151
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Geny S, Moreno PMD, Krzywkowski T, Gissberg O, Andersen NK, Isse AJ, El-Madani AM, Lou C, Pabon YV, Anderson BA, Zaghloul EM, Zain R, Hrdlicka PJ, Jørgensen PT, Nilsson M, Lundin KE, Pedersen EB, Wengel J, Smith CIE. Next-generation bis-locked nucleic acids with stacking linker and 2'-glycylamino-LNA show enhanced DNA invasion into supercoiled duplexes. Nucleic Acids Res 2016; 44:2007-19. [PMID: 26857548 PMCID: PMC4797291 DOI: 10.1093/nar/gkw021] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 01/08/2016] [Indexed: 12/17/2022] Open
Abstract
Targeting and invading double-stranded DNA with synthetic oligonucleotides under physiological conditions remain a challenge. Bis-locked nucleic acids (bisLNAs) are clamp-forming oligonucleotides able to invade into supercoiled DNA via combined Hoogsteen and Watson–Crick binding. To improve the bisLNA design, we investigated its mechanism of binding. Our results suggest that bisLNAs bind via Hoogsteen-arm first, followed by Watson–Crick arm invasion, initiated at the tail. Based on this proposed hybridization mechanism, we designed next-generation bisLNAs with a novel linker able to stack to adjacent nucleobases, a new strategy previously not applied for any type of clamp-constructs. Although the Hoogsteen-arm limits the invasion, upon incorporation of the stacking linker, bisLNA invasion is significantly more efficient than for non-clamp, or nucleotide-linker containing LNA-constructs. Further improvements were obtained by substituting LNA with 2′-glycylamino-LNA, contributing a positive charge. For regular bisLNAs a 14-nt tail significantly enhances invasion. However, when two stacking linkers were incorporated, tail-less bisLNAs were able to efficiently invade. Finally, successful targeting of plasmids inside bacteria clearly demonstrates that strand invasion can take place in a biologically relevant context.
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Affiliation(s)
- Sylvain Geny
- Department of Laboratory Medicine, Karolinska Institutet and Clinical Research Center, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden
| | - Pedro M D Moreno
- Department of Laboratory Medicine, Karolinska Institutet and Clinical Research Center, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden INEB-Instituto de Engenharia Biomedica, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal
| | - Tomasz Krzywkowski
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SE-171 21, Sweden
| | - Olof Gissberg
- Department of Laboratory Medicine, Karolinska Institutet and Clinical Research Center, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden
| | - Nicolai K Andersen
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, Nucleic Acid Centre, University of Southern Denmark, 5230 Odense, Denmark
| | - Abdirisaq J Isse
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, Nucleic Acid Centre, University of Southern Denmark, 5230 Odense, Denmark
| | - Amro M El-Madani
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, Nucleic Acid Centre, University of Southern Denmark, 5230 Odense, Denmark
| | - Chenguang Lou
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, Nucleic Acid Centre, University of Southern Denmark, 5230 Odense, Denmark
| | - Y Vladimir Pabon
- Department of Laboratory Medicine, Karolinska Institutet and Clinical Research Center, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden
| | | | - Eman M Zaghloul
- Department of Laboratory Medicine, Karolinska Institutet and Clinical Research Center, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden
| | - Rula Zain
- Department of Laboratory Medicine, Karolinska Institutet and Clinical Research Center, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden Centre for Rare Diseases, Department of Clinical Genetics, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | | | - Per T Jørgensen
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, Nucleic Acid Centre, University of Southern Denmark, 5230 Odense, Denmark
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SE-171 21, Sweden
| | - Karin E Lundin
- Department of Laboratory Medicine, Karolinska Institutet and Clinical Research Center, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden
| | - Erik B Pedersen
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, Nucleic Acid Centre, University of Southern Denmark, 5230 Odense, Denmark
| | - Jesper Wengel
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, Nucleic Acid Centre, University of Southern Denmark, 5230 Odense, Denmark
| | - C I Edvard Smith
- Department of Laboratory Medicine, Karolinska Institutet and Clinical Research Center, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden
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152
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Silva NJ, Machado FBC, Lischka H, Aquino AJA. π–π stacking between polyaromatic hydrocarbon sheets beyond dispersion interactions. Phys Chem Chem Phys 2016; 18:22300-10. [DOI: 10.1039/c6cp03749f] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A slipped parallel structure of a stacked graphene flake showing a biconcave curvature.
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Affiliation(s)
- Nadeesha J. Silva
- Department of Chemistry and Biochemistry
- Texas Tech University
- Lubbock Texas 79409
- USA
| | | | - Hans Lischka
- Department of Chemistry and Biochemistry
- Texas Tech University
- Lubbock Texas 79409
- USA
- Institute for Theoretical Chemistry
| | - Adelia J. A. Aquino
- Department of Chemistry and Biochemistry
- Texas Tech University
- Lubbock Texas 79409
- USA
- School of Pharmaceutical Sciences and Technology
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153
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Kamaladevi A, Balamurugan K. Lipopolysaccharide of Klebsiella pneumoniae attenuates immunity of Caenorhabditis elegans and evades by altering its supramolecular structure. RSC Adv 2016. [DOI: 10.1039/c5ra18206a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Given the prominence of lipopolysaccharide (LPS) in the pathogenesis of Gram-negative bacteria, investigations at the molecular level in in vivo conditions are in dire need to understand its role in provoking infection.
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Affiliation(s)
- Arumugam Kamaladevi
- Department of Biotechnology
- Science Campus
- Alagappa University
- Karaikudi 630 004
- India
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154
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Choi JS, Dasari A, Hu P, Benkovic SJ, Berdis AJ. The use of modified and non-natural nucleotides provide unique insights into pro-mutagenic replication catalyzed by polymerase eta. Nucleic Acids Res 2015; 44:1022-35. [PMID: 26717984 PMCID: PMC4756837 DOI: 10.1093/nar/gkv1509] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 12/10/2015] [Indexed: 12/25/2022] Open
Abstract
This report evaluates the pro-mutagenic behavior of 8-oxo-guanine (8-oxo-G) by quantifying the ability of high-fidelity and specialized DNA polymerases to incorporate natural and modified nucleotides opposite this lesion. Although high-fidelity DNA polymerases such as pol δ and the bacteriophage T4 DNA polymerase replicating 8-oxo-G in an error-prone manner, they display remarkably low efficiencies for TLS compared to normal DNA synthesis. In contrast, pol η shows a combination of high efficiency and low fidelity when replicating 8-oxo-G. These combined properties are consistent with a pro-mutagenic role for pol η when replicating this DNA lesion. Studies using modified nucleotide analogs show that pol η relies heavily on hydrogen-bonding interactions during translesion DNA synthesis. However, nucleobase modifications such as alkylation to the N2 position of guanine significantly increase error-prone synthesis catalyzed by pol η when replicating 8-oxo-G. Molecular modeling studies demonstrate the existence of a hydrophobic pocket in pol η that participates in the increased utilization of certain hydrophobic nucleotides. A model is proposed for enhanced pro-mutagenic replication catalyzed by pol η that couples efficient incorporation of damaged nucleotides opposite oxidized DNA lesions created by reactive oxygen species. The biological implications of this model toward increasing mutagenic events in lung cancer are discussed.
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Affiliation(s)
- Jung-Suk Choi
- Department of Chemistry, Cleveland State University, 2351 Euclid Avenue, Cleveland, OH 44115, USA
| | - Anvesh Dasari
- Department of Chemistry, Cleveland State University, 2351 Euclid Avenue, Cleveland, OH 44115, USA
| | - Peter Hu
- Department of Chemistry, The Pennsylvania State University, 413 Wartik Building, University Park, PA 16802, USA
| | - Stephen J Benkovic
- Department of Chemistry, The Pennsylvania State University, 413 Wartik Building, University Park, PA 16802, USA
| | - Anthony J Berdis
- Department of Chemistry, Cleveland State University, 2351 Euclid Avenue, Cleveland, OH 44115, USA Center for Gene Regulation in Health and Disease, Cleveland State University, 2351 Euclid Avenue, Cleveland, OH 44115, USA Case Comprehensive Cancer Center, 10900 Euclid Avenue, Cleveland OH 44106, USA
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155
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156
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Topkaya SN, Serindere G, Ozder M. Determination of DNA Hypermethylation Using Anti-cancer Drug-Temozolomide. ELECTROANAL 2015. [DOI: 10.1002/elan.201501027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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157
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Mak CH. Atomistic Free Energy Model for Nucleic Acids: Simulations of Single-Stranded DNA and the Entropy Landscape of RNA Stem-Loop Structures. J Phys Chem B 2015; 119:14840-56. [PMID: 26548372 DOI: 10.1021/acs.jpcb.5b08077] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While single-stranded (ss) segments of DNAs and RNAs are ubiquitous in biology, details about their structures have only recently begun to emerge. To study ssDNA and RNAs, we have developed a new Monte Carlo (MC) simulation using a free energy model for nucleic acids that has the atomisitic accuracy to capture fine molecular details of the sugar-phosphate backbone. Formulated on the basis of a first-principle calculation of the conformational entropy of the nucleic acid chain, this free energy model correctly reproduced both the long and short length-scale structural properties of ssDNA and RNAs in a rigorous comparison against recent data from fluorescence resonance energy transfer, small-angle X-ray scattering, force spectroscopy and fluorescence correlation transport measurements on sequences up to ∼100 nucleotides long. With this new MC algorithm, we conducted a comprehensive investigation of the entropy landscape of small RNA stem-loop structures. From a simulated ensemble of ∼10(6) equilibrium conformations, the entropy for the initiation of different size RNA hairpin loops was computed and compared against thermodynamic measurements. Starting from seeded hairpin loops, constrained MC simulations were then used to estimate the entropic costs associated with propagation of the stem. The numerical results provide new direct molecular insights into thermodynaimc measurement from macroscopic calorimetry and melting experiments.
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Affiliation(s)
- Chi H Mak
- Department of Chemistry and Center of Applied Mathematical Sciences, University of Southern California , Los Angeles, California 90089, United States
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158
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Langkjær N, Wengel J, Pasternak A. Watson-Crick hydrogen bonding of unlocked nucleic acids. Bioorg Med Chem Lett 2015; 25:5064-6. [PMID: 26497284 DOI: 10.1016/j.bmcl.2015.10.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 10/08/2015] [Accepted: 10/09/2015] [Indexed: 12/31/2022]
Abstract
We herein describe the synthesis of two new unlocked nucleic acid building blocks containing hypoxanthine and 2,6-diaminopurine as nucleobase moieties and their incorporation into oligonucleotides. The modified oligonucleotides were used to examine the thermodynamic properties of UNA against unmodified oligonucleotides and the resulting thermodynamic data support that the hydrogen bonding face of UNA is Watson-Crick like.
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Affiliation(s)
- Niels Langkjær
- Nucleic Acid Center, University of Southern Denmark, Campusvej 55, Odense 5230, Denmark
| | - Jesper Wengel
- Nucleic Acid Center, University of Southern Denmark, Campusvej 55, Odense 5230, Denmark.
| | - Anna Pasternak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland.
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159
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Abstract
All biological information, since the last common ancestor of all life on Earth, has been encoded by a genetic alphabet consisting of only four nucleotides that form two base pairs. Long-standing efforts to develop two synthetic nucleotides that form a third, unnatural base pair (UBP) have recently yielded three promising candidates, one based on alternative hydrogen bonding, and two based on hydrophobic and packing forces. All three of these UBPs are replicated and transcribed with remarkable efficiency and fidelity, and the latter two thus demonstrate that hydrogen bonding is not unique in its ability to underlie the storage and retrieval of genetic information. This Review highlights these recent developments as well as the applications enabled by the UBPs, including the expansion of the evolution process to include new functionality and the creation of semi-synthetic life that stores increased information.
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Affiliation(s)
- Denis A Malyshev
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - Floyd E Romesberg
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA).
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160
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Park JH, Shin C. Slicer-independent mechanism drives small-RNA strand separation during human RISC assembly. Nucleic Acids Res 2015; 43:9418-33. [PMID: 26384428 PMCID: PMC4627090 DOI: 10.1093/nar/gkv937] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 09/08/2015] [Indexed: 11/17/2022] Open
Abstract
Small RNA silencing is mediated by the effector RNA-induced silencing complex (RISC) that consists of an Argonaute protein (AGOs 1–4 in humans). A fundamental step during RISC assembly involves the separation of two strands of a small RNA duplex, whereby only the guide strand is retained to form the mature RISC, a process not well understood. Despite the widely accepted view that ‘slicer-dependent unwinding’ via passenger-strand cleavage is a prerequisite for the assembly of a highly complementary siRNA into the AGO2-RISC, here we show by careful re-examination that ‘slicer-independent unwinding’ plays a more significant role in human RISC maturation than previously appreciated, not only for a miRNA duplex, but, unexpectedly, for a highly complementary siRNA as well. We discovered that ‘slicer-dependency’ for the unwinding was affected primarily by certain parameters such as temperature and Mg2+. We further validate these observations in non-slicer AGOs (1, 3 and 4) that can be programmed with siRNAs at the physiological temperature of humans, suggesting that slicer-independent mechanism is likely a common feature of human AGOs. Our results now clearly explain why both miRNA and siRNA are found in all four human AGOs, which is in striking contrast to the strict small-RNA sorting system in Drosophila.
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Affiliation(s)
- June Hyun Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Republic of Korea
| | - Chanseok Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Republic of Korea Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Republic of Korea
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161
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Yoosefian M, Mola A. Solvent effects on binding energy, stability order and hydrogen bonding of guanine–cytosine base pair. J Mol Liq 2015. [DOI: 10.1016/j.molliq.2015.06.029] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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162
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Armani A, Giusti A, Guardone L, Castigliego L, Gianfaldoni D, Guidi A. Universal Primers Used for Species Identification of Foodstuff of Animal Origin: Effects of Oligonucleotide Tails on PCR Amplification and Sequencing Performance. FOOD ANAL METHOD 2015. [DOI: 10.1007/s12161-015-0301-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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163
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Cai S, Cao Z, Lau C, Lu J. Label-free technology for the amplified detection of microRNA based on the allosteric hairpin DNA switch and hybridization chain reaction. Analyst 2015; 139:6022-7. [PMID: 25270599 DOI: 10.1039/c4an01178c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
By using the allosteric hairpin DNA switch, a novel assay for the detection of microRNA (miRNA) let-7a via a hybridization chain reaction (HCR) was introduced. Briefly, the hairpin DNA switch probe is a single-stranded DNA consisting of a streptavidin (SA) aptamer sequence, a target binding sequence and a certain sequence that acts as a trigger of the HCR. In the presence of target let-7a, the hairpin DNA switch would open and expose the stem region sequences, where a part of this sequence acts as initiator sequence strands for the HCR and triggers a cascade of hybridization events that yields nicked double helices analogous to alternating copolymers, another part is the SA aptamer sequence which activates its binding affinity to SA on SA-coated magnetic particles. The hybridization event could be sensitively detected via an instantaneous derivatization reaction between a special chemiluminescence (CL) reagent, 3,4,5-trimethoxylphenylglyoxal (TMPG) and the guanine nucleotides within the target, the hairpin DNA switch probe, and HCR helices to form an unstable CL intermediate for the generation of light. Our results show that the coupling of the hairpin DNA switch probe and the HCR for the amplified detection of let-7a achieves a better performance (e.g. wide linear response range: 0.1-1000 fmol, low detection limit: 0.1 fmol, and high specificity). Furthermore, this approach could be easily applied to the detection of let-7a in human lung cells, and extended to detect other types of miRNA and proteins such as PDGF based on aptamers. We believe such advancements will represent a significant step towards improved diagnostics and more personalized medical treatment.
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Affiliation(s)
- Sheng Cai
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China.
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164
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165
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Tamura K. Beyond the Frozen Accident: Glycine Assignment in the Genetic Code. J Mol Evol 2015; 81:69-71. [PMID: 26289730 DOI: 10.1007/s00239-015-9694-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 08/11/2015] [Indexed: 10/23/2022]
Abstract
tRNA with a terminal UCCA-3' forms a structure in which the 3'-sequence folds back. The adenine of glycyl-AMP can base-pair with the uridine of the UCCA-3' region, which places the glycine residue in close proximity to the 3'-terminal adenosine of tRNA, possibly enabling the transfer of glycine from glycyl-AMP to tRNA. Thus, the UCCA-3'-containing tRNA (as seen in eubacterial tRNA(Gly)s) would possess an intrinsic property of glycylation by glycyl-AMP. This model provides a new perspective on the origins of the glycine assignment in the genetic code, beyond the "frozen accident" hypothesis.
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Affiliation(s)
- Koji Tamura
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan. .,Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan.
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166
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Mak CH, Sani LL, Villa AN. Residual Conformational Entropies on the Sugar–Phosphate Backbone of Nucleic Acids: An Analysis of the Nucleosome Core DNA and the Ribosome. J Phys Chem B 2015. [DOI: 10.1021/acs.jpcb.5b04839] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Chi H. Mak
- Department of Chemistry and ‡Center of Applied Mathematical
Sciences, University of Southern California, Los Angeles, California 90089, United States
| | - Levana L. Sani
- Department of Chemistry and ‡Center of Applied Mathematical
Sciences, University of Southern California, Los Angeles, California 90089, United States
| | - Amber N. Villa
- Department of Chemistry and ‡Center of Applied Mathematical
Sciences, University of Southern California, Los Angeles, California 90089, United States
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167
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168
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miR-1322 Binding Sites in Paralogous and Orthologous Genes. BIOMED RESEARCH INTERNATIONAL 2015; 2015:962637. [PMID: 26114118 PMCID: PMC4465656 DOI: 10.1155/2015/962637] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 11/19/2014] [Indexed: 12/26/2022]
Abstract
We searched for 2,563 microRNA (miRNA) binding sites in 17,494 mRNA sequences of human genes. miR-1322 has more than 2,000 binding sites in 1,058 genes with ΔG/ΔGm ratio of 85% and more. miR-1322 has 1,889 binding sites in CDSs, 215 binding sites in 5′ UTRs, and 160 binding sites in 3′ UTRs. From two to 28 binding sites have arranged localization with the start position through three nucleotides of each following binding site. The nucleotide sequences of these sites in CDSs encode oligopeptides with the same and/or different amino acid sequences. We found that 33% of the target genes encoded transcription factors. miR-1322 has arranged binding sites in the CDSs of orthologous MAMLD1, MAML2, and MAML3 genes. These sites encode a polyglutamine oligopeptide ranging from six to 47 amino acids in length. The properties of miR-1322 binding sites in orthologous and paralogous target genes are discussed.
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169
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Elder RM, Pfaendtner J, Jayaraman A. Effect of Hydrophobic and Hydrophilic Surfaces on the Stability of Double-Stranded DNA. Biomacromolecules 2015; 16:1862-9. [DOI: 10.1021/acs.biomac.5b00469] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Robert M. Elder
- U.S. Army Research
Laboratory, Aberdeen Proving
Ground, MD 21005, United States
- Department
of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
| | - Jim Pfaendtner
- Department
of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Arthi Jayaraman
- Department
of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
- Departments
of Chemical and Biomolecular Engineering and Materials Science and
Engineering, University of Delaware, Newark, Delaware 19716, United States
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170
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Domingo O, Hellmuth I, Jäschke A, Kreutz C, Helm M. Intermolecular 'cross-torque': the N4-cytosine propargyl residue is rotated to the 'CH'-edge as a result of Watson-Crick interaction. Nucleic Acids Res 2015; 43:5275-83. [PMID: 25934805 PMCID: PMC4477647 DOI: 10.1093/nar/gkv285] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 03/24/2015] [Indexed: 12/13/2022] Open
Abstract
Propargyl groups are attractive functional groups for labeling purposes, as they allow CuAAC-mediated bioconjugation. Their size minimally exceeds that of a methyl group, the latter being frequent in natural nucleotide modifications. To understand under which circumstances propargyl-containing oligodeoxynucleotides preserve base pairing, we focused on the exocyclic amine of cytidine. Residues attached to the exocyclic N4 may orient away from or toward the Watson-Crick face, ensuing dramatic alteration of base pairing properties. ROESY-NMR experiments suggest a uniform orientation toward the Watson-Crick face of N(4)-propargyl residues in derivatives of both deoxycytidine and 5-methyl-deoxycytidine. In oligodeoxynucleotides, however, UV-melting indicated that N(4)-propargyl-deoxycytidine undergoes standard base pairing. This implies a rotation of the propargyl moiety toward the 'CH'-edge as a result of base pairing on the Watson-Crick face. In oligonucleotides containing the corresponding 5-methyl-deoxycytidine derivative, dramatically reduced melting temperatures indicate impaired Watson-Crick base pairing. This was attributed to a steric clash of the propargyl moiety with the 5-methyl group, which prevents back rotation to the 'CH'-edge, consequently preventing Watson-Crick geometry. Our results emphasize the tendency of an opposing nucleic acid strand to mechanically rotate single N(4)-substituents to make way for Watson-Crick base pairing, providing no steric hindrance is present on the 'CH'-edge.
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Affiliation(s)
- Olwen Domingo
- Department of Pharmaceutical Chemistry, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, 55128 Mainz, Rhineland-Palatinate, Germany
| | - Isabell Hellmuth
- Department of Pharmaceutical Chemistry, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, 55128 Mainz, Rhineland-Palatinate, Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, 69120 Heidelberg, Baden-Wuerttemberg, Germany
| | - Christoph Kreutz
- Institute of Organic Chemistry, University of Innsbruck, 6020 Innsbruck, Tyrol, Austria
| | - Mark Helm
- Department of Pharmaceutical Chemistry, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, 55128 Mainz, Rhineland-Palatinate, Germany
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171
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Shen Y, Tian F, Chen Z, Li R, Ge Q, Lu Z. Amplification-based method for microRNA detection. Biosens Bioelectron 2015; 71:322-331. [PMID: 25930002 DOI: 10.1016/j.bios.2015.04.057] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 04/17/2015] [Accepted: 04/18/2015] [Indexed: 12/20/2022]
Abstract
Over the last two decades, the study of miRNAs has attracted tremendous attention since they regulate gene expression post-transcriptionally and have been demonstrated to be dysregulated in many diseases. Detection methods with higher sensitivity, specificity and selectivity between precursors and mature microRNAs are urgently needed and widely studied. This review gave an overview of the amplification-based technologies including traditional methods, current modified methods and the cross-platforms of them combined with other techniques. Many progresses were found in the modified amplification-based microRNA detection methods, while traditional platforms could not be replaced until now. Several sample-specific normalizers had been validated, suggesting that the different normalizers should be established for different sample types and the combination of several normalizers might be more appropriate than a single universal normalizer. This systematic overview would be useful to provide comprehensive information for subsequent related studies and could reduce the un-necessary repetition in the future.
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Affiliation(s)
- Yanting Shen
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Fei Tian
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Zhenzhu Chen
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Rui Li
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Qinyu Ge
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China; State Key Laboratory of Bioelectronics, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Zuhong Lu
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China; State Key Laboratory of Bioelectronics, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
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172
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Temprano I, Thomas G, Haq S, Dyer MS, Latter EG, Darling GR, Uvdal P, Raval R. 1D self-assembly of chemisorbed thymine on Cu(110) driven by dispersion forces. J Chem Phys 2015; 142:101916. [DOI: 10.1063/1.4907721] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- I. Temprano
- Surface Science Research Centre and the Department of Chemistry, University of Liverpool, Liverpool L69 3BX, United Kingdom
| | - G. Thomas
- Surface Science Research Centre and the Department of Chemistry, University of Liverpool, Liverpool L69 3BX, United Kingdom
| | - S. Haq
- Surface Science Research Centre and the Department of Chemistry, University of Liverpool, Liverpool L69 3BX, United Kingdom
| | - M. S. Dyer
- Surface Science Research Centre and the Department of Chemistry, University of Liverpool, Liverpool L69 3BX, United Kingdom
| | - E. G. Latter
- Surface Science Research Centre and the Department of Chemistry, University of Liverpool, Liverpool L69 3BX, United Kingdom
| | - G. R. Darling
- Surface Science Research Centre and the Department of Chemistry, University of Liverpool, Liverpool L69 3BX, United Kingdom
| | - P. Uvdal
- Chemical Physics, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
- MAX-IV Laboratory, Lund University, P.O. Box 118, SE-221 00 Lund, Sweden
| | - R. Raval
- Surface Science Research Centre and the Department of Chemistry, University of Liverpool, Liverpool L69 3BX, United Kingdom
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173
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Sochacka E, Szczepanowski RH, Cypryk M, Sobczak M, Janicka M, Kraszewska K, Bartos P, Chwialkowska A, Nawrot B. 2-Thiouracil deprived of thiocarbonyl function preferentially base pairs with guanine rather than adenine in RNA and DNA duplexes. Nucleic Acids Res 2015; 43:2499-512. [PMID: 25690900 PMCID: PMC4357714 DOI: 10.1093/nar/gkv109] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 01/30/2015] [Accepted: 02/02/2015] [Indexed: 12/12/2022] Open
Abstract
2-Thiouracil-containing nucleosides are essential modified units of natural and synthetic nucleic acids. In particular, the 5-substituted-2-thiouridines (S2Us) present in tRNA play an important role in tuning the translation process through codon-anticodon interactions. The enhanced thermodynamic stability of S2U-containing RNA duplexes and the preferred S2U-A versus S2U-G base pairing are appreciated characteristics of S2U-modified molecular probes. Recently, we have demonstrated that 2-thiouridine (alone or within an RNA chain) is predominantly transformed under oxidative stress conditions to 4-pyrimidinone riboside (H2U) and not to uridine. Due to the important biological functions and various biotechnological applications for sulfur-containing nucleic acids, we compared the thermodynamic stabilities of duplexes containing desulfured products with those of 2-thiouracil-modified RNA and DNA duplexes. Differential scanning calorimetry experiments and theoretical calculations demonstrate that upon 2-thiouracil desulfuration to 4-pyrimidinone, the preferred base pairing of S2U with adenosine is lost, with preferred base pairing with guanosine observed instead. Therefore, biological processes and in vitro assays in which oxidative desulfuration of 2-thiouracil-containing components occurs may be altered. Moreover, we propose that the H2U-G base pair is a suitable model for investigation of the preferred recognition of 3'-G-ending versus A-ending codons by tRNA wobble nucleosides, which may adopt a 4-pyrimidinone-type structural motif.
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Affiliation(s)
- Elzbieta Sochacka
- Institute of Organic Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland
| | - Roman H Szczepanowski
- International Institute of Molecular and Cell Biology, Ks. J. Trojdena 4, 02-109 Warsaw, Poland
| | - Marek Cypryk
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Milena Sobczak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Magdalena Janicka
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Karina Kraszewska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Paulina Bartos
- Institute of Organic Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland
| | - Anna Chwialkowska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Barbara Nawrot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
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174
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Wu EY, Walsh AR, Materne EC, Hiltner EP, Zielinski B, Miller BR, Mawby L, Modeste E, Parish CA, Barnes WM, Kermekchiev MB. A conservative isoleucine to leucine mutation causes major rearrangements and cold sensitivity in KlenTaq1 DNA polymerase. Biochemistry 2015; 54:881-9. [PMID: 25537790 PMCID: PMC4310628 DOI: 10.1021/bi501198f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Assembly of polymerase chain reactions at room temperature can sometimes lead to low yields or unintentional products due to mispriming. Mutation of isoleucine 707 to leucine in DNA polymerase I from Thermus aquaticus substantially decreases its activity at room temperature without compromising its ability to amplify DNA. To understand why a conservative change to the enzyme over 20 Å from the active site can have a large impact on its activity at low temperature, we solved the X-ray crystal structure of the large (5'-to-3' exonuclease-deleted) fragment of Taq DNA polymerase containing the cold-sensitive mutation in the ternary (E-DNA-ddNTP) and binary (E-DNA) complexes. The I707L KlenTaq1 ternary complex was identical to the wild-type in the closed conformation except for the mutation and a rotamer change in nearby phenylalanine 749, suggesting that the enzyme should remain active. However, soaking out of the nucleotide substrate at low temperature results in an altered binary complex made possible by the rotamer change at F749 near the tip of the polymerase O-helix. Surprisingly, two adenosines in the 5'-template overhang fill the vacated active site by stacking with the primer strand, thereby blocking the active site at low temperature. Replacement of the two overhanging adenosines with pyrimidines substantially increased activity at room temperature by keeping the template overhang out of the active site, confirming the importance of base stacking. These results explain the cold-sensitive phenotype of the I707L mutation in KlenTaq1 and serve as an example of a large conformational change affected by a conservative mutation.
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Affiliation(s)
- Eugene Y Wu
- Department of Biology and ‡Department of Chemistry, University of Richmond , Richmond, Virginia 23173, United States
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175
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Aakeröy CB, Wijethunga TK, Desper J. Molecular electrostatic potential dependent selectivity of hydrogen bonding. NEW J CHEM 2015. [DOI: 10.1039/c4nj01324g] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A molecular electrostatic potential based approach for anticipating the outcome of hydrogen-bond interactions in a competitive scenario is described.
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Affiliation(s)
| | | | - John Desper
- Department of Chemistry
- Kansas State University
- Manhattan
- USA
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176
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Jena NR, Gaur V, Mishra PC. The R- and S-diastereoisomeric effects on the guanidinohydantoin-induced mutations in DNA. Phys Chem Chem Phys 2015; 17:18111-20. [DOI: 10.1039/c5cp02636a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Although, Gh (Gh1 or Gh2) in DNA would induce mainly G to C mutations, other mutations cannot be ignored.
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Affiliation(s)
- N. R. Jena
- Discipline of Natural Sciences
- Indian Institute of Information Technology
- Design and Manufacturing
- Jabalpur-482005
- India
| | - Vivek Gaur
- Discipline of Mechanical Engineering
- Indian Institute of Information Technology
- Design and Manufacturing
- Jabalpur-482005
- India
| | - P. C. Mishra
- NASI Senior Scientist
- Department of Physics
- Banaras Hindu University
- Varanasi-221005
- India
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177
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Wang B, Opron K, Burton ZF, Cukier RI, Feig M. Five checkpoints maintaining the fidelity of transcription by RNA polymerases in structural and energetic details. Nucleic Acids Res 2014; 43:1133-46. [PMID: 25550432 PMCID: PMC4333413 DOI: 10.1093/nar/gku1370] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Transcriptional fidelity, which prevents the misincorporation of incorrect nucleoside monophosphates in RNA, is essential for life. Results from molecular dynamics (MD) simulations of eukaryotic RNA polymerase (RNAP) II and bacterial RNAP with experimental data suggest that fidelity may involve as many as five checkpoints. Using MD simulations, the effects of different active site NTPs in both open and closed trigger loop (TL) structures of RNAPs are compared. Unfavorable initial binding of mismatched substrates in the active site with an open TL is proposed to be the first fidelity checkpoint. The leaving of an incorrect substrate is much easier than a correct one energetically from the umbrella sampling simulations. Then, the closing motion of the TL, required for catalysis, is hindered by the presence of mismatched NTPs. Mismatched NTPs also lead to conformational changes in the active site, which perturb the coordination of magnesium ions and likely affect the ability to proceed with catalysis. This step appears to be the most important checkpoint for deoxy-NTP discrimination. Finally, structural perturbations in the template DNA and the nascent RNA in the presence of mismatches likely hinder nucleotide addition and provide the structural foundation for backtracking followed by removing erroneously incorporated nucleotides during proofreading.
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Affiliation(s)
- Beibei Wang
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Kristopher Opron
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Zachary F Burton
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Robert I Cukier
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Michael Feig
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
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178
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Zahurancik WJ, Klein SJ, Suo Z. Significant contribution of the 3'→5' exonuclease activity to the high fidelity of nucleotide incorporation catalyzed by human DNA polymerase ϵ. Nucleic Acids Res 2014; 42:13853-60. [PMID: 25414327 PMCID: PMC4267634 DOI: 10.1093/nar/gku1184] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 11/02/2014] [Accepted: 11/03/2014] [Indexed: 11/30/2022] Open
Abstract
Most eukaryotic DNA replication is performed by A- and B-family DNA polymerases which possess a faithful polymerase activity that preferentially incorporates correct over incorrect nucleotides. Additionally, many replicative polymerases have an efficient 3'→5' exonuclease activity that excises misincorporated nucleotides. Together, these activities contribute to overall low polymerase error frequency (one error per 10(6)-10(8) incorporations) and support faithful eukaryotic genome replication. Eukaryotic DNA polymerase ϵ (Polϵ) is one of three main replicative DNA polymerases for nuclear genomic replication and is responsible for leading strand synthesis. Here, we employed pre-steady-state kinetic methods and determined the overall fidelity of human Polϵ (hPolϵ) by measuring the individual contributions of its polymerase and 3'→5' exonuclease activities. The polymerase activity of hPolϵ has a high base substitution fidelity (10(-4)-10(-7)) resulting from large decreases in both nucleotide incorporation rate constants and ground-state binding affinities for incorrect relative to correct nucleotides. The 3'→5' exonuclease activity of hPolϵ further enhances polymerization fidelity by an unprecedented 3.5 × 10(2) to 1.2 × 10(4)-fold. The resulting overall fidelity of hPolϵ (10(-6)-10(-11)) justifies hPolϵ to be a primary enzyme to replicate human nuclear genome (0.1-1.0 error per round). Consistently, somatic mutations in hPolϵ, which decrease its exonuclease activity, are connected with mutator phenotypes and cancer formation.
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Affiliation(s)
- Walter J Zahurancik
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Seth J Klein
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Zucai Suo
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
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179
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Abstract
Mutational heterogeneity must be taken into account when reconstructing evolutionary histories, calibrating molecular clocks, and predicting links between genes and disease. Selective pressures and various DNA transactions have been invoked to explain the heterogeneous distribution of genetic variation between species, within populations, and in tissue-specific tumors. To examine relationships between such heterogeneity and variations in leading- and lagging-strand replication fidelity and mismatch repair, we accumulated 40,000 spontaneous mutations in eight diploid yeast strains in the absence of selective pressure. We found that replicase error rates vary by fork direction, coding state, nucleosome proximity, and sequence context. Further, error rates and DNA mismatch repair efficiency both vary by mismatch type, responsible polymerase, replication time, and replication origin proximity. Mutation patterns implicate replication infidelity as one driver of variation in somatic and germline evolution, suggest mechanisms of mutual modulation of genome stability and composition, and predict future observations in specific cancers.
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180
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Binding sites of miR-1273 family on the mRNA of target genes. BIOMED RESEARCH INTERNATIONAL 2014; 2014:620530. [PMID: 25243165 PMCID: PMC4160624 DOI: 10.1155/2014/620530] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 07/11/2014] [Accepted: 07/23/2014] [Indexed: 11/17/2022]
Abstract
This study examined binding sites of 2,578 miRNAs in the mRNAs of 12,175 human genes using the MirTarget program. It found that the miRNAs of miR-1273 family have between 33 and 1,074 mRNA target genes, with a free hybridization energy of 90% or more of its maximum value. The miR-1273 family consists of miR-1273a, miR-1273c, miR-1273d, miR-1273e, miR-1273f, miR-1273g-3p, miR-1273g-5p, miR-1273h-3p, and miR-1273h-5p. Unique miRNAs (miR-1273e, miR-1273f, and miR-1273g-3p) have more than 400 target genes. We established 99 mRNA nucleotide sequences that contain arranged binding sites for the miR-1273 family. High conservation of each miRNA binding site in the mRNA of the target genes was found. The arranged binding sites of the miR-1273 family are located in the 5′UTR, CDS, or 3′UTR of many mRNAs. Five repeating sites containing some of the miR-1273 family's binding sites were found in the 3′UTR of several target genes. The oligonucleotide sequences of miR-1273 binding sites located in CDSs code for homologous amino acid sequences in the proteins of target genes. The biological role of unique miRNAs was also discussed.
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181
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Sassi M, Carter DJ, Uberuaga BP, Stanek CR, Mancera RL, Marks NA. Hydrogen Bond Disruption in DNA Base Pairs from 14C Transmutation. J Phys Chem B 2014; 118:10430-5. [DOI: 10.1021/jp508118f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Michel Sassi
- Nanochemistry Research Institute & Department of Chemistry, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
- Fundamental
and Computational Sciences Directorate, Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Damien J. Carter
- Nanochemistry Research Institute & Department of Chemistry, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
| | - Blas P. Uberuaga
- Material
Science and Technology Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Christopher R. Stanek
- Material
Science and Technology Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Ricardo L. Mancera
- School
of Biomedical Sciences, CHIRI Biosciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
| | - Nigel A. Marks
- Discipline of Physics & Astronomy, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
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182
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Gaur V, Vyas R, Fowler JD, Efthimiopoulos G, Feng JY, Suo Z. Structural and kinetic insights into binding and incorporation of L-nucleotide analogs by a Y-family DNA polymerase. Nucleic Acids Res 2014; 42:9984-95. [PMID: 25104018 PMCID: PMC4150803 DOI: 10.1093/nar/gku709] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Considering that all natural nucleotides (D-dNTPs) and the building blocks (D-dNMPs) of DNA chains possess D-stereochemistry, DNA polymerases and reverse transcriptases (RTs) likely possess strongD-stereoselectivity by preferably binding and incorporating D-dNTPs over unnatural L-dNTPs during DNA synthesis. Surprisingly, a structural basis for the discrimination against L-dNTPs by DNA polymerases or RTs has not been established although L-deoxycytidine analogs (lamivudine and emtricitabine) and L-thymidine (telbivudine) have been widely used as antiviral drugs for years. Here we report seven high-resolution ternary crystal structures of a prototype Y-family DNA polymerase, DNA, and D-dCTP, D-dCDP, L-dCDP, or the diphosphates and triphosphates of lamivudine and emtricitabine. These structures reveal that relative to D-dCTP, each of these L-nucleotides has its sugar ring rotated by 180° with an unusual O4'-endo sugar puckering and exhibits multiple triphosphate-binding conformations within the active site of the polymerase. Such rare binding modes significantly decrease the incorporation rates and efficiencies of these L-nucleotides catalyzed by the polymerase.
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Affiliation(s)
- Vineet Gaur
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Rajan Vyas
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Jason D Fowler
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Georgia Efthimiopoulos
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Joy Y Feng
- Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94044, USA
| | - Zucai Suo
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
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183
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Ding Y, Zhang X, Tham KW, Qin PZ. Experimental mapping of DNA duplex shape enabled by global lineshape analyses of a nucleotide-independent nitroxide probe. Nucleic Acids Res 2014; 42:e140. [PMID: 25092920 PMCID: PMC4191381 DOI: 10.1093/nar/gku695] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Sequence-dependent variation in structure and dynamics of a DNA duplex, collectively referred to as ‘DNA shape’, critically impacts interactions between DNA and proteins. Here, a method based on the technique of site-directed spin labeling was developed to experimentally map shapes of two DNA duplexes that contain response elements of the p53 tumor suppressor. An R5a nitroxide spin label, which was covalently attached at a specific phosphate group, was scanned consecutively through the DNA duplex. X-band continuous-wave electron paramagnetic resonance spectroscopy was used to monitor rotational motions of R5a, which report on DNA structure and dynamics at the labeling site. An approach based on Pearson's coefficient analysis was developed to collectively examine the degree of similarity among the ensemble of R5a spectra. The resulting Pearson's coefficients were used to generate maps representing variation of R5a mobility along the DNA duplex. The R5a mobility maps were found to correlate with maps of certain DNA helical parameters, and were capable of revealing similarity and deviation in the shape of the two closely related DNA duplexes. Collectively, the R5a probe and the Pearson's coefficient-based lineshape analysis scheme yielded a generalizable method for examining sequence-dependent DNA shapes.
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Affiliation(s)
- Yuan Ding
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Xiaojun Zhang
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Kenneth W Tham
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Peter Z Qin
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
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184
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The properties of binding sites of miR-619-5p, miR-5095, miR-5096, and miR-5585-3p in the mRNAs of human genes. BIOMED RESEARCH INTERNATIONAL 2014; 2014:720715. [PMID: 25162022 PMCID: PMC4137733 DOI: 10.1155/2014/720715] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 07/03/2014] [Accepted: 07/03/2014] [Indexed: 11/17/2022]
Abstract
The binding of 2,578 human miRNAs with the mRNAs of 12,175 human genes was studied. It was established that miR-619-5p, miR-5095, miR-5096, and miR-5585-3p bind with high affinity to the mRNAs of the 1215, 832, 725, and 655 genes, respectively. These unique miRNAs have binding sites in the coding sequences and untranslated regions of mRNAs. The mRNAs of many genes have multiple miR-619-5p, miR-5095, miR-5096, and miR-5585-3p binding sites. Groups of mRNAs in which the ordering of the miR-619-5p, miR-5095, miR-5096, and miR-5585-3p binding sites differ were established. The possible functional and evolutional properties of unique miRNAs are discussed.
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185
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Poudel L, Rulis P, Liang L, Ching WY. Electronic structure, stacking energy, partial charge, and hydrogen bonding in four periodic B-DNA models. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:022705. [PMID: 25215756 DOI: 10.1103/physreve.90.022705] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Indexed: 05/12/2023]
Abstract
We present a theoretical study of the electronic structure of four periodic B-DNA models labeled (AT)(10), (GC)(10), (AT)(5)(GC)(5), and (AT-GC)(5) where A denotes adenine, T denotes thymine, G denotes guanine, and C denotes cytosine. Each model has ten base pairs with Na counterions to neutralize the negative phosphate group in the backbone. The (AT)(5)(GC)(5) and (AT-GC)(5) models contain two and five AT-GC bilayers, respectively. When compared against the average of the two pure models, we estimate the AT-GC bilayer interaction energy to be 19.015 Kcal/mol, which is comparable to the hydrogen bonding energy between base pairs obtained from the literature. Our investigation shows that the stacking of base pairs plays a vital role in the electronic structure, relative stability, bonding, and distribution of partial charges in the DNA models. All four models show a highest occupied molecular orbital (HOMO) to lowest unoccupied molecular orbital (LUMO) gap ranging from 2.14 to 3.12 eV with HOMO states residing on the PO(4) + Na functional group and LUMO states originating from the bases. Our calculation implies that the electrical conductance of a DNA molecule should increase with increased base-pair mixing. Interatomic bonding effects in these models are investigated in detail by analyzing the distributions of the calculated bond order values for every pair of atoms in the four models including hydrogen bonding. The counterions significantly affect the gap width, the conductivity, and the distribution of partial charge on the DNA backbone. We also evaluate quantitatively the surface partial charge density on each functional group of the DNA models.
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Affiliation(s)
- Lokendra Poudel
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, Missouri 64110, USA
| | - Paul Rulis
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, Missouri 64110, USA
| | - Lei Liang
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, Missouri 64110, USA
| | - W Y Ching
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, Missouri 64110, USA
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186
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Ivashchenko A, Berillo O, Pyrkova A, Niyazova R, Atambayeva S. MiR-3960 binding sites with mRNA of human genes. Bioinformation 2014; 10:423-7. [PMID: 25187682 PMCID: PMC4135290 DOI: 10.6026/97320630010423] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 07/07/2014] [Indexed: 12/20/2022] Open
Abstract
The importance of miRNA in cellular regulation is gaining momentum. Therefore, it is of interest to study miRNA in human genes. Hence, the humanmRNA sequences (12,175) were searched for miRNA binding sites and 2,563predicted sites were found. We observed that the miR-3960 has more than 1000mRNA binding sites with high affinity (with ΔG/ΔGm values greater than or equal to 90%) for 375genes. The miR-3960 has 565 binding sites in the 5'UTRs and 515 sites in theCDS of mRNAs. Nucleotide sequences of the binding sites in CDS encode for polyalanine orpolyproline. It is observed that miR-3960 has binding sites in 73 mRNAs of target genesencoded transcription factors. Thus, we document predictedproperties (polysites, sites in CDS) of uncharacterized miR-3960 binding sites. The studying of the miRNA properties is important for creation of diagnostic methods of cancer.
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Affiliation(s)
- Anatoly Ivashchenko
- National Nanotechnology Laboratory, al-Farabi Kazakh National University, Almaty-050038, Kazakhstan
| | - Olga Berillo
- National Nanotechnology Laboratory, al-Farabi Kazakh National University, Almaty-050038, Kazakhstan
| | - Anna Pyrkova
- National Nanotechnology Laboratory, al-Farabi Kazakh National University, Almaty-050038, Kazakhstan
| | - Raigul Niyazova
- National Nanotechnology Laboratory, al-Farabi Kazakh National University, Almaty-050038, Kazakhstan
| | - Shara Atambayeva
- National Nanotechnology Laboratory, al-Farabi Kazakh National University, Almaty-050038, Kazakhstan
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187
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Grabkowska-Drużyc M, Balzarini J, Piotrowska DG. Design, synthesis, antiviral, and cytostatic evaluation of novel isoxazolidine analogues of C-nucleotides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2014; 32:682-99. [PMID: 24328565 DOI: 10.1080/15257770.2013.851794] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
5-Aryl-2-methylisoxazolidin-3-yl-3-phosphonates have been synthesised from N-methyl-C-diethoxyphosphorylnitrone and vinyl aryls in good yields. Isoxazolidine phosphonates obtained herein were evaluated for activity against a broad range of DNA and RNA viruses. None of the compounds were endowed with antiviral activity nor cytostatic activity at 100 to 250 μM concentrations.
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188
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Nath S, Modi T, Mishra RK, Giri D, Mandal BP, Kumar S. Statistical mechanics of DNA rupture: theory and simulations. J Chem Phys 2014; 139:165101. [PMID: 24182082 DOI: 10.1063/1.4824796] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
We study the effects of the shear force on the rupture mechanism on a double stranded DNA. Motivated by recent experiments, we perform the atomistic simulations with explicit solvent to obtain the distributions of extension in hydrogen and covalent bonds below the rupture force. We obtain a significant difference between the atomistic simulations and the existing results in the literature based on the coarse-grained models (theory and simulations). We discuss the possible reasons and improve the coarse-grained model by incorporating the consequences of semi-microscopic details of the nucleotides in its description. The distributions obtained by the modified model (simulations and theoretical) are qualitatively similar to the one obtained using atomistic simulations.
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Affiliation(s)
- S Nath
- Department of Physics, Banaras Hindu University, Varanasi 221005, India
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189
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Ekmekci Z, Saha K, Moyano DF, Tonga GY, Wang H, Mout R, Rotello VM. Probing the Protein-Nanoparticle Interface: The Role of Aromatic Substitution Pattern on Affinity. Supramol Chem 2014; 27:123-126. [PMID: 27122961 DOI: 10.1080/10610278.2014.914627] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
A new class of cationic gold nanoparticles has been synthesized bearing benzyl moieties featuring -NO2 and -OMe groups to investigate the regioisomeric control of aromatic nanoparticle-protein recognition. In general, nanoparticles bearing electron withdrawing group demonstrated higher binding affinities towards green fluorescent protein (GFP) compared to electron-donating groups. Significantly, a ~7.5 and ~4.3 fold increase in binding with GFP was observed for -NO2 groups in meta- and para-position respectively, while ortho-substitution showed similar binding compared to the unsubstituted ring. These findings demonstrated that nanoparticle-protein interaction can be controlled by the tuning the spatial orientation and the relative electronic properties of the aromatic substituents. This improved biomolecular recognition provides opportunities for enhanced biosensing and functional protein delivery to the cells.
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Affiliation(s)
- Zeynep Ekmekci
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, MA 01003, USA; Department of Biomedical Engineering, Suleyman Demirel University, 32260, Cunur, Isparta, Turkey
| | - Krishnendu Saha
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, MA 01003, USA
| | - Daniel F Moyano
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, MA 01003, USA
| | - Gulen Yesilbag Tonga
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, MA 01003, USA
| | - Hao Wang
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, MA 01003, USA
| | - Rubul Mout
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, MA 01003, USA
| | - Vincent M Rotello
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, MA 01003, USA
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190
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Abstract
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This review will summarize our structural
and kinetic studies of
RB69 DNA polymerase (RB69pol) as well as selected variants of the
wild-type enzyme that were undertaken to obtain a deeper understanding
of the exquisitely high fidelity of B family replicative DNA polymerases.
We discuss how the structures of the various RB69pol ternary complexes
can be used to rationalize the results obtained from pre-steady-state
kinetic assays. Our main findings can be summarized as follows. (i)
Interbase hydrogen bond interactions can increase catalytic efficiency
by 5000-fold; meanwhile, base selectivity is not solely determined
by the number of hydrogen bonds between the incoming dNTP and the
templating base. (ii) Minor-groove hydrogen bond interactions at positions n – 1 and n – 2 of the primer
strand and position n – 1 of the template
strand in RB69pol ternary complexes are essential for efficient primer
extension and base selectivity. (iii) Partial charge interactions
among the incoming dNTP, the penultimate base pair, and the hydration
shell surrounding the incoming dNTP modulate nucleotide insertion
efficiency and base selectivity. (iv) Steric clashes between mismatched
incoming dNTPs and templating bases with amino acid side chains in
the nascent base pair binding pocket (NBP) as well as weak interactions
and large gaps between the incoming dNTPs and the templating base
are some of the reasons that incorrect dNTPs are incorporated so inefficiently
by wild-type RB69pol. In addition, we developed a tC°–tCnitro Förster resonance energy transfer assay to monitor
partitioning of the primer terminus between the polymerase and exonuclease
subdomains.
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Affiliation(s)
- Shuangluo Xia
- Department of Molecular Biophysics and Biochemistry, Yale University , New Haven, Connecticut 06520-8024, United States
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191
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Bats JW, Żivković A, Parsch J, Engels JW. Three different fluoro- or chloro-substituted 1'-deoxy-1'-phenyl-β-D-ribofuranoses. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2014; 70:400-4. [PMID: 24705057 DOI: 10.1107/s2053229614004999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 03/04/2014] [Indexed: 11/10/2022]
Abstract
Crystal structures are reported for three fluoro- or chloro-substituted 1'-deoxy-1'-phenyl-β-D-ribofuranoses, namely 1'-deoxy-1'-(2,4,5-trifluorophenyl)-β-D-ribofuranose, C11H11F3O4, (I), 1'-deoxy-1'-(2,4,6-trifluorophenyl)-β-D-ribofuranose, C11H11F3O4, (II), and 1'-(4-chlorophenyl)-1'-deoxy-β-D-ribofuranose, C11H13ClO4, (III). The five-membered furanose ring of the three compounds has a conformation between a C2'-endo,C3'-exo twist and a C2'-endo envelope. The ribofuranose groups of (I) and (III) are connected by intermolecular O-H···O hydrogen bonds to six symmetry-related molecules to form double layers, while the ribofuranose group of (II) is connected by O-H···O hydrogen bonds to four symmetry-related molecules to form single layers. The O···O contact distance of the O-H···O hydrogen bonds ranges from 2.7172 (15) to 2.8895 (19) Å. Neighbouring double layers of (I) are connected by a very weak intermolecular C-F···π contact. The layers of (II) are connected by one C-H···O and two C-H···F contacts, while the double layers of (III) are connected by a C-H···Cl contact. The conformations of the molecules are compared with those of seven related molecules. The orientation of the benzene ring is coplanar with the H-C1' bond or bisecting the H-C1'-C2' angle, or intermediate between these positions. The orientation of the benzene ring is independent of the substitution pattern of the ring and depends mainly on crystal-packing effects.
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Affiliation(s)
- Jan W Bats
- Institut für Organische Chemie und Chemische Biologie, Universität Frankfurt, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
| | - Aleksandra Żivković
- Institut für Organische Chemie und Chemische Biologie, Universität Frankfurt, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
| | - Jörg Parsch
- Institut für Organische Chemie und Chemische Biologie, Universität Frankfurt, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
| | - Joachim W Engels
- Institut für Organische Chemie und Chemische Biologie, Universität Frankfurt, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany
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192
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Yu CY, Yin BC, Ye BC. A universal real-time PCR assay for rapid quantification of microRNAs via the enhancement of base-stacking hybridization. Chem Commun (Camb) 2014; 49:8247-9. [PMID: 23925039 DOI: 10.1039/c3cc44125c] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Via the base-stacking hybridization strategy, we have developed a universal, one-step real-time quantitative PCR assay for sensitive and selective detection of microRNAs. This proposed assay has several intrinsic features including rapid response, low cost, simple handling procedures, etc.
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Affiliation(s)
- Cui-Yuan Yu
- Lab of Biosystem and Microanalysis, East China University of Science & Technology, Shanghai 200237, PR China
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193
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Dupuis NF, Holmstrom ED, Nesbitt DJ. Single-molecule kinetics reveal cation-promoted DNA duplex formation through ordering of single-stranded helices. Biophys J 2014; 105:756-66. [PMID: 23931323 DOI: 10.1016/j.bpj.2013.05.061] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Revised: 05/16/2013] [Accepted: 05/30/2013] [Indexed: 01/05/2023] Open
Abstract
In this work, the kinetics of short, fully complementary oligonucleotides are investigated at the single-molecule level. Constructs 6-9 bp in length exhibit single exponential kinetics over 2 orders of magnitude time for both forward (kon, association) and reverse (koff, dissociation) processes. Bimolecular rate constants for association are weakly sensitive to the number of basepairs in the duplex, with a 2.5-fold increase between 9 bp (k'on = 2.1(1) × 10(6) M(-1) s(-1)) and 6 bp (k'on = 5.0(1) × 10(6) M(-1) s(-1)) sequences. In sharp contrast, however, dissociation rate constants prove to be exponentially sensitive to sequence length, varying by nearly 600-fold over the same 9 bp (koff = 0.024 s(-1)) to 6 bp (koff = 14 s(-1)) range. The 8 bp sequence is explored in more detail, and the NaCl dependence of kon and koff is measured. Interestingly, kon increases by >40-fold (kon = 0.10(1) s(-1) to 4.0(4) s(-1) between [NaCl] = 25 mM and 1 M), whereas in contrast, koff decreases by fourfold (0.72(3) s(-1) to 0.17(7) s(-1)) over the same range of conditions. Thus, the equilibrium constant (Keq) increases by ≈160, largely due to changes in the association rate, kon. Finally, temperature-dependent measurements reveal that increased [NaCl] reduces the overall exothermicity (ΔΔH° > 0) of duplex formation, albeit by an amount smaller than the reduction in entropic penalty (-TΔΔS° < 0). This reduced entropic cost is attributed to a cation-facilitated preordering of the two single-stranded species, which lowers the association free-energy barrier and in turn accelerates the rate of duplex formation.
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194
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Oertell K, Chamberlain BT, Wu Y, Ferri E, Kashemirov BA, Beard WA, Wilson SH, McKenna CE, Goodman MF. Transition state in DNA polymerase β catalysis: rate-limiting chemistry altered by base-pair configuration. Biochemistry 2014; 53:1842-8. [PMID: 24580380 PMCID: PMC3985788 DOI: 10.1021/bi500101z] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
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Kinetics
studies of dNTP analogues having pyrophosphate-mimicking
β,γ-pCXYp leaving groups with variable X and Y substitution
reveal striking differences in the chemical transition-state energy
for DNA polymerase β that depend on all aspects of base-pairing
configurations, including whether the incoming dNTP is a purine or
pyrimidine and if base-pairings are right (T•A and G•C)
or wrong (T•G and G•T). Brønsted plots of the catalytic
rate constant (log(kpol)) versus pKa4 for the leaving group exhibit linear free
energy relationships (LFERs) with negative slopes ranging from −0.6
to −2.0, consistent with chemical rate-determining transition-states
in which the active-site adjusts to charge-stabilization demand during
chemistry depending on base-pair configuration. The Brønsted
slopes as well as the intercepts differ dramatically and provide the
first direct evidence that dNTP base recognition by the enzyme–primer–template
complex triggers a conformational change in the catalytic region of
the active-site that significantly modifies the rate-determining chemical
step.
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Affiliation(s)
- Keriann Oertell
- Department of Biological Sciences and ‡Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California , University Park Campus, Los Angeles, California 90089-0744, United States
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195
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Naserian-Nik AM, Tahani M, Karttunen M. Molecular dynamics study of DNA oligomers under angled pulling. RSC Adv 2014. [DOI: 10.1039/c3ra45604h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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196
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197
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Yu C, Guan J, Chen K, Bae SC, Granick S. Single-molecule observation of long jumps in polymer adsorption. ACS NANO 2013; 7:9735-9742. [PMID: 24168181 DOI: 10.1021/nn4049039] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Single-molecule fluorescence imaging of adsorption onto initially bare surfaces shows that polymer chains need not localize immediately after arrival. In a system optimized to present limited adsorption sites (quartz surface to which polyethylene glycol (PEG) chains adsorb from aqueous solution at pH 8.2), we find that some chains diffuse back into bulk solution and readsorb at some distance away, sometimes multiple times before they either localize at a stable position or diffuse away into bulk solution. This mechanism of surface diffusion is considerably more rapid than the classical model in which adsorbed polymers crawl on surfaces while the entire molecule remains adsorbed, suggesting the conceptual generality of a recent report ( Phys. Rev. Lett. 2013 , 110 , 256101 ) but in a new experimental system and with comparison of different chain lengths. We find the trajectories with jumps to follow a truncated Lévy distribution of step size with limiting slope -2.5, consistent with a well-defined, rapid surface diffusion coefficient over the times we observe. The broad waiting time distribution appears to reflect that polymer chains possess a broad distribution of bound fraction: the smaller the bound fraction of a given chain, the shorter the surface residence time before executing the next surface jump.
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Affiliation(s)
- Changqian Yu
- Departments of †Materials Science and Engineering, ‡Chemical and Biomolecular Engineering, §Chemistry, and ⊥Physics, University of Illinois , Urbana, Illinois 61801, United States
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198
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Golden J, Motea E, Zhang X, Choi JS, Feng Y, Xu Y, Lee I, Berdis AJ. Development and characterization of a non-natural nucleoside that displays anticancer activity against solid tumors. ACS Chem Biol 2013; 8:2452-65. [PMID: 23992753 DOI: 10.1021/cb400350h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nucleoside analogs are an important class of anticancer agent that historically show better efficacy against hematological cancers versus solid tumors. This report describes the development and characterization of a new class of nucleoside analog that displays anticancer effects against both hematological and adherent cancer cell lines. These new analogs lack canonical hydrogen-bonding groups yet are effective nucleotide substrates for several high-fidelity DNA polymerases. Permutations in the position of the non-hydrogen-bonding functional group greatly influence the kinetic behavior of these nucleosides. One particular analog designated 4-nitroindolyl-2'-deoxynucleoside triphosphate (4-NITP) is unique as it is incorporated opposite C and T with high catalytic efficiencies. In addition, this analog functions as a nonobligate chain terminator of DNA synthesis, since it is poorly elongated. Consistent with this mechanism, the corresponding nucleoside, 4-nitroindolyl-2'-deoxynucleoside (4-NIdR), produces antiproliferative effects against leukemia cells. 4-NIdR also produces cytostatic and cytotoxic effects against several adherent cancer cell lines, especially those that are deficient in mismatch repair and p53. Cell death in this case appears to occur via mitotic catastrophe, a specialized form of apoptosis. Mass spectroscopy experiments performed on nucleic acid isolated from cells treated with 4-NIdR validate that the non-natural nucleoside is stably incorporated into DNA. Xenograft mouse studies demonstrate that administration of 4-NIdR delays tumor growth without producing adverse side effects such as anemia and thrombocytopenia. Collectively, the results of in vitro, cell-based, and animal studies provide evidence for the development of a novel nucleoside analog that shows enhanced effectiveness against solid tumors.
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Affiliation(s)
- Jackelyn Golden
- Departments of Pharmacology and ‡Chemistry, Case Western Reserve University , 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
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200
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Martin-Pintado N, Deleavey GF, Portella G, Campos-Olivas R, Orozco M, Damha MJ, González C. Backbone FCH⋅⋅⋅O Hydrogen Bonds in 2′F-Substituted Nucleic Acids. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201305710] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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