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Kamble N, Wolfrum M, Halbritter T, Sigurdsson ST, Richert C. Noncovalent Spin-Labeling of DNA and RNA Triplexes. Chem Biodivers 2019; 17:e1900676. [PMID: 31872549 DOI: 10.1002/cbdv.201900676] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 12/23/2019] [Indexed: 11/07/2022]
Abstract
Studying nucleic acids often requires labeling. Many labeling approaches require covalent bonds between the nucleic acid and the label, which complicates experimental procedures. Noncovalent labeling avoids the need for highly specific reagents and reaction conditions, and the effort of purifying bioconjugates. Among the least invasive techniques for studying biomacromolecules are NMR and EPR. Here, we report noncovalent labeling of DNA and RNA triplexes with spin labels that are nucleobase derivatives. Spectroscopic signals indicating strong binding were detected in EPR experiments in the cold, and filtration assays showed micromolar dissociation constants for complexes between a guanine-derived label and triplex motifs containing a single-nucleotide gap in the oligopurine strand. The advantages and challenges of noncovalent labeling via this approach that complements techniques relying on covalent links are discussed.
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Affiliation(s)
- Nilesh Kamble
- Science Institute, University of Iceland, Dunhaga 3, 107 R, eykjavik, Iceland
| | - Manpreet Wolfrum
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Thomas Halbritter
- Science Institute, University of Iceland, Dunhaga 3, 107 R, eykjavik, Iceland
| | - Snorri T Sigurdsson
- Science Institute, University of Iceland, Dunhaga 3, 107 R, eykjavik, Iceland
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
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2
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Feldner T, Wolfrum M, Richert C. Turning DNA Binding Motifs into a Material for Flow Cells. Chemistry 2019; 25:15288-15294. [PMID: 31483908 PMCID: PMC6916365 DOI: 10.1002/chem.201903631] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/03/2019] [Indexed: 01/18/2023]
Abstract
Nanoscale assemblies of DNA strands are readily designed and can be generated in a wide range of shapes and sizes. Turning them into solids that bind biomolecules reversibly, so that they can act as active material in flow cells, is a challenge. Among the biomolecular ligands, cofactors are of particular interest because they are often the most expensive reagents of biochemical transformations, for which controlled release and recycling are desirable. We have recently described DNA triplex motifs that bind adenine-containing cofactors, such as NAD, FAD and ATP, reversibly with low micromolar affinity. We sought ways to convert the soluble DNA motifs into a macroporous solid for cofactor binding. While assemblies of linear and branched DNA motifs produced hydrogels with undesirable properties, long DNA triplexes treated with protamine gave materials suitable for flow cells. Using exchangeable cells in a flow system, thermally controlled loading and discharge were demonstrated. Employing a flow cell loaded with ATP, bioluminescence was induced through thermal release of the cofactor. The results show that materials generated from functional DNA structures can be successfully employed in macroscopic devices.
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Affiliation(s)
- Tobias Feldner
- Institut für Organische ChemieUniversität StuttgartPfaffenwaldring 5570569StuttgartGermany
| | - Manpreet Wolfrum
- Institut für Organische ChemieUniversität StuttgartPfaffenwaldring 5570569StuttgartGermany
| | - Clemens Richert
- Institut für Organische ChemieUniversität StuttgartPfaffenwaldring 5570569StuttgartGermany
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3
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Schwarz RJ, Richert C. A four-helix bundle DNA nanostructure with binding pockets for pyrimidine nucleotides. NANOSCALE 2017; 9:7047-7054. [PMID: 28327725 DOI: 10.1039/c7nr00094d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Designed DNA nanostructures of impressive size have been described, but designed structures of the size of protein enzymes that bind organic ligands with high specificity are rare. Here we report a four-helix motif consisting of three synthetic strands with 65 base pairs and 165 nucleotides in total that folds well. Furthermore, we show that in the interior of this small folded DNA nanostructure, cavities can be set up that bind pyrimidine nucleotides with micromolar affinity. Base-specific binding for both thymidine and cytidine derivatives is demonstrated. The binding affinity depends on the position in the structure, as expected for recognition beyond simple base pairing. The folding motif reported here can help to expand DNA nanotechnology into the realm of selective molecular recognition that is currently dominated by protein-based enzymes and receptors.
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Affiliation(s)
- Rainer Joachim Schwarz
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany.
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4
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Göckel A, Richert C. Synthesis of an oligonucleotide with a nicotinamide mononucleotide residue and its molecular recognition in DNA helices. Org Biomol Chem 2016; 13:10303-9. [PMID: 26371420 DOI: 10.1039/c5ob01714a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nicotinamide adenine dinucleotide (NAD) is a pivotal redox cofactor of primary metabolism. Its redox reactivity is based on the nicotinamide mononucleotide (NMN) moiety. We investigated whether NMN(+) can engage in pairing interactions, when incorporated into an oligonucleotide. Here we describe the incorporation of NMN(+) at the 3'-terminus of an oligodeoxynucleotide via a phosphoramidate coupling in solution. The stability of duplexes and triplexes with the NMN(+)-containing strand was measured in UV-melting curves. While the melting points of duplexes with different bases facing the nicotinamide were similar, triplex stabilities varied greatly between different base combinations, suggesting specific pairing. The most stable triplexes were found when a guanine and an adenine were facing the NMN(+) residue. Their triplex melting points were higher than those of the corresponding triplexes with a thymidine residue at the same position. These results show that NMN(+) residues can be recognized selectively in DNA helices and are thus compatible with the molecular recognition in nucleic acids.
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Affiliation(s)
- A Göckel
- Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany.
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5
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Hu Y, Lin F, Wu T, Wang Y, Zhou XS, Shao Y. Fluorescently Sensing of DNA Triplex Assembly Using an Isoquinoline Alkaloid as Selector, Stabilizer, Inducer, and Switch-On Emitter. Chem Asian J 2016; 11:2041-8. [DOI: 10.1002/asia.201600459] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Indexed: 01/07/2023]
Affiliation(s)
- Yuehua Hu
- Institute of Physical Chemistry; Zhejiang Normal University; Jinhua 321004 Zhejiang People's Republic of China
| | - Fan Lin
- Institute of Physical Chemistry; Zhejiang Normal University; Jinhua 321004 Zhejiang People's Republic of China
| | - Tao Wu
- Institute of Physical Chemistry; Zhejiang Normal University; Jinhua 321004 Zhejiang People's Republic of China
| | - Ying Wang
- Institute of Physical Chemistry; Zhejiang Normal University; Jinhua 321004 Zhejiang People's Republic of China
| | - Xiao-Shun Zhou
- Institute of Physical Chemistry; Zhejiang Normal University; Jinhua 321004 Zhejiang People's Republic of China
| | - Yong Shao
- Institute of Physical Chemistry; Zhejiang Normal University; Jinhua 321004 Zhejiang People's Republic of China
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6
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Kalinowski M, Haug R, Said H, Piasecka S, Kramer M, Richert C. Phosphoramidate Ligation of Oligonucleotides in Nanoscale Structures. Chembiochem 2016; 17:1150-5. [PMID: 27225865 DOI: 10.1002/cbic.201600061] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Indexed: 01/25/2023]
Abstract
The folding of long DNA strands into designed nanostructures has evolved into an art. Being based on linear chains only, the resulting nanostructures cannot readily be transformed into covalently linked frameworks. Covalently linking strands in the context of folded DNA structures requires a robust method that avoids sterically demanding reagents or enzymes. Here we report chemical ligation of the 3'-amino termini of oligonucleotides and 5'-phosphorylated partner strands in templated reactions that produce phosphoramidate linkages. These reactions produce inter-nucleotide linkages that are isoelectronic and largely isosteric to phosphodiesters. Ligations were performed at three levels of complexity, including the extension of branched DNA hybrids and the ligation of six scaffold strands in a small origami.
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Affiliation(s)
- Matthäus Kalinowski
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Rüdiger Haug
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Hassan Said
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Sylwia Piasecka
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Markus Kramer
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Clemens Richert
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany.
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Goldsmith G, Rathinavelan T, Yathindra N. Selective Preference of Parallel DNA Triplexes Is Due to the Disruption of Hoogsteen Hydrogen Bonds Caused by the Severe Nonisostericity between the G*GC and T*AT Triplets. PLoS One 2016; 11:e0152102. [PMID: 27010368 PMCID: PMC4807104 DOI: 10.1371/journal.pone.0152102] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 03/08/2016] [Indexed: 12/14/2022] Open
Abstract
Implications of DNA, RNA and RNA.DNA hybrid triplexes in diverse biological functions, diseases and therapeutic applications call for a thorough understanding of their structure-function relationships. Despite exhaustive studies mechanistic rationale for the discriminatory preference of parallel DNA triplexes with G*GC & T*AT triplets still remains elusive. Here, we show that the highest nonisostericity between the G*GC & T*AT triplets imposes extensive stereochemical rearrangements contributing to context dependent triplex destabilisation through selective disruption of Hoogsteen scheme of hydrogen bonds. MD simulations of nineteen DNA triplexes with an assortment of sequence milieu reveal for the first time fresh insights into the nature and extent of destabilization from a single (non-overlapping), double (overlapping) and multiple pairs of nonisosteric base triplets (NIBTs). It is found that a solitary pair of NIBTs, feasible either at a G*GC/T*AT or T*AT/G*GC triplex junction, does not impinge significantly on triplex stability. But two overlapping pairs of NIBTs resulting from either a T*AT or a G*GC interruption disrupt Hoogsteen pair to a noncanonical mismatch destabilizing the triplex by ~10 to 14 kcal/mol, implying that their frequent incidence in multiples, especially, in short sequences could even hinder triplex formation. The results provide (i) an unambiguous and generalised mechanistic rationale for the discriminatory trait of parallel triplexes, including those studied experimentally (ii) clarity for the prevalence of antiparallel triplexes and (iii) comprehensive perspectives on the sequence dependent influence of nonisosteric base triplets useful in the rational design of TFO's against potential triplex target sites.
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Affiliation(s)
- Gunaseelan Goldsmith
- Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronics City Phase I, Bangalore, India
- Manipal University, Manipal, India
| | | | - Narayanarao Yathindra
- Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronics City Phase I, Bangalore, India
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8
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Wang Y, Hu Y, Wu T, Zhou X, Shao Y. Triggered Excited-State Intramolecular Proton Transfer Fluorescence for Selective Triplex DNA Recognition. Anal Chem 2015; 87:11620-4. [DOI: 10.1021/acs.analchem.5b02851] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ying Wang
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
| | - Yuehua Hu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
| | - Tao Wu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
| | - Xiaoshun Zhou
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
| | - Yong Shao
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
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9
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Vollmer S, Richert C. DNA Triplexes That Bind Several Cofactor Molecules. Chemistry 2015; 21:18613-22. [PMID: 26561335 DOI: 10.1002/chem.201503220] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Indexed: 12/29/2022]
Abstract
Cofactors are critical for energy-consuming processes in the cell. Harnessing such processes for practical applications requires control over the concentration of cofactors. We have recently shown that DNA triplex motifs with a designed binding site can be used to capture and release nucleotides with low micromolar dissociation constants. In order to increase the storage capacity of such triplex motifs, we have explored the limits of ligand binding through designed cavities in the oligopurine tract. Oligonucleotides with up to six non-nucleotide bridges between purines were synthesized and their ability to bind ATP, cAMP or FAD was measured. Triplex motifs with several single-nucleotide binding sites were found to bind purines more tightly than triplexes with one large binding site. The optimized triplex consists of 59 residues and four C3-bridges. It can bind up to four equivalents of ligand with apparent Kd values of 52 µM for ATP, 9 µM for FAD, and 2 µM for cAMP. An immobilized version fuels bioluminescence via release of ATP at body temperature. These results show that motifs for high-density capture, storage and release of energy-rich biomolecules can be constructed from synthetic DNA.
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Affiliation(s)
- Sven Vollmer
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany), Fax: (+49) 711-685-64321
| | - Clemens Richert
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany), Fax: (+49) 711-685-64321.
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10
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Vollmer S, Richert C. Effect of preorganization on the affinity of synthetic DNA binding motifs for nucleotide ligands. Org Biomol Chem 2015; 13:5734-42. [PMID: 25902412 DOI: 10.1039/c5ob00508f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Triplexes with a gap in the purine strand have been shown to bind adenosine or guanosine derivatives through a combination of Watson-Crick and Hoogsteen base pairing. Rigidifying the binding site should be advantageous for affinity. Here we report that clamps delimiting the binding site have a modest effect on affinity, while bridging the gap of the purine strand can strongly increase affinity for ATP, cAMP, and FAD. The lowest dissociation constants were measured for two-strand triple helical motifs with a propylene bridge or an abasic nucleoside analog, with Kd values as low as 30 nM for cAMP in the latter case. Taken together, our data suggest that improving preorganization through covalent bridges increases the affinity for nucleotide ligands. But, a bulky bridge may also block one of two alternative binding modes for the adenine base. The results may help to design new receptors, switches, or storage motifs for purine-containing ligands.
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Affiliation(s)
- S Vollmer
- Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany.
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11
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Zhuang Z, Pan R, Zhang Q, Huang H. Molecular recognition of pyrimidine nucleobases by triplex DNA receptors. Bioorg Med Chem Lett 2015; 25:1520-4. [DOI: 10.1016/j.bmcl.2015.02.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 02/05/2015] [Accepted: 02/09/2015] [Indexed: 11/29/2022]
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12
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Abstract
Incorporation of a 5-methyl-2-thiocytosine base to the parallel homopyrimidine region of a triplex DNA receptor enabled selective molecular recognition of an inosine ligand.
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Affiliation(s)
- Haidong Huang
- Department of Chemistry and Environmental Science
- New Jersey Institute of Technology
- Newark
- USA
| | - Peter C. Tlatelpa
- Department of Chemistry and Environmental Science
- New Jersey Institute of Technology
- Newark
- USA
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13
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Kröner C, Thunemann M, Vollmer S, Kinzer M, Feil R, Richert C. Endless: a purine-binding RNA motif that can be expressed in cells. Angew Chem Int Ed Engl 2014; 53:9198-202. [PMID: 25045108 DOI: 10.1002/anie.201403579] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 04/29/2014] [Indexed: 01/16/2023]
Abstract
It is becoming increasingly clear that nature uses RNAs extensively for regulating vital functions of the cell, and short sequences are frequently used to suppress gene expression. However, controlling the concentration of small molecules intracellularly through designed RNA sequences that fold into ligand-binding structures is difficult. The development of "endless", a triplex-based folding motif that can be expressed in mammalian cells and binds the second messenger 3',5'-cyclic guanosine monophosphate (cGMP), is described. In vitro, DNA or RNA versions of endless show low micromolar to nanomolar dissociation constants for cGMP. To test its functionality in vivo, four endless RNA motifs arranged in tandem were co-expressed with a fluorescent cGMP sensor protein in murine vascular smooth muscle cells. Nitric oxide induced endogenous cGMP signals were suppressed in endless-expressing cells compared to cells expressing a control motif, which suggests that endless can act as a genetically encoded cGMP sink to modulate signal transduction in cells.
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Affiliation(s)
- Christoph Kröner
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany)
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14
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Kröner C, Thunemann M, Vollmer S, Kinzer M, Feil R, Richert C. Endless: A Purine-Binding RNA Motif that Can Be Expressed in Cells. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403579] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Curtis EA, Liu DR. A naturally occurring, noncanonical GTP aptamer made of simple tandem repeats. RNA Biol 2014; 11:682-92. [PMID: 24824832 PMCID: PMC4156500 DOI: 10.4161/rna.28798] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Recently, we used in vitro selection to identify a new class of naturally occurring GTP aptamer called the G motif. Here we report the discovery and characterization of a second class of naturally occurring GTP aptamer, the “CA motif.” The primary sequence of this aptamer is unusual in that it consists entirely of tandem repeats of CA-rich motifs as short as three nucleotides. Several active variants of the CA motif aptamer lack the ability to form consecutive Watson-Crick base pairs in any register, while others consist of repeats containing only cytidine and adenosine residues, indicating that noncanonical interactions play important roles in its structure. The circular dichroism spectrum of the CA motif aptamer is distinct from that of A-form RNA and other major classes of nucleic acid structures. Bioinformatic searches indicate that the CA motif is absent from most archaeal and bacterial genomes, but occurs in at least 70 percent of approximately 400 eukaryotic genomes examined. These searches also uncovered several phylogenetically conserved examples of the CA motif in rodent (mouse and rat) genomes. Together, these results reveal the existence of a second class of naturally occurring GTP aptamer whose sequence requirements, like that of the G motif, are not consistent with those of a canonical secondary structure. They also indicate a new and unexpected potential biochemical activity of certain naturally occurring tandem repeats.
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Affiliation(s)
- Edward A Curtis
- Department of Chemistry and Chemical Biology and Howard Hughes Medical Institute; Harvard University; Cambridge, MA USA
| | - David R Liu
- Department of Chemistry and Chemical Biology and Howard Hughes Medical Institute; Harvard University; Cambridge, MA USA
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