoxy-L-ribose, the Z-DNA duplex is right-handed, as confirmed by the ultrahigh-resolution crystal structure determined at 0.69 Å resolution. Although the X-ray diffraction data were collected at a very short wavelength (0.7085 Å), where the anomalous signal of the P and K atoms is very weak, the signal was sufficiently outstanding to clearly indicate the wrong hand when the structure was mistakenly solved assuming the presence of 2'-deoxy-D-ribose. The electron density clearly shows the entire cadaverinium dication, which has an occupancy of 0.53 and interacts with one Z-DNA duplex. The K+ cation, with an occupancy of 0.32, has an irregular coordination sphere that is formed by three OP atoms of two symmetry-related Z-DNA duplexes and one O5' hydroxyl O atom, and is completed by three water sites, one of which is twofold disordered. The K+ site is complemented by a partial water molecule, the hydrogen bonds of which have the same lengths as the K-O bonds. The sugar-phosphate backbone assumes two conformations, but the base pairs do not show any sign of disorder.
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Affiliation(s)
- Pawel Drozdzal
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Tomasz Manszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Miroslaw Gilski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland,Department of Crystallography, Faculty of Chemistry, Adam Mickiewicz University, Poznan, Poland
| | | | - Mariusz Jaskolski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland,Department of Crystallography, Faculty of Chemistry, Adam Mickiewicz University, Poznan, Poland,Correspondence e-mail:
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Mandal PK, Collie GW, Kauffmann B, Huc I. Racemic crystal structures of A-DNA duplexes. ACTA CRYSTALLOGRAPHICA SECTION D STRUCTURAL BIOLOGY 2022; 78:709-715. [PMID: 35647918 PMCID: PMC9159285 DOI: 10.1107/s2059798322003928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 04/10/2022] [Indexed: 11/20/2022]
Abstract
Racemic crystallography benefits the identification of a structural form of a DNA sequence that was not previously observed for the enantiopure equivalent. The ease with which racemic mixtures crystallize compared with the equivalent chiral systems is routinely taken advantage of to produce crystals of small molecules. However, biological macromolecules such as DNA and proteins are naturally chiral, and thus the limited range of chiral space groups available hampers the crystallization of such molecules. Inspiring work over the past 15 years has shown that racemic mixtures of proteins, which were made possible by impressive advances in protein chemical synthesis, can indeed improve the success rate of protein crystallization experiments. More recently, the racemic crystallization approach was extended to include nucleic acids as a possible aid in the determination of enantiopure DNA crystal structures. Here, findings are reported that suggest that the benefits may extend beyond this. Two racemic crystal structures of the DNA sequence d(CCCGGG) are described which were found to fold into A-form DNA. This form differs from the Z-form DNA conformation adopted by the chiral equivalent in the solid state, suggesting that the use of racemates may also favour the emergence of new conformations. Importantly, the racemic mixture forms interactions in the solid state that differ from the chiral equivalent (including the formation of racemic pseudo-helices), suggesting that the use of racemic DNA mixtures could provide new possibilities for the design of precise self-assembled nanomaterials and nanostructures.
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Dantsu Y, Zhang Y, Zhang W. Advances in Therapeutic L-Nucleosides and L-Nucleic Acids with Unusual Handedness. Genes (Basel) 2021; 13:46. [PMID: 35052385 PMCID: PMC8774879 DOI: 10.3390/genes13010046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 12/19/2022] Open
Abstract
Nucleic-acid-based small molecule and oligonucleotide therapies are attractive topics due to their potential for effective target of disease-related modules and specific control of disease gene expression. As the non-naturally occurring biomolecules, modified DNA/RNA nucleoside and oligonucleotide analogues composed of L-(deoxy)riboses, have been designed and applied as innovative therapeutics with superior plasma stability, weakened cytotoxicity, and inexistent immunogenicity. Although all the chiral centers in the backbone are mirror converted from the natural D-nucleic acids, L-nucleic acids are equipped with the same nucleobases (A, G, C and U or T), which are critical to maintain the programmability and form adaptable tertiary structures for target binding. The types of L-nucleic acid drugs are increasingly varied, from chemically modified nucleoside analogues that interact with pathogenic polymerases to nanoparticles containing hundreds of repeating L-nucleotides that circulate durably in vivo. This article mainly reviews three different aspects of L-nucleic acid therapies, including pharmacological L-nucleosides, Spiegelmers as specific target-binding aptamers, and L-nanostructures as effective drug-delivery devices.
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Affiliation(s)
- Yuliya Dantsu
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA; (Y.D.); (Y.Z.)
| | - Ying Zhang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA; (Y.D.); (Y.Z.)
| | - Wen Zhang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA; (Y.D.); (Y.Z.)
- Melvin and Bren Simon Cancer Center, 535 Barnhill Drive, Indianapolis, IN 46202, USA
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Through the looking glass: milestones on the road towards mirroring life. Trends Biochem Sci 2021; 46:931-943. [PMID: 34294544 DOI: 10.1016/j.tibs.2021.06.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 06/05/2021] [Accepted: 06/18/2021] [Indexed: 12/24/2022]
Abstract
Naturally occurring DNA, RNA, and proteins predominantly exist in only one enantiomeric form (homochirality). Advances in biotechnology and chemical synthesis allow the production of the respective alternate enantiomeric form, enabling access to mirror-image versions of these natural biopolymers. Exploiting the unique properties of such mirror molecules has already led to many applications, such as biostable and nonimmunogenic therapeutics or sensors. However, a 'roadblock' for unlocking the mirror world is the lack of biological systems capable of synthesizing critical building blocks including mirror oligonucleotides and oligopeptides to reducing cost and improve purity. Here, we provide an overview of the current progress, applications, and challenges of the molecular mirror world by identifying milestones towards mirroring life.
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Schaudy E, Lietard J, Somoza MM. Sequence Preference and Initiator Promiscuity for De Novo DNA Synthesis by Terminal Deoxynucleotidyl Transferase. ACS Synth Biol 2021; 10:1750-1760. [PMID: 34156829 PMCID: PMC8291772 DOI: 10.1021/acssynbio.1c00142] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The untemplated activity
of terminal deoxynucleotidyl transferase
(TdT) represents its most appealing feature. Its use is well established
in applications aiming for extension of a DNA initiator strand, but
a more recent focus points to its potential in enzymatic de
novo synthesis of DNA. Whereas its low substrate specificity
for nucleoside triphosphates has been studied extensively, here we
interrogate how the activity of TdT is modulated by the nature of
the initiating strands, in particular their length, chemistry, and
nucleotide composition. Investigation of full permutational libraries
of mono- to pentamers of d-DNA, l-DNA, and 2′O-methyl-RNA
of differing directionality immobilized to glass surfaces, and generated via photolithographic in situ synthesis,
shows that the efficiency of extension strongly depends on the nucleobase
sequence. We also show TdT being catalytically active on a non-nucleosidic
substrate, hexaethylene glycol. These results offer new perspectives
on constraints and strategies for de novo synthesis
of DNA using TdT regarding the requirements for initiation of enzymatic
generation of DNA.
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Affiliation(s)
- Erika Schaudy
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Jory Lietard
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Mark M. Somoza
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
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McKenzie LK, El-Khoury R, Thorpe JD, Damha MJ, Hollenstein M. Recent progress in non-native nucleic acid modifications. Chem Soc Rev 2021; 50:5126-5164. [DOI: 10.1039/d0cs01430c] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
While Nature harnesses RNA and DNA to store, read and write genetic information, the inherent programmability, synthetic accessibility and wide functionality of these nucleic acids make them attractive tools for use in a vast array of applications.
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Affiliation(s)
- Luke K. McKenzie
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
| | | | | | | | - Marcel Hollenstein
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
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Schaudy E, Somoza MM, Lietard J. l-DNA Duplex Formation as a Bioorthogonal Information Channel in Nucleic Acid-Based Surface Patterning. Chemistry 2020; 26:14310-14314. [PMID: 32515523 PMCID: PMC7702103 DOI: 10.1002/chem.202001871] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Indexed: 01/02/2023]
Abstract
Photolithographic in situ synthesis of nucleic acids enables extremely high oligonucleotide sequence density as well as complex surface patterning and combined spatial and molecular information encoding. No longer limited to DNA synthesis, the technique allows for total control of both chemical and Cartesian space organization on surfaces, suggesting that hybridization patterns can be used to encode, display or encrypt informative signals on multiple chemically orthogonal levels. Nevertheless, cross-hybridization reduces the available sequence space and limits information density. Here we introduce an additional, fully independent information channel in surface patterning with in situ l-DNA synthesis. The bioorthogonality of mirror-image DNA duplex formation prevents both cross-hybridization on chimeric l-/d-DNA microarrays and also results in enzymatic orthogonality, such as nuclease-proof DNA-based signatures on the surface. We show how chimeric l-/d-DNA hybridization can be used to create informative surface patterns including QR codes, highly counterfeiting resistant authenticity watermarks, and concealed messages within high-density d-DNA microarrays.
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Affiliation(s)
- Erika Schaudy
- Institute of Inorganic ChemistryFaculty of ChemistryUniversity of ViennaAlthanstraße 14, UZA II1090ViennaAustria
| | - Mark M. Somoza
- Institute of Inorganic ChemistryFaculty of ChemistryUniversity of ViennaAlthanstraße 14, UZA II1090ViennaAustria
- Chair of Food Chemistry and Molecular and Sensory ScienceTechnical University of MunichLise-Meitner-Straße 3485354FreisingGermany
- Leibniz-Institute for Food Systems BiologyTechnical University of MunichLise-Meitner-Straße 3485354FreisingGermany
| | - Jory Lietard
- Institute of Inorganic ChemistryFaculty of ChemistryUniversity of ViennaAlthanstraße 14, UZA II1090ViennaAustria
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