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Degtyareva NN, Reddish MJ, Sengupta B, Petty JT. Structural studies of a trinucleotide repeat sequence using 2-aminopurine. Biochemistry 2010; 48:2340-6. [PMID: 19170594 DOI: 10.1021/bi802225y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The secondary structure of repeated trinucleotide sequences results in the development of several neurodegenerative diseases, and these studies consider the (CAG)(8) sequence that forms a stem-loop hairpin. The structural and thermodynamic properties of this hairpin are assessed using 2-aminopurine substitutions for adenine at six positions in this repeated sequence. Circular dichroism spectra and thermal denaturation experiments show that the secondary structure is not disturbed by the modifications. The local structure of the hairpin was monitored using the fluorescence intensities of 2-aminopurines, the changes in the intensity relative to the denatured state, and the sensitivity of the fluorescence to quenching by acrylamide. To establish the stem and loop characteristics in (CAG)(8), known reference points for stem, loop, and exposed base motifs were used. In the vicinity of the loop, the bases become more solvent exposed, which suggests that the instability associated with this repeated hairpin influences the global secondary structure. These results provide the basis to interpret the structures adopted by other repeated (CAG) structures.
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Affiliation(s)
- Natalya N Degtyareva
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, USA
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2
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Tamulaitis G, Zaremba M, Szczepanowski RH, Bochtler M, Siksnys V. Nucleotide flipping by restriction enzymes analyzed by 2-aminopurine steady-state fluorescence. Nucleic Acids Res 2007; 35:4792-9. [PMID: 17617640 PMCID: PMC1950555 DOI: 10.1093/nar/gkm513] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Many DNA modification and repair enzymes require access to DNA bases and therefore flip nucleotides. Restriction endonucleases (REases) hydrolyze the phosphodiester backbone within or in the vicinity of the target recognition site and do not require base extrusion for the sequence readout and catalysis. Therefore, the observation of extrahelical nucleotides in a co-crystal of REase Ecl18kI with the cognate sequence, CCNGG, was unexpected. It turned out that Ecl18kI reads directly only the CCGG sequence and skips the unspecified N nucleotides, flipping them out from the helix. Sequence and structure conservation predict nucleotide flipping also for the complexes of PspGI and EcoRII with their target DNAs (/CCWGG), but data in solution are limited and indirect. Here, we demonstrate that Ecl18kI, the C-terminal domain of EcoRII (EcoRII-C) and PspGI enhance the fluorescence of 2-aminopurines (2-AP) placed at the centers of their recognition sequences. The fluorescence increase is largest for PspGI, intermediate for EcoRII-C and smallest for Ecl18kI, probably reflecting the differences in the hydrophobicity of the binding pockets within the protein. Omitting divalent metal cations and mutation of the binding pocket tryptophan to alanine strongly increase the 2-AP signal in the Ecl18kI–DNA complex. Together, our data provide the first direct evidence that Ecl18kI, EcoRII-C and PspGI flip nucleotides in solution.
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Affiliation(s)
- Gintautas Tamulaitis
- Institute of Biotechnology, Graiciuno 8, LT-02241, Vilnius, Lithuania, International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland and Max-Planck-Institute for Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01309 Dresden, Germany
| | - Mindaugas Zaremba
- Institute of Biotechnology, Graiciuno 8, LT-02241, Vilnius, Lithuania, International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland and Max-Planck-Institute for Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01309 Dresden, Germany
| | - Roman H. Szczepanowski
- Institute of Biotechnology, Graiciuno 8, LT-02241, Vilnius, Lithuania, International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland and Max-Planck-Institute for Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01309 Dresden, Germany
| | - Matthias Bochtler
- Institute of Biotechnology, Graiciuno 8, LT-02241, Vilnius, Lithuania, International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland and Max-Planck-Institute for Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01309 Dresden, Germany
| | - Virginijus Siksnys
- Institute of Biotechnology, Graiciuno 8, LT-02241, Vilnius, Lithuania, International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland and Max-Planck-Institute for Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01309 Dresden, Germany
- *To whom correspondence should be addressed.+370 5 2602108+370 5 2602116
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Sowers LC, Mhaskar DN, Khwaja TA, Goodman MF. Preparation of Imino and Amino N-15 Enriched 2-Aminopurine Deoxynucleoside. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328318908054155] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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4
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Gargallo R, Vives M, Tauler R, Eritja R. Protonation studies and multivariate curve resolution on oligodeoxynucleotides carrying the mutagenic base 2-aminopurine. Biophys J 2001; 81:2886-96. [PMID: 11606299 PMCID: PMC1301753 DOI: 10.1016/s0006-3495(01)75929-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
2-Aminopurine (P) is a mutagen causing A.T to G.C transitions in prokaryotic systems. To study the base-pairing schemes between P and cytosine (C) or thymine (T), two self-complementary dodecamers containing P paired with either C or T were synthesized, and their protonation equilibria were studied by acid-base titrations and melting experiments. The mismatches were incorporated into the self-complementary sequence d(CGCPCCGGXGCG), where X was C or T. Spectroscopic data obtained from molecular absorption, circular dichroism (CD), and molecular fluorescence spectroscopy were analyzed by a factor-analysis-based method, multivariate curve resolution based on the alternating least squares optimization procedure (MCR-ALS). This procedure allows determination of the number of acid-base species or conformations present in an acid-base or melting experiment and the resolution of the concentration profiles and pure spectra for each of them. Acid-base experiments have shown that at pH 7, 150 mM ionic strength, and 37 degrees C, both C and P are deprotonated. At pH near 4, the majority of species shows C protonated and P deprotonated. Finally, at pH values near 3, the majority of species shows both protonated C and P. These results are in agreement with NMR studies showing a wobble geometry for the P x C base pair and a Watson-Crick geometry for the P x T base pair at neutral pH. Melting experiments were carried out to confirm the proposed acid-base distribution profile. For the sequence including the P x T mismatch, only one transition was observed at neutral pH. However, for the sequence including the P x C mismatch, two transitions were detected by CD but only one by molecular absorption. This behavior agrees with that observed by other authors for oligonucleotides of similar sequence and suggests the following sequence of conformational changes during melting: duplex --> hairpin --> random coil.
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Affiliation(s)
- R Gargallo
- Department of Analytical Chemistry, University of Barcelona, E-08028 Barcelona, Spain.
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5
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Organization, Replication, Transposition, and Repair of DNA. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50030-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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6
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Sherer EC, Cramer CJ. Quantum chemical characterization of the cytosine: 2-Aminopurine base pair. J Comput Chem 2001. [DOI: 10.1002/jcc.1075] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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7
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Luyten I, Herdewijn P. Hybridization properties of base-modified oligonucleotides within the double and triple helix motif. Eur J Med Chem 1998. [DOI: 10.1016/s0223-5234(98)80016-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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8
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Molecular electric field mapping of some anions and cations of 2- aminopurine and 6- thioguanine. J CHEM SCI 1994. [DOI: 10.1007/bf02840750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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9
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Goodman MF, Creighton S, Bloom LB, Petruska J. Biochemical basis of DNA replication fidelity. Crit Rev Biochem Mol Biol 1993; 28:83-126. [PMID: 8485987 DOI: 10.3109/10409239309086792] [Citation(s) in RCA: 391] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
DNA polymerase is the critical enzyme maintaining genetic integrity during DNA replication. Individual steps in the replication process that contribute to DNA synthesis fidelity include nucleotide insertion, exonucleolytic proofreading, and binding to and elongation of matched and mismatched primer termini. Each process has been investigated using polyacrylamide gel electrophoresis (PAGE) to resolve 32P-labeled primer molecules extended by polymerase. We describe how integrated gel band intensities can be used to obtain site-specific velocities for addition of correct and incorrect nucleotides, extending mismatched compared to correctly matched primer termini and measuring polymerase dissociation rates and equilibrium DNA binding constants. The analysis is based on steady-state "single completed hit conditions", where polymerases encounter many DNA molecules but where each DNA encounters an enzyme at most once. Specific topics addressed include nucleotide misinsertion, mismatch extension, exonucleolytic proofreading, single nucleotide discrimination using PCR, promiscuous mismatch extension by HIV-1 and AMV reverse transcriptases, sequence context effects on fidelity and polymerase dissociation, structural and kinetic properties of mispairs relating to fidelity, error avoidance mechanisms, kinetics of copying template lesions, the "A-rule" for insertion at abasic template lesions, an interesting exception to the "A-rule", thermodynamic and kinetic determinants of base pair discrimination by polymerases.
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Affiliation(s)
- M F Goodman
- University of Southern California, Department of Biological Sciences, Los Angeles 90089-1340
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Letić-Gavrilović A, Abe K. Localization of chromogranins, non-neuron-specific enolase, and different forms of somatostatins in the submandibular salivary glands of mice. J Dent Res 1990; 69:1494-9. [PMID: 1974558 DOI: 10.1177/00220345900690080901] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The localizations of chromogranins A, B, and C, neuron-specific enolase (NSE, gamma gamma-type) and non-NSE (alpha alpha-type), and different forms of somatostatins were immunocytochemically identified. The localizations were compared with those of epidermal growth factor (EGF) and nerve growth factor (NGF) in the submandibular salivary glands (SMG) of male mice at five to six weeks of age, with use of a variety of antibodies and the peroxidase-antiperoxidase (PAP) and avidin-biotin complex (ABC) detection methods. In the SMG of male mice, the major chromogranin present was chromogranin A, whereas chromogranins B and C were not detected at these ages by either method. Chromogranin A-like immunoreactivity was located in the granular convoluted tubule (GCT) cells of the SMG, whereas non-NSE immunoreactivity was observed throughout the duct system and in some acinar-associated cells. NSE was not detected in any part of the SMG. The distribution of chromogranin A and somatostatins in the GCT cells was similar to that of EGF and NGF. Our results strongly suggest that chromogranin A and somatostatins, but not chromogranin B or C, may be useful as a means of differentiation of the cells in the duct system of the SMG responsible for the production of biologically-active factors.
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Nagata C, Aida M. Ab initio molecular orbital study on the pairing and stacking interactions between nucleic acid bases in relation to the biological activities. ACTA ACUST UNITED AC 1988. [DOI: 10.1016/0166-1280(88)80141-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Abstract
The nature of hydrogen bonding between normal and modified bases has been re-examined. It is proposed that hydrogen-bonding schemes may involve tautomeric, ionized or conformational forms (syn, anti and wobble). Several important cases are presented or reviewed in which physical evidence indicates the existence of ionized base pairs. When thermodynamic values determined in aqueous solution under physiological conditions are considered, it can be argued that base ionization will contribute substantially to the stability of many biologically relevant base pairs containing modified bases. A significant incidence of ionized bases in DNA may have important kinetic ramifications for the further chemical reactivity of both the modified base and its cross-strand pairing partner. Moreover, DNA structure at and surrounding ionized base pairs may be altered. For this reason, the model presented in this study should be useful as DNA-sequence analysis becomes more commonly applied to the study of mutagenesis.
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Takahashi M, Negishi K, Hayatsu H. Proofreading of a mutagenic nucleotide, N4-aminodeoxycytidylic acid, by Escherichia coli DNA polymerase I. Biochem Biophys Res Commun 1987; 143:104-9. [PMID: 3548722 DOI: 10.1016/0006-291x(87)90636-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
N4-Aminodeoxycytidine triphosphate, a putative metabolite of N4-aminocytidine which is a potent mutagen, is incorporated, in vitro, into polynucleotides in place of dCTP and at a much lesser extent, but significantly, in place of dTTP by E. coli DNA polymerase I large fragment. The activity of the polymerase to proofread this unnatural nucleotide has now been investigated. The results indicate that the 3'-5' exonuclease in the polymerase recognizes N4-aminocytosine as an incorrect base when N4-aminocytosine is incorporated opposite adenine but the enzyme cannot distinguish N4-aminocytosine from cytosine when it is incorporated opposite guanine.
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Aida M, Yamane K, Nagata C. An explanation of the induction of mutations by 2-aminopurine from an ab initio molecular orbital study. Mutat Res 1986; 173:49-54. [PMID: 3941679 DOI: 10.1016/0165-7992(86)90010-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The molecular mechanism of induction of mutations by 2-aminopurine (AP) was studied by an ab initio molecular orbital method. Cytosine (C) is converted to its disfavored imino tautomer more easily than AP, judging from the calculated total energies of the bases and the base analogue. This suggests that a stable AP:C base mispair via two hydrogen bonds can be formed with the imino tautomer of C. These results stress the importance of the imino form of C in AP-induced mutagenesis and support the 'trigger mechanism', in which formation of one hydrogen bond between AP and C is considered to stimulate the tautomeric shift of AP or C. The calculated relative stabilities of various base pairs and mispairs were in good agreement with experimental findings.
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16
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New light on tautomerism of purines and pyrimidines and its biological and genetic implications. J Biosci 1985. [DOI: 10.1007/bf02702764] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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17
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Hopkins RL, Goodman MF. Ribonucleoside and deoxyribonucleoside triphosphate pools during 2-aminopurine mutagenesis in T4 mutator-, wild type-, and antimutator-infected Escherichia coli. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(18)88826-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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18
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Mhaskar DN, Goodman MF. On the molecular basis of transition mutations. Frequency of forming 2-aminopurine-cytosine base mispairs in the G X C—-A X T mutational pathway by T4 DNA polymerase in vitro. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(20)71268-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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