1
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Benitah A, Qualley DF, Woski SA. Substituent effects on indole universal bases in DNA. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2022; 41:1187-1204. [PMID: 35921554 DOI: 10.1080/15257770.2022.2105354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/25/2022] [Accepted: 06/25/2022] [Indexed: 06/15/2023]
Abstract
A series of eleven 5-substituted-indole nucleoside residues were synthesized and incorporated into 15-mer oligodeoxynucleotide duplexes with each of the four natural bases (A, G, C, T) paired with the non-natural residues. The universal base properties of these residues were evaluated by comparing the stabilities of these complexes determined by UV thermal denaturation experiments. All of the substituted indoles were more stable than an unsubstituted indole residue, and measures of electronic influences of substituents on the indole pi system correlate with stability. Several residues were more promiscuous than the previously studied 5-nitroindole residue, but the relationship between substituents and selectivity is not clear.
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Affiliation(s)
- Avi Benitah
- Department of Chemistry & Biochemistry, The University of Alabama, Tuscaloosa, AL, USA
| | - Dominic F Qualley
- Department of Chemistry & Biochemistry, The University of Alabama, Tuscaloosa, AL, USA
| | - Stephen A Woski
- Department of Chemistry & Biochemistry, The University of Alabama, Tuscaloosa, AL, USA
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2
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Guide RNAs containing universal bases enable Cas9/Cas12a recognition of polymorphic sequences. Nat Commun 2022; 13:1617. [PMID: 35338140 PMCID: PMC8956631 DOI: 10.1038/s41467-022-29202-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 03/03/2022] [Indexed: 12/15/2022] Open
Abstract
CRISPR/Cas complexes enable precise gene editing in a wide variety of organisms. While the rigid identification of DNA sequences by these systems minimizes the potential for off-target effects, it consequently poses a problem for the recognition of sequences containing naturally occurring polymorphisms. The presence of genetic variance such as single nucleotide polymorphisms (SNPs) in a gene sequence can compromise the on-target activity of CRISPR systems. Thus, when attempting to target multiple variants of a human gene, or evolved variants of a pathogen gene using a single guide RNA, more flexibility is desirable. Here, we demonstrate that Cas9 can tolerate the inclusion of universal bases in individual guide RNAs, enabling simultaneous targeting of polymorphic sequences. Crucially, we find that specificity is selectively degenerate at the site of universal base incorporation, and remains otherwise preserved. We demonstrate the applicability of this technology to targeting multiple naturally occurring human SNPs with individual guide RNAs and to the design of Cas12a/Cpf1-based DETECTR probes capable of identifying multiple evolved variants of the HIV protease gene. Our findings extend the targeting capabilities of CRISPR/Cas systems beyond their canonical spacer sequences and highlight a use of natural and synthetic universal bases.
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3
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Tabatabaei SK, Pham B, Pan C, Liu J, Chandak S, Shorkey SA, Hernandez AG, Aksimentiev A, Chen M, Schroeder CM, Milenkovic O. Expanding the Molecular Alphabet of DNA-Based Data Storage Systems with Neural Network Nanopore Readout Processing. NANO LETTERS 2022; 22:1905-1914. [PMID: 35212544 PMCID: PMC8915253 DOI: 10.1021/acs.nanolett.1c04203] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 02/22/2022] [Indexed: 05/23/2023]
Abstract
DNA is a promising next-generation data storage medium, but challenges remain with synthesis costs and recording latency. Here, we describe a prototype of a DNA data storage system that uses an extended molecular alphabet combining natural and chemically modified nucleotides. Our results show that MspA nanopores can discriminate different combinations and ordered sequences of natural and chemically modified nucleotides in custom-designed oligomers. We further demonstrate single-molecule sequencing of the extended alphabet using a neural network architecture that classifies raw current signals generated by Oxford Nanopore sequencers with an average accuracy exceeding 60% (39× larger than random guessing). Molecular dynamics simulations show that the majority of modified nucleotides lead to only minor perturbations of the DNA double helix. Overall, the extended molecular alphabet may potentially offer a nearly 2-fold increase in storage density and potentially the same order of reduction in the recording latency, thereby enabling new implementations of molecular recorders.
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Affiliation(s)
- S Kasra Tabatabaei
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
| | - Bach Pham
- Department of Chemistry, University of Massachusetts at Amherst, Amherst, Massachusetts 01003, United States
| | - Chao Pan
- Department of Electrical and Computer Engineering, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
| | - Jingqian Liu
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
| | - Shubham Chandak
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, United States
| | - Spencer A Shorkey
- Department of Chemistry, University of Massachusetts at Amherst, Amherst, Massachusetts 01003, United States
| | - Alvaro G Hernandez
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
| | - Aleksei Aksimentiev
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
- Department of Physics, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
| | - Min Chen
- Department of Chemistry, University of Massachusetts at Amherst, Amherst, Massachusetts 01003, United States
| | - Charles M Schroeder
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
- Department of Materials Science and Engineering, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
| | - Olgica Milenkovic
- Department of Electrical and Computer Engineering, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
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4
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Kolganova NA, Tsvetkov VB, Smirnov IP, Timofeev EN. Probing the Nitroindole-Modified Central Loop of Thrombin Aptamer HD1 as a Recognition Site. Nucleic Acid Ther 2019; 29:208-217. [PMID: 30864877 DOI: 10.1089/nat.2018.0757] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Thrombin-binding aptamer HD1 is a DNA-based thrombin inhibitor that features an antiparallel G-quadruplex (GQ) structure. We recently reported a single-nucleotide G8 to 5-nitroindole (NI) modification of HD1 (N8) that notably improves the anticoagulant properties and binding affinity of the aptamer. Based on molecular modeling and binding studies, it was originally proposed that N8 may acquire the ability to bind thrombin by a modified central loop. To verify this possibility, in this study, we report new variations of the N8 aptamer with intact or damaged TT loops. Anomeric alpha-thymidine was used as a "damaging" residue to disable the primary recognition site of N8. Biophysical characterization of modified aptamers supports the formation of HD1-like antiparallel GQs with varying stability by all studied variants. Binding experiments showed that N8 variants with impaired TT loops lost the ability to bind thrombin, suggesting the primary role of thymines in TT loops for the thrombin-N8 interaction. Aptamer N8α(7/9) bearing NI at position 8 and damaged thymidines 7 and 9 retained thrombin affinity, which was intermediate between N8 and HD1. Fluorescence polarization studies suggest 1:1 stoichiometry for thrombin complexes with either HD1, N8, or N8α(7/9). Further molecular dynamics (MD) study of complexes formed by these three aptamers with thrombin disproves the idea of direct interaction between central loop residues and the protein. Based on MD results, the origin of the NI tuning effect is associated with its ability to promote the formation of compact and rigid structures through hydrophobic interactions with the GQ core and loop thymines.
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Affiliation(s)
- Natalia A Kolganova
- 1Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir B Tsvetkov
- 2Research and Clinical Center for Physical Chemical Medicine, Moscow, Russia.,3Smorodintsev Research Institute of Influenza, St. Petersburg, Russia.,4I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Igor P Smirnov
- 2Research and Clinical Center for Physical Chemical Medicine, Moscow, Russia
| | - Edward N Timofeev
- 1Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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Inde T, Masaki Y, Maruyama A, Ito Y, Makio N, Miyatake Y, Tomori T, Sekine M, Seio K. Synthesis of oligonucleotides containing 2-N-heteroarylguanine residues and their effect on duplex/triplex stability. Org Biomol Chem 2018; 15:8371-8383. [PMID: 28937703 DOI: 10.1039/c7ob01875d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To systematically understand the effect of 2-N-heteroarylguanine (GHA) modification on the stability of higher-order DNA structures, nucleoside derivatives and oligodeoxyribonucleotides containing guanine residues modified with four kinds of hereroaryl groups on the 2-amino group were synthesized. The stabilities of the DNA duplex and the parallel-oriented DNA triplex containing these GHAs were studied by measuring their melting temperatures (Tm). Tm experiments and DFT calculations of the modified guanine nucleobases suggested that the base pair formation energy and stability of the two conformations, i.e., the open- and closed-type conformations, are key to determining the stability of the DNA duplex. Finally, the DNA triplex was destabilized when modified guanine residues were introduced into triplex-forming oligonucleotides.
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Affiliation(s)
- Takeshi Inde
- Department of Life Science and Technology, Tokyo Institute of Technology, J2-16, 4259 Nagatsuta-cho Midoriku, Yokohama, Japan.
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6
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Zargarian L, Ben Imeddourene A, Gavvala K, Barthes NPF, Michel BY, Kenfack CA, Morellet N, René B, Fossé P, Burger A, Mély Y, Mauffret O. Structural and Dynamical Impact of a Universal Fluorescent Nucleoside Analogue Inserted Into a DNA Duplex. J Phys Chem B 2017; 121:11249-11261. [PMID: 29172512 DOI: 10.1021/acs.jpcb.7b08825] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recently, a 3-hydroxychromone based nucleoside 3HCnt has been developed as a highly environment-sensitive nucleoside surrogate to investigate protein-DNA interactions. When it is incorporated in DNA, the probe is up to 50-fold brighter than 2-aminopurine, the reference fluorescent nucleoside. Although the insertion of 3HCnt in DNA was previously shown to not alter the overall DNA structure, the possibility of the probe inducing local effects cannot be ruled out. Hence, a systematic structural and dynamic study is required to unveil the 3HCnt's limitations and to properly interpret the data obtained with this universal probe. Here, we investigated by NMR a 12-mer duplex, in which a central adenine was replaced by 3HCnt. The chemical shifts variations and nOe contacts revealed that the 3HCnt is well inserted in the DNA double helix with extensive stacking interactions with the neighbor base pairs. These observations are in excellent agreement with the steady-state and time-resolved fluorescence properties indicating that the 3HCnt fluorophore is protected from the solvent and does not exhibit rotational motion. The 3HCnt insertion in DNA is accompanied by the extrusion of the opposite nucleobase from the double helix. Molecular dynamics simulations using NMR-restraints demonstrated that 3HCnt fluorophore exhibits only translational dynamics. Taken together, our data showed an excellent intercalation of 3HCnt in the DNA double helix, which is accompanied by localized perturbations. This confirms 3HCnt as a highly promising tool for nucleic acid labeling and sensing.
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Affiliation(s)
- Loussiné Zargarian
- LBPA, Ecole normale supérieure Paris-Saclay, UMR 8113 CNRS, Université Paris-Saclay , 61 Avenue du Pdt Wilson 94235 Cachan cedex, France
| | - Akli Ben Imeddourene
- LBPA, Ecole normale supérieure Paris-Saclay, UMR 8113 CNRS, Université Paris-Saclay , 61 Avenue du Pdt Wilson 94235 Cachan cedex, France
| | - Krishna Gavvala
- Laboratoire de Biophotonique et Pharmacologie, Faculté de Pharmacie, UMR 7213 CNRS, Université de Strasbourg , 74 route du Rhin, 67401 Illkirch, France
| | - Nicolas P F Barthes
- Institut de Chimie de Nice, UMR 7272, Université Côte d'Azur, CNRS , Parc Valrose, 06108 Nice Cedex 2, France
| | - Benoit Y Michel
- Institut de Chimie de Nice, UMR 7272, Université Côte d'Azur, CNRS , Parc Valrose, 06108 Nice Cedex 2, France
| | - Cyril A Kenfack
- Laboratoire d'Optique et Applications, Centre de Physique Atomique Moléculaire et Optique Quantique, Université de Douala , BP 85580, Douala, Cameroon
| | - Nelly Morellet
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris Saclay , 1 Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Brigitte René
- LBPA, Ecole normale supérieure Paris-Saclay, UMR 8113 CNRS, Université Paris-Saclay , 61 Avenue du Pdt Wilson 94235 Cachan cedex, France
| | - Philippe Fossé
- LBPA, Ecole normale supérieure Paris-Saclay, UMR 8113 CNRS, Université Paris-Saclay , 61 Avenue du Pdt Wilson 94235 Cachan cedex, France
| | - Alain Burger
- Institut de Chimie de Nice, UMR 7272, Université Côte d'Azur, CNRS , Parc Valrose, 06108 Nice Cedex 2, France
| | - Yves Mély
- Laboratoire de Biophotonique et Pharmacologie, Faculté de Pharmacie, UMR 7213 CNRS, Université de Strasbourg , 74 route du Rhin, 67401 Illkirch, France
| | - Olivier Mauffret
- LBPA, Ecole normale supérieure Paris-Saclay, UMR 8113 CNRS, Université Paris-Saclay , 61 Avenue du Pdt Wilson 94235 Cachan cedex, France
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7
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Spring-Connell AM, Evich MG, Debelak H, Seela F, Germann MW. Using NMR and molecular dynamics to link structure and dynamics effects of the universal base 8-aza, 7-deaza, N8 linked adenosine analog. Nucleic Acids Res 2016; 44:8576-8587. [PMID: 27566150 PMCID: PMC5062995 DOI: 10.1093/nar/gkw736] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 08/10/2016] [Indexed: 12/30/2022] Open
Abstract
A truly universal nucleobase enables a host of novel applications such as simplified templates for PCR primers, randomized sequencing and DNA based devices. A universal base must pair indiscriminately to each of the canonical bases with little or preferably no destabilization of the overall duplex. In reality, many candidates either destabilize the duplex or do not base pair indiscriminatingly. The novel base 8-aza-7-deazaadenine (pyrazolo[3,4-d]pyrimidin- 4-amine) N8-(2'deoxyribonucleoside), a deoxyadenosine analog (UB), pairs with each of the natural DNA bases with little sequence preference. We have utilized NMR complemented with molecular dynamic calculations to characterize the structure and dynamics of a UB incorporated into a DNA duplex. The UB participates in base stacking with little to no perturbation of the local structure yet forms an unusual base pair that samples multiple conformations. These local dynamics result in the complete disappearance of a single UB proton resonance under native conditions. Accommodation of the UB is additionally stabilized via heightened backbone conformational sampling. NMR combined with various computational techniques has allowed for a comprehensive characterization of both structural and dynamic effects of the UB in a DNA duplex and underlines that the UB as a strong candidate for universal base applications.
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Affiliation(s)
| | - Marina G Evich
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Harald Debelak
- Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069 Osnabrück, Germany
| | - Frank Seela
- Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069 Osnabrück, Germany Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster, Germany
| | - Markus W Germann
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
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Abstract
In this study we describe new modified analogs of the thrombin binding aptamer (TBA) containing 5-nitroindole residues. It has been shown that all modified TBAs form an anti-parallel G-quadruplex structure and retain the ability to inhibit thrombin. The most advanced TBA variant (TBA-N8) has a substantially increased clotting time and two-fold lower IC50 value compared to the unmodified prototype. Molecular modelling studies suggest that the improved anticoagulant properties of TBA-N8 result from changes in the binding mode of the analog. A modified central loop in TBA-N8 is presumed to participate in the binding of the target protein. Studies of FAM labelled TBA and TBA-N8 showed an improved binding affinity of the modified aptamer and provided evidence of a direct interaction between the modified central loop and thrombin. Our findings have implications for the design of new aptamers with improved binding affinities.
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9
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Ingale SA, Leonard P, Yang H, Seela F. 5-Nitroindole oligonucleotides with alkynyl side chains: universal base pairing, triple bond hydration and properties of pyrene "click" adducts. Org Biomol Chem 2015; 12:8519-32. [PMID: 25236942 DOI: 10.1039/c4ob01478b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Oligonucleotides with 3-ethynyl-5-nitroindole and 3-octadiynyl-5-nitroindole 2'-deoxyribonucleosides were prepared by solid-phase synthesis. To this end, nucleoside phosphoramidites with clickable side chains were synthesized. The 3-ethynylated 5-nitroindole nucleoside was hydrated during automatized DNA synthesis to 3-acetyl-5-nitroindole 2'-deoxyribonucleoside. Side product formation was circumvented by triisopropylsilyl protection of the ethynyl side chain and was removed with TBAF after oligonucleotide synthesis. All compounds with a clickable 5-nitroindole skeleton show universal base pairing and can be functionalized with almost any azide in any position of the DNA chain. Functionalization of the side chain with 1-azidomethylpyrene afforded click adducts in which the fluorescence was quenched by the 5-nitroindole moieties. However, fluorescence was slightly recovered during duplex formation. Oligonucleotides with a pyrene residue and a long linker arm are stabilized over those with non-functionalized side chains. From the UV red shift of the pyrene residue in oligonucleotides and modelling studies, pyrene intercalation was established for the long linker adduct showing increased duplex stability over those with a short side chain.
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Affiliation(s)
- Sachin A Ingale
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
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10
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Kowal EA, Lad RR, Pallan PS, Dhummakupt E, Wawrzak Z, Egli M, Sturla SJ, Stone MP. Recognition of O6-benzyl-2'-deoxyguanosine by a perimidinone-derived synthetic nucleoside: a DNA interstrand stacking interaction. Nucleic Acids Res 2013; 41:7566-76. [PMID: 23748954 PMCID: PMC3753623 DOI: 10.1093/nar/gkt488] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The 2'-deoxynucleoside containing the synthetic base 1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)-tetrahydrofuran-2-yl)-1H-perimidin-2(3H)-one] (dPer) recognizes in DNA the O(6)-benzyl-2'-deoxyguanosine nucleoside (O(6)-Bn-dG), formed by exposure to N-benzylmethylnitrosamine. Herein, we show how dPer distinguishes between O(6)-Bn-dG and dG in DNA. The structure of the modified Dickerson-Drew dodecamer (DDD) in which guanine at position G(4) has been replaced by O(6)-Bn-dG and cytosine C(9) has been replaced with dPer to form the modified O(6)-Bn-dG:dPer (DDD-XY) duplex [5'-d(C(1)G(2)C(3)X(4)A(5)A(6)T(7)T(8)Y(9)G(10)C(11)G(12))-3']2 (X = O(6)-Bn-dG, Y = dPer) reveals that dPer intercalates into the duplex and adopts the syn conformation about the glycosyl bond. This provides a binding pocket that allows the benzyl group of O(6)-Bn-dG to intercalate between Per and thymine of the 3'-neighbor A:T base pair. Nuclear magnetic resonance data suggest that a similar intercalative recognition mechanism applies in this sequence in solution. However, in solution, the benzyl ring of O(6)-Bn-dG undergoes rotation on the nuclear magnetic resonance time scale. In contrast, the structure of the modified DDD in which cytosine at position C(9) is replaced with dPer to form the dG:dPer (DDD-GY) [5'-d(C(1)G(2)C(3)G(4)A(5)A(6)T(7)T(8)Y(9)G(10)C(11)G(12))-3']2 duplex (Y = dPer) reveals that dPer adopts the anti conformation about the glycosyl bond and forms a less stable wobble pairing interaction with guanine.
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Affiliation(s)
- Ewa A. Kowal
- Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Center in Structural Biology, Vanderbilt University, Nashville, TN 37235, USA, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, CH-8092 Zürich, Switzerland, Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA and Department of Health Sciences and Technology, Synchrotron Research Center, Northwestern University, 9700 S Cass Ave, Argonne, IL 60439, USA
| | - Rahul R. Lad
- Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Center in Structural Biology, Vanderbilt University, Nashville, TN 37235, USA, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, CH-8092 Zürich, Switzerland, Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA and Department of Health Sciences and Technology, Synchrotron Research Center, Northwestern University, 9700 S Cass Ave, Argonne, IL 60439, USA
| | - Pradeep S. Pallan
- Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Center in Structural Biology, Vanderbilt University, Nashville, TN 37235, USA, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, CH-8092 Zürich, Switzerland, Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA and Department of Health Sciences and Technology, Synchrotron Research Center, Northwestern University, 9700 S Cass Ave, Argonne, IL 60439, USA
| | - Elizabeth Dhummakupt
- Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Center in Structural Biology, Vanderbilt University, Nashville, TN 37235, USA, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, CH-8092 Zürich, Switzerland, Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA and Department of Health Sciences and Technology, Synchrotron Research Center, Northwestern University, 9700 S Cass Ave, Argonne, IL 60439, USA
| | - Zdzislaw Wawrzak
- Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Center in Structural Biology, Vanderbilt University, Nashville, TN 37235, USA, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, CH-8092 Zürich, Switzerland, Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA and Department of Health Sciences and Technology, Synchrotron Research Center, Northwestern University, 9700 S Cass Ave, Argonne, IL 60439, USA
| | - Martin Egli
- Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Center in Structural Biology, Vanderbilt University, Nashville, TN 37235, USA, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, CH-8092 Zürich, Switzerland, Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA and Department of Health Sciences and Technology, Synchrotron Research Center, Northwestern University, 9700 S Cass Ave, Argonne, IL 60439, USA
| | - Shana J. Sturla
- Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Center in Structural Biology, Vanderbilt University, Nashville, TN 37235, USA, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, CH-8092 Zürich, Switzerland, Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA and Department of Health Sciences and Technology, Synchrotron Research Center, Northwestern University, 9700 S Cass Ave, Argonne, IL 60439, USA,*To whom correspondence should be addressed. Tel: +1 615 322 2589; Fax: +1 615 322 7591;
| | - Michael P. Stone
- Department of Chemistry, Center in Molecular Toxicology, Vanderbilt-Ingram Cancer Center, Center in Structural Biology, Vanderbilt University, Nashville, TN 37235, USA, Department of Health Sciences and Technology, Institute of Food, Nutrition and Health, ETH Zürich, CH-8092 Zürich, Switzerland, Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA and Department of Health Sciences and Technology, Synchrotron Research Center, Northwestern University, 9700 S Cass Ave, Argonne, IL 60439, USA,Correspondence may also be addressed to Shana J. Sturla. Tel: +41 44 632 9175; Fax: +41 44 632 1123;
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11
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Liang F, Liu YZ, Zhang P. Universal base analogues and their applications in DNA sequencing technology. RSC Adv 2013. [DOI: 10.1039/c3ra41492b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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12
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Wang X, Wang X, Cui S, Wang Y, Chen G, Guo Z. Specific recognition of DNA depurination by a luminescent terbium(iii) complex. Chem Sci 2013. [DOI: 10.1039/c3sc51781k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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13
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Zhang J, Zheng J, Lu C, Du Q, Liang Z, Xi Z. Modification of the siRNA passenger strand by 5-nitroindole dramatically reduces its off-target effects. Chembiochem 2012; 13:1940-5. [PMID: 22887813 DOI: 10.1002/cbic.201200349] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Indexed: 12/16/2022]
Abstract
During the formation of RNA-induced silencing complex (RISC), the passenger and guide strand of an siRNA duplex separate from each other to generate an active RISC complex. Accumulating evidence shows that an siRNA passenger strand can also assemble into a RISC complex and mediate RNA interference, thereby causing undesired off-target effects. To reduce this effect, the so-called "universal base" 5-nitroindole nucleotides were incorporated into an siRNA passenger strand. Melting temperature and circular dichroism spectrum measurements showed no significant changes compared to the unmodified duplex, thus indicating the formation of normal A-form conformation. Using a dual luciferase reporter assay, we have further shown that 5-nitroindole modification at position 15 of the siRNA passenger strand drastically decreased the RNAi (RNA interfering) potency of this strand, whereas the potency of the RNA guide strand was not much affected. These results could provide a practical approach for reducing off-target effects mediated by the siRNA passenger strand.
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Affiliation(s)
- Junbin Zhang
- Department of Chemical Biology and State Key Laboratory of Elemento-organic Chemistry, Nankai University, Tianjin, China
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Rutledge LR, Wetmore SD. A computational proposal for the experimentally observed discriminatory behavior of hypoxanthine, a weak universal nucleobase. Phys Chem Chem Phys 2012; 14:2743-53. [PMID: 22270716 DOI: 10.1039/c2cp23600a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A computational model composed of six nucleobases was used to investigate why hypoxanthine does not yield duplexes of equal stability when paired opposite each of the natural DNA nucleobases. The magnitudes of all nearest-neighbor interactions in a DNA helix were calculated, including hydrogen-bonding, intra- and interstrand stacking interactions, as well as 1-3 intrastrand stacking interactions. Although the stacking interactions in DNA relevant arrangements are significant and account for at least one third of the total stabilization energy in our nucleobase complexes, the trends in the magnitude of the stacking interactions cannot explain the relative experimental melting temperatures previously reported in the literature. Furthermore, although the total hydrogen-bonding interactions explain why hypoxanthine preferentially pairs with cytosine, the experimental trend for the remaining nucleobases (A, T, G) is not explained. In fact, the calculated pairing preference of hypoxanthine matches that determined experimentally only when the sum of all types of nearest-neighbor interactions is considered. This finding highlights a strong correlation between the relative magnitude of the total nucleobase-nucleobase interactions and measured melting temperatures for DNA strands containing hypoxanthine despite the potential role of other factors (including hydration, temperature, sugar-phosphate backbone). By considering a large range of sequence combinations, we reveal that the binding preference of hypoxanthine is strongly dependent on the nucleobase sequence, which may explain the varied ability of hypoxanthine to universally bind to the natural bases. As a result, we propose that future work should closely examine the interplay between the dominant nucleobase-nucleobase interactions and the overall strand stability to fully understand how sequence context affects the universal binding properties of modified bases and to aid the design of new molecules with ambiguous pairing properties.
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Affiliation(s)
- Lesley R Rutledge
- Department of Chemistry & Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
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15
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Cravens SL, Navapanich AC, Geierstanger BH, Tahmassebi DC, Dwyer TJ. NMR Solution Structure of a DNA−Actinomycin D Complex Containing a Non-Hydrogen-Bonding Pair in the Binding Site. J Am Chem Soc 2010; 132:17588-98. [DOI: 10.1021/ja107575f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Shannen L. Cravens
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, California 92110, United States, and Genomics Institute of the Novartis Research Institute, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Alyssa C. Navapanich
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, California 92110, United States, and Genomics Institute of the Novartis Research Institute, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Bernhard H. Geierstanger
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, California 92110, United States, and Genomics Institute of the Novartis Research Institute, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Deborah C. Tahmassebi
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, California 92110, United States, and Genomics Institute of the Novartis Research Institute, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
| | - Tammy J. Dwyer
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, California 92110, United States, and Genomics Institute of the Novartis Research Institute, 10675 John Jay Hopkins Drive, San Diego, California 92121, United States
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16
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Thayer JR, Flook KJ, Woodruff A, Rao S, Pohl CA. New monolith technology for automated anion-exchange purification of nucleic acids. J Chromatogr B Analyt Technol Biomed Life Sci 2010; 878:933-41. [PMID: 20226746 DOI: 10.1016/j.jchromb.2010.01.030] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Revised: 01/14/2010] [Accepted: 01/21/2010] [Indexed: 11/27/2022]
Abstract
Synthetic nucleic acid analysis often employs pellicular anion-exchange (AE) chromatography because it supports very high efficiency separations while offering means to control secondary structure, retention and resolution by readily modifiable chromatographic conditions. However, these pellicular anion-exchange (pAE) phases do not offer capacity sufficient for lab-scale oligonucleotide (ON) purification. In contrast, monolithic phases produce fast separations at capacities exceeding their pellicular counterparts, but do not exhibit capacities typical of fully porous, bead-based, anion-exchangers. In order to further increase monolith capacity and obtain the selectivity and mass transfer characteristics of pellicular phases, a surface-functionalized monolith was coated with pAE nanobeads (latexes) usually employed on the pellicular DNAPac phase. The nanobead-coated monolith exhibited chromatographic behaviors typical of polymer AE phases. Based on this observation the monolithic substrate surface porosity and latex diameters were co-optimized to produce a hybrid monolith harboring capacity similar to that of fully porous bead-based phases and peak shape approaching that of the pAE phases. We tested the hybrid monolith on a variety of previously developed pAE capabilities including control of ON selectivity, resolution of derivatized ONs, the ability to resolve RNA ONs harboring aberrant linkages at different positions in a single sequence and separation of phosphorothioate diastereoisomers. We compared the yield and purity of an 8 mg ON sample purified on both the new hybrid monolith and a benchmark AE column based on fully porous monodisperse beads. This comparison included an assessment of the relative selectivities of both columns. Finally, we demonstrated the ability to couple AE ON separations with ESI-MS using an automated desalting protocol. This protocol is also useful for preparing ONs for other assays, such as enzyme treatments, that may be sensitive to high salt levels.
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Affiliation(s)
- J R Thayer
- Dionex Corporation, 445 Lakeside Drive, Sunnyvale, CA 94085, USA.
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17
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Loakes D, Gallego J, Pinheiro VB, Kool ET, Holliger P. Evolving a polymerase for hydrophobic base analogues. J Am Chem Soc 2009; 131:14827-37. [PMID: 19778048 PMCID: PMC2762193 DOI: 10.1021/ja9039696] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrophobic base analogues (HBAs) have shown great promise for the expansion of the chemical and coding potential of nucleic acids but are generally poor polymerase substrates. While extensive synthetic efforts have yielded examples of HBAs with favorable substrate properties, their discovery has remained challenging. Here we describe a complementary strategy for improving HBA substrate properties by directed evolution of a dedicated polymerase using compartmentalized self-replication (CSR) with the archetypal HBA 5-nitroindole (d5NI) and its derivative 5-nitroindole-3-carboxamide (d5NIC) as selection substrates. Starting from a repertoire of chimeric polymerases generated by molecular breeding of DNA polymerase genes from the genus Thermus, we isolated a polymerase (5D4) with a generically enhanced ability to utilize HBAs. The selected polymerase. 5D4 was able to form and extend d5NI and d5NIC (d5NI(C)) self-pairs as well as d5NI(C) heteropairs with all four bases with efficiencies approaching, or exceeding, those of the cognate Watson-Crick pairs, despite significant distortions caused by the intercalation of the d5NI(C) heterocycles into the opposing strand base stack, as shown by nuclear magnetic resonance spectroscopy (NMR). Unlike Taq polymerase, 5D4 was also able to extend HBA pairs such as Pyrene: varphi (abasic site), d5NI: varphi, and isocarbostyril (ICS): 7-azaindole (7AI), allowed bypass of a chemically diverse spectrum of HBAs, and enabled PCR amplification with primers comprising multiple d5NI(C)-substitutions, while maintaining high levels of catalytic activity and fidelity. The selected polymerase 5D4 promises to expand the range of nucleobase analogues amenable to replication and should find numerous applications, including the synthesis and replication of nucleic acid polymers with expanded chemical and functional diversity.
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Affiliation(s)
- David Loakes
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - José Gallego
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Vitor B. Pinheiro
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Eric T. Kool
- Stanford University, Department of Chemistry, Stanford, CA 94305, USA
| | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
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Timofeev EN, Kolganova NA, Smirnov IP, Kochetkova SV, Florent'ev VL. [Oligodeoxynucleotides containing substituted 4-nitroindoles: synthesis and study of their DNA duplexes]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2008; 34:220-6. [PMID: 18522278 DOI: 10.1134/s106816200802009x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The synthesis of oligonucleotides containing 1-(2-deoxy-beta-D-ribofuranosyl)-2-methyl-4-nitroindole and 1-(2-deoxy-beta-D-ribofuranosyl)-2-phenyl-4-nitroindole is described. The synthesized modified oligonucleotides were used for studying the stability of intermolecular DNA duplexes with one unnatural strand and for evaluation of discriminating potential of 2-methyl- and 2-phenyl-4-nitroindoles toward nucleic bases. For comparison, an unmodified oligonucleotide and oligonucleotides bearing 5-nitroindole were used. It was shown that 2-methyl-4-nitroindole was only insignificantly inferior in stability to 5-nitroindole and characterized by a similar discriminating potential. 2-Phenyl-4-nitroindole provided a more pronounced duplex destabilization, the discrimination toward natural bases being decreased. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2008, vol. 34, no. 2; see also http:// www.maik.ru.
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Model systems for understanding DNA base pairing. Curr Opin Chem Biol 2007; 11:588-94. [PMID: 17967435 DOI: 10.1016/j.cbpa.2007.09.019] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2007] [Accepted: 09/28/2007] [Indexed: 11/23/2022]
Abstract
The fact that nucleic acid bases recognize each other to form pairs is a canonical part of the dogma of biology. However, they do not recognize each other well enough in water to account for the selectivity and efficiency that is needed in the transmission of biological information through a cell. Thus proteins assist in this recognition in multiple ways, and recent data suggest that these mechanisms of recognition can vary widely with context. To probe how the chemical differences of the four nucleobases are defined in various biological contexts, chemists and biochemists have developed modified versions that differ in their polarity, shape, size, and functional groups. This brief review covers recent advances in this field of research.
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Harki DA, Graci JD, Edathil JP, Castro C, Cameron CE, Peterson BR. Synthesis of a universal 5-nitroindole ribonucleotide and incorporation into RNA by a viral RNA-dependent RNA polymerase. Chembiochem 2007; 8:1359-62. [PMID: 17600792 PMCID: PMC2194811 DOI: 10.1002/cbic.200700160] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2007] [Indexed: 11/10/2022]
Affiliation(s)
- Daniel A. Harki
- Dr. D. A. Harki, J. P. Edathil, Prof. B. R. Peterson, Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, PA 16802 (USA), Fax: (+1) 814-863-5319, E-mail:
| | - Jason D. Graci
- J. D. Graci, Dr. C. Castro, Prof. C. E. Cameron, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802 (USA)
| | - Jocelyn P. Edathil
- Dr. D. A. Harki, J. P. Edathil, Prof. B. R. Peterson, Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, PA 16802 (USA), Fax: (+1) 814-863-5319, E-mail:
| | - Christian Castro
- J. D. Graci, Dr. C. Castro, Prof. C. E. Cameron, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802 (USA)
| | - Craig E. Cameron
- J. D. Graci, Dr. C. Castro, Prof. C. E. Cameron, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802 (USA)
| | - Blake R. Peterson
- Dr. D. A. Harki, J. P. Edathil, Prof. B. R. Peterson, Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, PA 16802 (USA), Fax: (+1) 814-863-5319, E-mail:
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