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Beyond the double helix: DNA structural diversity and the PDB. J Biol Chem 2021; 296:100553. [PMID: 33744292 PMCID: PMC8063756 DOI: 10.1016/j.jbc.2021.100553] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/15/2021] [Accepted: 03/16/2021] [Indexed: 12/11/2022] Open
Abstract
The determination of the double helical structure of DNA in 1953 remains the landmark event in the development of modern biological and biomedical science. This structure has also been the starting point for the determination of some 2000 DNA crystal structures in the subsequent 68 years. Their structural diversity has extended to the demonstration of sequence-dependent local structure in duplex DNA, to DNA bending in short and long sequences and in the DNA wound round the nucleosome, and to left-handed duplex DNAs. Beyond the double helix itself, in circumstances where DNA sequences are or can be induced to unwind from being duplex, a wide variety of topologies and forms can exist. Quadruplex structures, based on four-stranded cores of stacked G-quartets, are prevalent though not randomly distributed in the human and other genomes and can play roles in transcription, translation, and replication. Yet more complex folds can result in DNAs with extended tertiary structures and enzymatic/catalytic activity. The Protein Data Bank is the depository of all these structures, and the resource where structures can be critically examined and validated, as well as compared one with another to facilitate analysis of conformational and base morphology features. This review will briefly survey the major structural classes of DNAs and illustrate their significance, together with some examples of how the use of the Protein Data Bank by for example, data mining, has illuminated DNA structural concepts.
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2
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Sarkar AK, Sarzynska J, Lahiri A. Ensemble Allosteric Model for the Modified Wobble Hypothesis. J Phys Chem Lett 2020; 11:6337-6343. [PMID: 32701298 DOI: 10.1021/acs.jpclett.0c00854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The residue 2-thiouridine (s2U) provides a remarkable example for the "modified wobble" hypothesis, which postulates that some post-transcriptional modifications at the wobble position of tRNAs restrict recognition of degenerate codons. Through extensive molecular dynamics simulations using our χIDRP force field parameters, we demonstrate how this modification shifts the conformational ensemble from a predominantly disordered, as in the case of an RNA pentamer (GUUUC), to a substantially ordered population in Gs2UUUC. Our simulations clearly showed that the van der Waals interaction of sulfur played a major role in driving the disorder-to-order transition. The conformational redistribution and the slowing down of the transition between the clusters within the population in the presence of s2U suggest ensemble allostery to be a key mechanism that may play a general role in the functioning of the wobble modifications of tRNAs.
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Affiliation(s)
- Aditya K Sarkar
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata 700 009, India
| | - Joanna Sarzynska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Ansuman Lahiri
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata 700 009, India
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3
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Devi M, Chingbiaknem E, Lyngdoh RHD. A molecular mechanics study on GA codon box translation. J Theor Biol 2018; 441:28-43. [PMID: 29305181 DOI: 10.1016/j.jtbi.2018.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 01/01/2018] [Accepted: 01/02/2018] [Indexed: 11/28/2022]
Abstract
The GA codon box incorporates the two-fold degeneracy of aspartic acid and of glutamic acid. Using the molecular mechanics approach of the AMBER suite, the four codons of the GA box are paired via H-bonding with two aspartic acid anticodons and two glutamic acid anticodons to yield 8 cognate and 11 non-cognate codon-anticodon duplexes. In addition four select non-cognate duplexes between the GA box codons and three alanine anticodons are also studied. These 23 duplexes display a variety of base-pairing possibilities at the wobble position. Cognate duplexes are differentiated from non-cognate duplexes on the grounds of structure and stability (chiefly the former). The results are in line with Crick's wobble hypothesis, and corroborate the observed reading properties of the aspartic acid anticodons GUC and QUC and of the glutamic acid anticodons CUC and SmnUC.
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Affiliation(s)
- Martina Devi
- Department of Chemistry, North-Eastern Hill University, Shillong 793022, India
| | - Esther Chingbiaknem
- Department of Chemistry, North-Eastern Hill University, Shillong 793022, India
| | - R H Duncan Lyngdoh
- Department of Chemistry, North-Eastern Hill University, Shillong 793022, India.
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4
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Devi M, Lyngdoh RD. Favored and less favored codon–anticodon duplexes arising from the GC codon family box encoding for alanine: some computational perspectives. J Biomol Struct Dyn 2017; 36:1029-1049. [DOI: 10.1080/07391102.2017.1308886] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Martina Devi
- Department of Chemistry, North-Eastern Hill University, Shillong 793022, India
| | - R.H. Duncan Lyngdoh
- Department of Chemistry, North-Eastern Hill University, Shillong 793022, India
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5
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Matsuura MF, Kim HJ, Takahashi D, Abboud KA, Benner SA. Crystal structures of deprotonated nucleobases from an expanded DNA alphabet. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2016; 72:952-959. [PMID: 27918296 DOI: 10.1107/s2053229616017071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 10/24/2016] [Indexed: 11/10/2022]
Abstract
Reported here is the crystal structure of a heterocycle that implements a donor-donor-acceptor hydrogen-bonding pattern, as found in the Z component [6-amino-5-nitropyridin-2(1H)-one] of an artificially expanded genetic information system (AEGIS). AEGIS is a new form of DNA from synthetic biology that has six replicable nucleotides, rather than the four found in natural DNA. Remarkably, Z crystallizes from water as a 1:1 complex of its neutral and deprotonated forms, and forms a `skinny' pyrimidine-pyrimidine pair in this structure. The pair resembles the known intercalated cytosine pair. The formation of the same pair in two different salts, namely poly[[aqua(μ6-2-amino-6-oxo-3-nitro-1,6-dihydropyridin-1-ido)sodium]-6-amino-5-nitropyridin-2(1H)-one-water (1/1/1)], denoted Z-Sod, {[Na(C5H4N3O3)(H2O)]·C5H5N3O3·H2O}n, and ammonium 2-amino-6-oxo-3-nitro-1,6-dihydropyridin-1-ide-6-amino-5-nitropyridin-2(1H)-one-water (1/1/1), denoted Z-Am, NH4+·C5H4N3O3-·C5H5N3O3·H2O, under two different crystallization conditions suggests that the pair is especially stable. Implications of this structure for the use of this heterocycle in artificial DNA are discussed.
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Affiliation(s)
- Mariko F Matsuura
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Hyo Joong Kim
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Daisuke Takahashi
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Khalil A Abboud
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
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6
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Deb I, Sarzynska J, Nilsson L, Lahiri A. Rapid communication capturing the destabilizing effect of dihydrouridine through molecular simulations. Biopolymers 2016; 101:985-91. [PMID: 24729441 DOI: 10.1002/bip.22495] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Revised: 04/04/2014] [Accepted: 04/07/2014] [Indexed: 01/08/2023]
Abstract
The structural effects of the commonly occurring modified nucleoside dihydrouridine (D) observed experimentally in model oligonucleotides include a strong destabilization of the C3'-endo sugar conformation of D, the disruption of stacking interactions of neighboring residues with D and a possible destabilization of the C3'-endo sugar pucker of the 5'-neighboring nucleoside. Our simulations with a combination of a set of parameters for modified RNA residues with the recently developed AMBER FF99χ force field having reoptimized glycosidic torsion angle parameters for standard nucleosides was found to reproduce the destabilizing effect of dihydrouridine better than with the AMBER FF99 force field for nucleic acids for which the parameters for the modified residues were originally developed.
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Affiliation(s)
- Indrajit Deb
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, 700009, West Bengal, India
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7
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Rooman M, Wintjens R. Sequence and conformation effects on ionization potential and charge distribution of homo-nucleobase stacks using M06-2X hybrid density functional theory calculations. J Biomol Struct Dyn 2013; 32:532-45. [PMID: 23582046 PMCID: PMC3919198 DOI: 10.1080/07391102.2013.783508] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
DNA is subject to oxidative damage due to radiation or by-products of cellular metabolism, thereby creating electron holes that migrate along the DNA stacks. A systematic computational analysis of the dependence of the electronic properties of nucleobase stacks on sequence and conformation was performed here, on the basis of single- and double-stranded homo-nucleobase stacks of 1-10 bases or 1-8 base pairs in standard A-, B-, and Z-conformation. First, several levels of theory were tested for calculating the vertical ionization potentials of individual nucleobases; the M06-2X/6-31G* hybrid density functional theory method was selected by comparison with experimental data. Next, the vertical ionization potential, and the Mulliken charge and spin density distributions were calculated and considered on all nucleobase stacks. We found that (1) the ionization potential decreases with the number of bases, the lowest being reached by Gua≡Cyt tracts; (2) the association of two single strands into a double-stranded tract lowers the ionization potential significantly (3) differences in ionization potential due to sequence variation are roughly three times larger than those due to conformational modifications. The charge and spin density distributions were found (1) to be located toward the 5'-end for single-stranded Gua-stacks and toward the 3'-end for Cyt-stacks and basically delocalized over all bases for Ade- and Thy-stacks; (2) the association into double-stranded tracts empties the Cyt- and Thy-strands of most of the charge and all the spin density and concentrates them on the Gua- and Ade-strands. The possible biological implications of these results for transcription are discussed.
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Affiliation(s)
- Marianne Rooman
- a BioModeling, BioInformatics and BioProcesses Department , CP 165/61 Université Libre de Bruxelles , 50 Roosevelt ave, 1050 Brussels , Belgium
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8
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Ghita A, Pascut FC, Mather M, Sottile V, Notingher I. Cytoplasmic RNA in Undifferentiated Neural Stem Cells: A Potential Label-Free Raman Spectral Marker for Assessing the Undifferentiated Status. Anal Chem 2012; 84:3155-62. [DOI: 10.1021/ac202994e] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Adrian Ghita
- School of
Physics and Astronomy, ‡School of Electrical and Electronic Engineering, and §School of Clinical Sciences, University of Nottingham, University
Park, Nottingham NG7 2RD, U.K
| | - Flavius C. Pascut
- School of
Physics and Astronomy, ‡School of Electrical and Electronic Engineering, and §School of Clinical Sciences, University of Nottingham, University
Park, Nottingham NG7 2RD, U.K
| | - Melissa Mather
- School of
Physics and Astronomy, ‡School of Electrical and Electronic Engineering, and §School of Clinical Sciences, University of Nottingham, University
Park, Nottingham NG7 2RD, U.K
| | - Virginie Sottile
- School of
Physics and Astronomy, ‡School of Electrical and Electronic Engineering, and §School of Clinical Sciences, University of Nottingham, University
Park, Nottingham NG7 2RD, U.K
| | - Ioan Notingher
- School of
Physics and Astronomy, ‡School of Electrical and Electronic Engineering, and §School of Clinical Sciences, University of Nottingham, University
Park, Nottingham NG7 2RD, U.K
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9
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10
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Lee CH, Tinoco I. Conformation studies of 13 trinucleoside diphosphates by 360 MHz PMR spectroscopy. A bulged base conformation. I. Base protons and H1' protons. Biophys Chem 2008; 11:283-94. [PMID: 16997249 DOI: 10.1016/0301-4622(80)80031-7] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/1979] [Revised: 01/02/1980] [Indexed: 11/23/2022]
Abstract
The 360 MHz NMR spectra of the base protons and the H1 protons of thirteen trinucleoside diphosphates have been analyzed. The sequences chosen represent all purine-pyrimidine sequences. The chemical shifts of the base protons give evidence for strong next nearest-neighbor effects in some oligonucleotides. Although increasing chain length usually increases nearest-neighbor base-base stacking, it is not always so. Comparing ApCpG, ApUpG and GpUpG to their component dimers, one finds a decrease in stacking of the center pyrimidine with the purine on either side. The coupling constants J 1'2' also show that these three trimers show less stacking for their terminal residues than expected from their component dimers. We conclude that the sequence Pu-Py-Pu favors a conformation in which the pyrimidine is bulged out and the two purines stack on each other.
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Affiliation(s)
- C H Lee
- Department of Chemistry and Laboratory of Chemical Biodynamics, University of California, Berkeley, California 94 720, USA
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11
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12
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Cusumano M, Di Pietro ML, Giannetto A, Vainiglia PA. DNA and RNA Noncovalent Interaction of Platinum(II) Polypyridine Complexes. Inorg Chem 2007; 46:7148-53. [PMID: 17655220 DOI: 10.1021/ic700495x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A comparative investigation of the noncovalent interaction of the platinum(II) polypyridine complexes [Pt(dipy)(n-Rpy)2]2+ and [Pt(4,4'-Me2dipy)(2-Rpy)2]2+ (dipy = 2,2'-dipyridine; Me = CH3; n = 2-4; R = H or CH3) with double-helical DNA (calf thymus) and RNA [poly(A).poly(U)] has been conducted. With the exception of [Pt(dipy)(2-Mepy)2]2+, all of the complexes interact strongly, by intercalation, with both nucleic acids giving rise to large changes in the electronic spectra and induced circular dichroism signals; in addition, viscosity experiments on rodlike DNA and RNA show that both biopolymers elongate upon interaction with the complexes. The binding constant values, KB, determined at 25 degrees C, indicate that, at 0.101 M ionic strength, the affinity for poly(A).poly(U) is strongly dependent on the complexes nature, while for DNA it is leveled off. [Pt(dipy)(2-Mepy)2]2+ binds to DNA but does not interact appreciably with poly(A).poly(U).
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Affiliation(s)
- Matteo Cusumano
- Dipartimento di Chimica Inorganica, Chimica Analitica e Chimica Fisica, University of Messina, 98166 Messina, Italy
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13
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Völker J, Klump HH, Breslauer KJ. DNA metastability and biological regulation: conformational dynamics of metastable omega-DNA bulge loops. J Am Chem Soc 2007; 129:5272-80. [PMID: 17397164 DOI: 10.1021/ja070258q] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dynamic interchange between DNA conformations, including metastable states, can be of importance to biological function. In this study, we use a combination of spectroscopic and calorimetric techniques to detect and characterize kinetically trapped, metastable states in strand exchange and strand displacement reactions for bulge loop DNA conformations, here referred to as Omega-DNAs. We show that such metastable, Omega-DNA bulge loop states can stably coexist below 50 degrees C, while rearranging irreversibly at elevated temperatures to thermodynamically more stable states. Such dynamic interchange between metastable and globally stable DNA conformational states can be of importance in biological regulatory mechanisms.
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Affiliation(s)
- Jens Völker
- Department of Chemistry and Chemical Biology, Rutgers--The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, USA
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14
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Cifuentes-Rojas C, Pavia P, Hernandez A, Osterwisch D, Puerta C, Cruz-Reyes J. Substrate determinants for RNA editing and editing complex interactions at a site for full-round U insertion. J Biol Chem 2007; 282:4265-4276. [PMID: 17158098 DOI: 10.1074/jbc.m605554200] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Multisubunit RNA editing complexes catalyze uridylate insertion/deletion RNA editing directed by complementary guide RNAs (gRNAs). Editing in trypanosome mitochondria is transcript-specific and developmentally controlled, but the molecular mechanisms of substrate specificity remain unknown. Here we used a minimal A6 pre-mRNA/gRNA substrate to define functional determinants for full-round insertion and editing complex interactions at the editing site 2 (ES2). Editing begins with pre-mRNA cleavage within an internal loop flanked by upstream and downstream duplexes with gRNA. We found that substrate recognition around the internal loop is sequence-independent and that completely artificial duplexes spanning a single helical turn are functional. Furthermore, after our report of cross-linking interactions at the deletion ES1 (35), we show for the first time editing complex contacts at an insertion ES. Our studies using site-specific ribose 2' substitutions defined 2'-hydroxyls within the (a) gRNA loop region and (b) flanking helixes that markedly stimulate both pre-mRNA cleavage and editing complex interactions at ES2. Modification of the downstream helix affected scissile bond specificity. Notably, a single 2'-hydroxyl at ES2 is essential for cleavage but dispensable for editing complex cross-linking. This study provides new insights on substrate recognition during full-round editing, including the relevance of secondary structure and the first functional association of specific (pre-mRNA and gRNA) riboses with both endonuclease cleavage and cross-linking activities of editing complexes at an ES. Importantly, most observed cross-linking interactions are both conserved and relatively stable at ES2 and ES1 in hybrid substrates. However, they were also detected as transient low-stability contacts in a non-edited transcript.
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Affiliation(s)
| | - Paula Pavia
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843 and
| | - Alfredo Hernandez
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843 and
| | - Daniel Osterwisch
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843 and
| | - Concepcion Puerta
- Laboratorio of Parasitologia Molecular, Pontificia Universidad Javeriana, Carrera 7a No. 43-82, Ed. 50, Lab 113, Bogota´, Colombia
| | - Jorge Cruz-Reyes
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843 and.
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Hunziker J, Roth HJ, Böhringer M, Giger A, Diederichsen U, Göbel M, Krishnan R, Jaun B, Leumann C, Eschenmoser A. Warum pentose-und nicht hexose-nucleinsäuren? Teil III. Oligo(2′,3′-dideoxy-β-D-glucopyranosyl) nucleotide (‘homo-DNS’): Paarungesigenschaften. Helv Chim Acta 2004. [DOI: 10.1002/hlca.19930760119] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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16
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Hossain MT, Kondo J, Ueno Y, Matsuda A, Takénaka A. X-Ray analysis of d(CGCGAATTXGCG)(2) containing a 2' or minute-deoxy-N(4)-methoxycytosine residue at X: a characteristic pattern of sugar puckers in the crystalline state of the Dickerson-Drew type DNA dodecamers. Biophys Chem 2002; 95:69-77. [PMID: 11880174 DOI: 10.1016/s0301-4622(01)00249-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In a series of structural studies on damaged DNA, a modified Dickerson-Drew dodecamer with the sequence d(CGCGAATTmo(4)CGCG), where mo(4)C is 2'-deoxy-N(4)-methoxycytidine, was synthesized and its structure in a new crystal form has been determined by the X-ray diffraction method. The two dodecamers form a B-form duplex, in which the two mo(4)C residues, respectively, form a wobble pair and a Watson-Crick type pair with the guanine residues of the opposite strand. A comparison of the sugar conformations with those of the other related Dickerson-Drew dodecamers indicates a common feature of their puckering patterns. The sugar pucker of the third residue always adopts an intermediate state (C4'-exo-O4'-endo) between the A-form and B-form. This deviation is ascribed to the stacking interaction of the ribose ring at the third residue with the guanine base at the 12th residue, which is brought about by an extra G12:G2 interaction between two duplexes related by a crystallographic 2(1) symmetry.
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Affiliation(s)
- M Tofazzal Hossain
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta, Midori-ku, 226-8501, Yokohama, Japan
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17
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Trantírek L, Milan Urbášek,, Štefl R, Feigon J, Sklenář V. A Method for Direct Determination of Helical Parameters in Nucleic Acids Using Residual Dipolar Couplings. J Am Chem Soc 2000. [DOI: 10.1021/ja0015702] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lukáš Trantírek
- Laboratory of Biomolecular Structure and Dynamics Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic Department of Computer Science and Engineering FEECS, Brno University of Technology Božetěchova 2, 602 00 Brno, Czech Republic Department of Chemistry and Biochemistry 405 Hilgard Avenue, University of California Los Angeles, California 90095
| | - Milan Urbášek,
- Laboratory of Biomolecular Structure and Dynamics Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic Department of Computer Science and Engineering FEECS, Brno University of Technology Božetěchova 2, 602 00 Brno, Czech Republic Department of Chemistry and Biochemistry 405 Hilgard Avenue, University of California Los Angeles, California 90095
| | - Richard Štefl
- Laboratory of Biomolecular Structure and Dynamics Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic Department of Computer Science and Engineering FEECS, Brno University of Technology Božetěchova 2, 602 00 Brno, Czech Republic Department of Chemistry and Biochemistry 405 Hilgard Avenue, University of California Los Angeles, California 90095
| | - Juli Feigon
- Laboratory of Biomolecular Structure and Dynamics Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic Department of Computer Science and Engineering FEECS, Brno University of Technology Božetěchova 2, 602 00 Brno, Czech Republic Department of Chemistry and Biochemistry 405 Hilgard Avenue, University of California Los Angeles, California 90095
| | - Vladimír Sklenář
- Laboratory of Biomolecular Structure and Dynamics Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic Department of Computer Science and Engineering FEECS, Brno University of Technology Božetěchova 2, 602 00 Brno, Czech Republic Department of Chemistry and Biochemistry 405 Hilgard Avenue, University of California Los Angeles, California 90095
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18
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Kato M. Structural bistability of repetitive DNA elements featuring CA/TG dinucleotide steps and mode of evolution of satellite DNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 1999; 265:204-9. [PMID: 10491175 DOI: 10.1046/j.1432-1327.1999.00714.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Satellite DNA sequences are known to be important components required for the construction of centromeres and are common to all higher eukaryotes. Nevertheless, their nucleotide sequences vary significantly, even in evolutionarily related species. In order to elucidate how the nucleotide sequences define the conformational character of centromeric satellite DNA, an evolutionary path toward repetitive units has been hypothesized. In that context, the DNA conformation of fish satellite DNA was evaluated in two ways: the organization of subrepeats and sequence characteristics were compared, and the differences in stacking energies between A-helix and B-helix and the sequence-dependent bendability of the helices were evaluated. Our findings suggest that the monomeric units making up currently observed repetitive sequences have evolved through stepwise amplification of shorter, ancestral sequences by increasing the length of the units. In addition, we suggest that potentially key sequences required for DNA amplification comprise highly flexible structures. Thus flexibility of the DNA structure may be a primary prerequisite for DNA amplification.
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Affiliation(s)
- M Kato
- Department of Life Sciences, College of Integrated Arts and Sciences, Osaka Prefecture University, Sakai, Japan.
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19
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Kosikov KM, Gorin AA, Zhurkin VB, Olson WK. DNA stretching and compression: large-scale simulations of double helical structures. J Mol Biol 1999; 289:1301-26. [PMID: 10373369 DOI: 10.1006/jmbi.1999.2798] [Citation(s) in RCA: 119] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Computer-simulated elongation and compression of A - and B -DNA structures beyond the range of thermal fluctuations provide new insights into high energy "activated" forms of DNA implicated in biochemical processes, such as recombination and transcription. All-atom potential energy studies of regular poly(dG).poly(dC) and poly(dA).poly(dT) double helices, stretched from compressed states of 2.0 A per base-pair step to highly extended forms of 7.0 A per residue, uncover four different hyperfamilies of right-handed structures that differ in mutual base-pair orientation and sugar-phosphate backbone conformation. The optimized structures embrace all currently known right-handed forms of double-helical DNA identified in single crystals as well as non-canonical forms, such as the original "Watson-Crick" duplex with trans conformations about the P-O5' and C5'-C4' backbone bonds. The lowest energy minima correspond to canonical A and B -form duplexes. The calculations further reveal a number of unusual helical conformations that are energetically disfavored under equilibrium conditions but become favored when DNA is highly stretched or compressed. The variation of potential energy versus stretching provides a detailed picture of dramatic conformational changes that accompany the transitions between various families of double-helical forms. In particular, the interchanges between extended canonical and non-canonical states are reminiscent of the cooperative transitions identified by direct stretching experiments. The large-scale, concerted changes in base-pair inclination, brought about by changes in backbone and glycosyl torsion angles, could easily give rise to the observed sharp increase in force required to stretch single DNA molecules more than 1.6-1.65 times their canonical extension. Our extended duplexes also help to tie together a number of previously known structural features of the RecA-DNA complex and offer a self-consistent stereochemical model for the single-stranded/duplex DNA recognition brought in register by recombination proteins. The compression of model duplexes, by contrast, yields non-canonical structures resembling the deformed steps in crystal complexes of DNA with the TATA-box binding protein (TBP). The crystalline TBP-bound DNA steps follow the calculated compression-elongation pattern of an unusual "vertical" duplex with base planes highly inclined with respect to the helical axis, exposed into the minor groove, and accordingly accessible for recognition.Significantly, the double helix can be stretched by a factor of two and compressed roughly in half before its computed internal energy rises sharply. The energy profiles show that DNA extension-compression is related not only to the variation of base-pair Rise but also to concerted changes of Twist, Roll, and Slide. We suggest that the high energy "activated" forms calculated here are critical for DNA processing, e.g. nucleo-protein recognition, DNA/RNA synthesis, and strand exchange.
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Affiliation(s)
- K M Kosikov
- Department of Chemistry, Rutgers, the State University of New Jersey, Wright-Rieman Laboratories, 610 Taylor Road, Piscataway, NJ, 08854-8087, USA
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20
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Yamaoka K, Ojima N, Fujita Y. Pulsed Electric Linear Dichroism of Double-Stranded Antiparallel Poly(rA)·Poly(rU) and Poly(dA)·Poly(dT) Helices in Solution. J Phys Chem B 1997. [DOI: 10.1021/jp9621235] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kiwamu Yamaoka
- Department of Materials Science and Graduate Department of Gene Science, Faculty of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739, Japan
| | - Noriyuki Ojima
- Department of Materials Science and Graduate Department of Gene Science, Faculty of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739, Japan
| | - Yoshimasa Fujita
- Department of Materials Science and Graduate Department of Gene Science, Faculty of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739, Japan
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21
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Yamaoka K, Yamamoto Y, Fujita Y, Ojima N. A Comparative Study on the Structure of Double-Stranded Antiparallel Poly(riboguanylic acid)·Poly(ribocytidylic acid) and Poly(deoxyriboguanylic acid)·Poly(deoxyribocytidylic acid) Helices in Solution by Pulsed Electric Linear Dichroism. J Phys Chem B 1997. [DOI: 10.1021/jp962590m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kiwamu Yamaoka
- Department of Materials Science and Graduate Department of Gene Science, Faculty of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739, Japan
| | - Yutaka Yamamoto
- Department of Materials Science and Graduate Department of Gene Science, Faculty of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739, Japan
| | - Yoshimasa Fujita
- Department of Materials Science and Graduate Department of Gene Science, Faculty of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739, Japan
| | - Noriyuki Ojima
- Department of Materials Science and Graduate Department of Gene Science, Faculty of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739, Japan
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22
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Abstract
In the years that have passed since the publication of Wolfram Saenger's classic book on nucleic acid structure (Saenger, 1984), a considerable amount of new data has been accumulated on the range of conformations which can be adopted by DNA. Many unusual species have joined the DNA zoo, including new varieties of two, three and four stranded helices. Much has been learnt about intrinsic DNA curvature, dynamics and conformational transitions and many types of damaged or deformed DNA have been investigated. In this article, we will try to summarise this progress, pointing out the scope of the various experimental techniques used to study DNA structure, and, where possible, trying to discern the rules which govern the behaviour of this subtle macromolecule. The article is divided into six major sections which begin with a general discussion of DNA structure and then present successively, B-DNA, DNA deformations, A-DNA, Z-DNA and DNARNA hybrids. An extensive set of references is included and should serve the reader who wishes to delve into greater detai.
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Affiliation(s)
- B Hartmann
- Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Paris, France
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23
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Swanson PC, Ackroyd C, Glick GD. Ligand recognition by anti-DNA autoantibodies. Affinity, specificity, and mode of binding. Biochemistry 1996; 35:1624-33. [PMID: 8634294 DOI: 10.1021/bi9516788] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Understanding the molecular basis of DNA recognition by anti-DNA autoantibodies is a key element in defining the role of antibody.DNA complexes in the pathogenesis of the autoimmune disorder systemic lupus erythematosus. As part of our efforts to relate anti-DNA affinity and specificity to antibody structure, and ultimately to disease pathogenesis, we have generated a panel of eight anti-DNA mAbs from an autoimmune MRL MpJ-lpr/lpr mouse and have assessed the binding properties of these antibodies. We find that none of our anti-DNA mAbs bind to RNA and only one low-affinity mAb cross-reacts with non-DNA antigens, albeit weakly. None of the mAbs in our panel bind double-stranded DNA exclusively. Antibodies that recognize single-stranded DNA can be categorized into two groups based on their affinity and apparent mode of binding. One group possesses relatively high affinity for oligo(dT) and may recognize single-stranded DNA ligands by accommodating thymine bases in hydrophobic pockets on the antigen binding site. The second group binds more weakly, apparently recognizes single-stranded DNA nonspecifically, and in some cases also binds double-stranded DNA. Although different mechanisms are used for binding single- and double-stranded ligands, the mode of DNA recognition appears conserved within groups of antibodies.
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Affiliation(s)
- P C Swanson
- Department of Chemistry, University of Michigan, Ann Arbor 48109-1055, USA
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24
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Džakula Ž, DeRider ML, Markley JL. Conformational Analysis of Molecules with Five-Membered Rings through NMR Determination of the Continuous Probability Distribution (CUPID) for Pseudorotation. J Am Chem Soc 1996. [DOI: 10.1021/ja962160+] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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25
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Berman HM, Gelbin A, Westbrook J. Nucleic acid crystallography: a view from the nucleic acid database. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1996; 66:255-88. [PMID: 9284453 DOI: 10.1016/s0079-6107(97)00019-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
What are the future directions of the field of nucleic acid crystallography? Although there have been many duplex structures determined, the sample is still relatively small. This is especially true if one wants to derive enough information about the relationships between sequence and structure. Indeed, there are data for all the possible 10 dimer steps, but for some steps it is very limited. If the structural code resides in trimers or tetrad steps then there is simply not enough data to do meaningful statistical analyses. So the first direction that needs to be explored is the determination of more structures with more varied sequences. The other noticeable thing about the data is the shortness of the strands. While it is probably true that attempts to crystallize very long sequences will not meet with success, the idea of crystallizing sequences engineered to fit together via sticky ends such as has been done for the CAP-DNA complex (Schultz et al., 1990) should give data about the behavior of much longer stretches of DNA. The question of the effects of environment on the structure of DNA continues to be a very important one to address since DNA is rarely alone. The preliminary data we have analysed from the current sample shows that the conformation of some steps are very sensitive to packing type. Numerous studies of the hydration around DNA shows that there is a real synergy between the hydration structure and the base conformation. More data will allow further quantitation of these observations. RNA structure is the next very exciting frontier. The emerging structures of duplexes with internal loops, the two hammerhead ribozyme structures and the group I intron ribozyme have given us a glimpse of the complexity and elegance of this class of molecules. With the technology now in place to allow the determination of the structures of these molecules, the expectation is that now we will see a large increase in the number of these structures in the NDB.
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Affiliation(s)
- H M Berman
- Department of Chemistry, Rutgers University, Piscataway, NJ 08855-0939, USA
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26
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Lewis JP, Sankey OF. Geometry and energetics of DNA basepairs and triplets from first principles quantum molecular relaxations. Biophys J 1995; 69:1068-76. [PMID: 8519960 PMCID: PMC1236334 DOI: 10.1016/s0006-3495(95)79980-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A first principles model for calculating hydrogen bonding interactions, previously applied to water, is here applied to the more difficult problem of interactions between DNA bases. We first consider the energetics and geometry for the A-T and the G-C basepairs, comparing our results to other calculated results as well as to experiment. Next, we study the interactions of isomorphic DNA base triplet structures, which are important because of their suggested role in the recombination process. We find that energetically the third base in the triplet tends to favor a position along the dyadic axis, where it is hydrogen bonded to both bases in the duplex.
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Affiliation(s)
- J P Lewis
- Department of Physics and Astronomy, Arizona State University, Tempe 85287-1504, USA
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27
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Holmes RR, Deiters JA, Gallucci JC. COMPUTER SIMULATION OF RIBONUCLEASE ACTION ON URIDYLYL-(3′-5′)-ADENOSINE. PHOSPHORUS SULFUR 1995. [DOI: 10.1080/10426509508036948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Robert R. Holmes
- a Contribution from the Department of Chemistry , University of Massachusetts , Amherst , Massachusetts , 01003
| | - Joan A. Deiters
- a Contribution from the Department of Chemistry , University of Massachusetts , Amherst , Massachusetts , 01003
| | - Judith C. Gallucci
- a Contribution from the Department of Chemistry , University of Massachusetts , Amherst , Massachusetts , 01003
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28
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Affiliation(s)
- N B Ulyanov
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco 94143, USA
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29
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Eilat D, Anderson WF. Structure-function correlates of autoantibodies to nucleic acids. Lessons from immunochemical, genetic and structural studies. Mol Immunol 1994; 31:1377-90. [PMID: 7529877 DOI: 10.1016/0161-5890(94)90154-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Nucleic acid binding autoantibodies are the hallmark of the human autoimmune disease, systemic lupus erythematosus (SLE) and are also prevalent in mouse models of this disease. The immunologic stimuli for the production of these antibodies as well as their pathogenic mechanisms are not well understood. However, extensive immunochemical and genetic studies, together with initial crystallographic analysis and computer modeling, have suggested several structure-function correlates which will form the basis for future research. The anti-DNA and anti-RNA autoantibodies comprise a continuous spectrum of specificities in which a delicate balance exists between the binding to the sugar-phosphate backbone and the interactions with the heterocyclic bases of the nucleic acid. Prominent in these interactions are the products of specific V-region immunoglobulin genes, some of which appear to be uniquely suitable for nucleic acid binding. Other structural elements encoded by D minigenes, N sequences and somatic mutations, help to increase the affinity of the binding interaction, and may also increase the repertoire of nucleic acid binding antibodies by combining with a relatively large number of additional V-gene products. Initial crystallographic analyses of anti-DNA antibodies indicate some fundamental differences in the structure and shape of ssDNA and dsDNA antibody combining sites. However, they also suggest a considerable degree of flexibility of both antibody and antigen, which is induced by their binding interaction.
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Affiliation(s)
- D Eilat
- Clinical Immunology Unit, Hadassah University Hospital, Jerusalem, Israel
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30
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Peterson CA, Gray DM, Gray HB, Legerski RJ. Evidence for a salt-induced conformational transition in UV-irradiated superhelical PM2 DNA. BIOCHIMICA ET BIOPHYSICA ACTA 1993; 1216:265-72. [PMID: 8241267 DOI: 10.1016/0167-4781(93)90153-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Upon treatment with UV irradiation, native (supercoiled) PM2 DNA undergoes an increase in electrophoretic mobility relative to the nicked circular form in the presence of 1 M NaCl or 5 mM CaCl2 or MgCl2. This effect is dependent upon supercoiling in that the relative electrophoretic mobility decreases with decreasing superhelical density of the molecule. These findings indicate that supercoil-dependent aspects of the secondary and tertiary structure of nonirradiated PM2 DNA can be altered by a combination of UV irradiation and any of the ionic environments above. We show that the alteration is not the result of a conversion of Z-DNA segments to a right-handed helix or to a renaturation of denatured regions in PM2 DNA. Circular dichroism studies do not support a simple model in which A-form DNA induced by superhelical stress is converted to B-form DNA by UV-induced photodamage and salt. We, therefore, present three alternative explanations for these observations two of which invoke conformational transitions in secondary structure and a third which requires a change in tertiary structure due to an increase in flexibility.
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Affiliation(s)
- C A Peterson
- Department of Molecular Genetics, University of Texas M.D. Anderson Cancer Center, Houston 77030
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31
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Eschenmoser A, Dobler M. Warum Pentose- und nicht Hexose-Nucleins�uren?? Teil I. Einleitung und Problemstellung, Konformationsanalyse f�r Oligonucleotid-Ketten aus 2?,3?-Dideoxyglucopyranosyl-Bausteinen (?Homo-DNS?) sowie Betrachtungen zur Konformation von A- und B-DNS. Helv Chim Acta 1992. [DOI: 10.1002/hlca.19920750120] [Citation(s) in RCA: 132] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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32
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Hall KB, McLaughlin LW. Thermodynamic and structural properties of pentamer DNA.DNA, RNA.RNA, and DNA.RNA duplexes of identical sequence. Biochemistry 1991; 30:10606-13. [PMID: 1931983 DOI: 10.1021/bi00108a002] [Citation(s) in RCA: 96] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Four pentamers with the general sequence 5'CU(T)GU(T)G/5'CACAG have been prepared by chemical synthesis in order to generate duplex structures with common sequences. The four duplexes studied include the DNA.DNA duplex (5'dCACAG/5'dCTGTG) and the RNA.RNA duplex (5'rCUGUG/5'rCACAG) as well as the two corresponding DNA.RNA heteroduplexes (5'rCUGUG/5'dCACAG and 5'CACAG/5'dCTGTG). The measured entropy, enthalpy, and free energy changes upon melting are reported for each pentamer and compared to the predicted values where possible. Results show that the two DNA.RNA heteroduplexes are destabilized (delta G degrees 25 = -4.2 +/- 0.4 kcal/mol) relative to either the DNA.DNA duplex (delta G degrees 25 = -4.8 +/- 0.5 kcal/mol) or the RNA.RNA duplex (delta G degrees 25 = -5.8 +/- 0.6 kcal/mol). Circular dichroism spectra indicate that the RNA and the two heteroduplexes adopt an A-form conformation, while the DNA conformation is B-form. Imino proton NMR spectra also show that the heteroduplex structures resemble the RNA.RNA duplex.
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Affiliation(s)
- K B Hall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis 63110
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33
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Benedetti G, Morosetti S. Three-dimensional folding of Tetrahymena thermophila rRNA IVS sequence: a proposal. J Biomol Struct Dyn 1991; 8:1045-55. [PMID: 1715170 DOI: 10.1080/07391102.1991.10507864] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We studied the Tetrahymena thermophila rRNA IVS sequence with the aim of obtaining a model of the structure characterized by the bases proximity of the self-reactions sites. The considered sequence kept up those fragments essential for its catalytic activity as demonstrated by deletion mutants. The first step was the theoretical analysis with a computer method previously proposed, to find optimal free energy secondary structures with the required features, under the suitable constrains. Then we tried folding the obtained secondary structures, in low resolution tertiary models, which kept up the proximity of the catalytic sites also in the space. The proposed tertiary folding seems to provide for a better explanation to the transesterification mechanisms and moreover it is in good agreement with the experimental data (activity of mutants, enzymatic cleavages, phylogenetically conserved regions).
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Affiliation(s)
- G Benedetti
- Department of Chemistry, University of Rome I, Italy
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34
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van Amerongen H, Kuil ME, Scheerhagen MA, van Grondelle R. Structure calculations for single-stranded DNA complexed with the single-stranded DNA binding protein GP32 of bacteriophage T4: a remarkable DNA structure. Biochemistry 1990; 29:5619-25. [PMID: 2386789 DOI: 10.1021/bi00475a029] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In this study it is established by calculation which regular conformations single-stranded DNA and RNA can adopt in the complex with the single-stranded DNA binding protein GP32 of bacteriophage T4. In order to do so, information from previous experiments about base orientations and the length and diameter of the complexes is used together with knowledge about bond lengths and valence angles between chemical bonds. It turns out that there is only a limited set of similar conformations which are in agreement with experimental data. The arrangement of neighboring bases is such that there is ample space for aromatic residues of the protein to partly intercalate between the bases, which is in agreement with a previously proposed model for the binding domain of the protein [Prigodich, R. V., Shamoo, Y., Williams, K. R., Chase, J. W., Konigsberg, W. H., & Coleman, J. E. (1986) Biochemistry 25, 3666-3671]. Both C2'endo and C3'endo sugar conformations lead to calculated DNA conformations that are consistent with experimental data. The orientation of the O2' atoms of the sugars in RNA can explain why the binding affinity of GP32 for polyribonucleotides is lower than for polydeoxyribonucleotides.
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Affiliation(s)
- H van Amerongen
- Department of Physics and Astronomy, Free University, Amsterdam, The Netherlands
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35
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Abstract
Bulge loops are commonly found in helical segments of cellular RNAs. When incorporated into long double-stranded RNAs, they may introduce points of flexibility or permanent bend that can be detected by the altered electrophoretic gel mobility of the RNA. We find that a single An or Un bulge loop near the middle of a long RNA helix significantly retards the RNA during polyacrylamide gel electrophoresis if n greater than or equal to 2. The mobility of an RNA containing two A2 bulges various periodically with the number of base pairs between the bulges. We interpret this to mean that A2 bulges varies periodically with the number of base pairs between the bulges. We interpret this to mean that Z2 bulges form torsionally stiff bends in the helix; the gel mobility reaches a minimum when the total helical twist between the bulges rotates the arms of the molecule into a cis conformation. The gel mobilities are proportional to the predicted end-to-end distance of the RNA if the average RNA helical repeat is 11.8 +/- 0.2 bp/turn and there is no helical twist (3 +/- 9 degrees) associated with the bulge (data obtained in 0.15 M Na+). Other sizes and sequences of bulges have very different effects on RNA helix conformation and flexibility. U2 bulges bend the helix to a much smaller degree than A2 bulges, while longer A or U bulge sequences probably allow bends of 90 degrees or more; all of these may be fairly flexible joints.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- R S Tang
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218
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36
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Il'ychova IA, Lysov YuP, Chernyi AA, Shchyolkina AK, Gottikh BP, Florentiev VA. Parallel double helices of DNA. Conformational analysis of regular helices with the second order symmetry axis. J Biomol Struct Dyn 1990; 7:879-97. [PMID: 2310521 DOI: 10.1080/07391102.1990.10508530] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We have performed a conformational analysis of DNA double helices with parallel directed backbone strands connected with the second order symmetry axis being at the same time the helix axis. The calculations were made for homopolymers poly(dA).poly(dA), poly(dC).poly(dC), poly(dG) poly(dG), and poly(dT).poly(dT). All possible variants of hydrogen bonding of base pairs of the same name were studied for each polymer. The maps of backbone chain geometrical existence were constructed. Conformational and helical parameters corresponding to local minima of conformational energy of "parallel" DNA helices, calculated at atom-atom approximation, were determined. The dependence of conformational energy on the base pair and on the hydrogen bond type was analysed. Two major conformational advantageous for "parallel" DNA's do not depend much on the hydrogen-bonded base pair type were indicated. One of them coincided with the conformational region typical for "antiparallel" DNA, in particular for the B-form DNA. Conformational energy of "parallel" DNA depends on the base pair type and for the most part is similar to the conformational energy of "antiparallel" B-DNA.
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Affiliation(s)
- I A Il'ychova
- V.A. Engelhard Institute of Molecular Biology, USSR Academy of Sciences, Moscow
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37
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van Amerongen H, van Grondelle R. Orientation of the bases of single-stranded DNA and polynucleotides in complexes formed with the gene 32 protein of bacteriophage T4. A linear dichroism study. J Mol Biol 1989; 209:433-45. [PMID: 2585494 DOI: 10.1016/0022-2836(89)90008-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Linear dichroism measurements were performed in the wavelength region 250 to 350 nm on complexes between the single-stranded DNA binding protein of bacteriophage T4 (gp32) and single-stranded DNA and a variety of homopolynucleotides in compressed polyacrylamide gels. The complexes appeared to orient well, giving rise to linear dichroism spectra that showed contributions from both the protein aromatic residues and the bases of the polynucleotides. In most cases the protein contribution appeared to be very similar, and the linear dichroism of the bases could be explained by similar orientations of the bases for most of the complexes. Assuming a similar, regular structure for most of the polynucleotides in complex, only a limited set of combinations of tilt and twist angles can explain the linear dichroism spectra. These values of tilt and twist are close to (-40 degrees, 30 degrees), (-40 degrees, 150 degrees), (40 degrees, -30 degrees) or (40 degrees, -150 degrees), with an uncertainty in both angles of about 15 degrees. Although the linear dichroism results do not allow a choice between these possible orientations, the latter two combinations are not in agreement with earlier circular dichroism calculations. For the complexes formed with poly(rC) and poly(rA), the linear dichroism spectra could not be explained by the same base orientations. In these two cases also the protein contribution to the linear dichroism appeared to be different, indicating that for some aromatic residues the orientations are not the same as those in the other complexes. The different structures of these complexes are possibly related to the relatively low binding affinity of gp32 to poly(rC), and to a lesser extent to poly(rA).
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Affiliation(s)
- H van Amerongen
- Department of Biophysics, Free University, Amsterdam, The Netherlands
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38
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Teplukhin AV, Poltev VI, Shulyupina NV, Malenkov GG. Monte Carlo simulation of hydration of the nucleic acid fragments. J Biomol Struct Dyn 1989; 7:75-99. [PMID: 2818872 DOI: 10.1080/07391102.1989.10507753] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Systems containing a base or a base pair and 25 water molecules, as well as a helical stack and 30 water molecules per base pair, have been simulated. Changes in the base hydration shell structure, after the bases have been included into the pair and then into the base pair stack, are discussed. Hydration shells of several configurations of the base pair stacks are discussed. Probabilities of formation of the hydrogen-bonded bridges of 1, 2 and 3 water molecules between hydrophilic centres have been estimated. The hydration shell structure was shown to depend on the nature of the base pair and on the stack configuration, while dependence of the global hydration shell characteristics on the stack configuration has been proved to be rather slight. The most typical structural elements of hydration shells, in the glycosidic (minor in B-like conformation) and non-glycosidic (major) grooves, for different configurations of AU and GC stacks, have been found and discussed. The number of hydrogen bonds between water molecules and bases per water molecule was shown to change upon transformation of the stack from A to B configuration. This result is discussed in connection with the reasons for B to A conformational transition and the concept of "water economy". Hydration shell patterns of NH2-groups of AU and GC helical stacks differ significantly.
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Affiliation(s)
- A V Teplukhin
- Research Computing Centre, USSR Academy of Sciences, Pushchino, MoscowRegion
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39
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Abstract
Double-stranded (ds) RNA and many viruses are inducers of interferon (IFN), the latter presumably because they contain, or can form, dsRNA. Concomitant with the induction of IFN in chicken embryo cells was the induction of a novel double-stranded ribonuclease (dsRNase), which was released into the medium and continued to accumulate long after IFN production ceased. Only avian cells (chicken, quail, turkey, or duck) expressed high levels of this dsRNase; mammalian, turtle, or fish cells did not. Production of the nuclease was inducer dose-dependent. Optimum pH and cation requirements distinguished it from other dsRNase activities. Degradation of dsRNA was endonucleolytic. Activity resided in a molecule of an Mr of approximately 34,500. Low levels of a single-stranded (ss) RNase activity were inseparable from the dsRNase. The role for a dsRNA-inducible dsRNase released from cells is unknown.
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Affiliation(s)
- J M Meegan
- Department of Molecular and Cell Biology, The University of Connecticut, Storrs 06269
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Lavery R, Sklenar H. Defining the structure of irregular nucleic acids: conventions and principles. J Biomol Struct Dyn 1989; 6:655-67. [PMID: 2619933 DOI: 10.1080/07391102.1989.10507728] [Citation(s) in RCA: 596] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The algorithm "Curves", that we have recently presented in this journal (J. Biolmol. Str. Dynam. 6, 63-91 (1988], is updated to take into account the conventions developed at the Cambridge meeting on DNA curvature (September 1988) and extended to the calculation of local parameters. In addition, the principles which govern the choices made in establishing the Curves algorithm are compared with the approaches adopted by other authors.
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Affiliation(s)
- R Lavery
- Institut de Biologie Physico-Chimique, Paris, France
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Gekko K, Sakaki T, Shindo H. Preferential Hydration and B–A Transition of Deoxyribonucleic Acid in Ethanol–Water Mixtures. Polym J 1988. [DOI: 10.1295/polymj.20.751] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Lavery R, Sklenar H. The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J Biomol Struct Dyn 1988; 6:63-91. [PMID: 2482765 DOI: 10.1080/07391102.1988.10506483] [Citation(s) in RCA: 783] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
An algorithm is presented which solves the problem of obtaining a rigorous helicoidal description of an irregular nucleic acid segment. Central to this approach is the definition of a function describing simultaneously the curvature of the nucleic acid segment in question and the corresponding stepwise variation of helicoidal parameters along the segment. Minimisation of this function leads to an optimal distribution of the conformational irregularity of the segment between these two components. Further, it is shown that this approach can be applied equally easily to single or double stranded nucleic acids. The results of this analysis yield both the absolute helicoidal parameters of individual bases/base pairs and the relative helicoidal parameters between successive bases/base pairs as well as the overall locus of the helical axis. The possibilities of this mathematical approach are demonstrated with the help of a computer program termed "Curves" which is applied to the study of a number of different nucleic acid structures.
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Affiliation(s)
- R Lavery
- Institut de Biologie Physico-Chimique, Paris, France
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Brimacombe R, Atmadja J, Stiege W, Schüler D. A detailed model of the three-dimensional structure of Escherichia coli 16 S ribosomal RNA in situ in the 30 S subunit. J Mol Biol 1988; 199:115-36. [PMID: 2451022 DOI: 10.1016/0022-2836(88)90383-x] [Citation(s) in RCA: 240] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A large body of intra-RNA and RNA-protein crosslinking data, obtained in this laboratory, was used to fold the phylogenetically and experimentally established secondary structure of Escherichia coli 16 S RNA into a three-dimensional model. All the crosslinks were induced in intact 30 S subunits (or in some cases in growing E. coli cells), and the sites of crosslinking were precisely localized on the RNA by oligonucleotide analysis. The RNA-protein crosslinking data (including 28 sites, and involving 13 of the 21 30S ribosomal were used to relate the RNA structure to the distribution of the proteins as determined by neutron scattering. The three-dimensional model of the 16 S RNA has overall dimensions of 220 A x 140 A x 90 A, in good agreement with electron microscopic estimates for the 30 S subunit. The shape of the model is also recognizably the same as that seen in electron micrographs, and the positions in the model of bases localized on the 30 S subunit by immunoelectron microscopy (the 5' and 3' termini, the m7G and m6(2)A residues, and C-1400) correspond closely to their experimentally observed positions. The distances between the RNA-protein crosslink sites in the model correlate well with the distances between protein centres of mass obtained by neutron scattering, only two out of 66 distances falling outside the expected tolerance limits. These two distances both involve protein S13, a protein noted for its anomalous behaviour. A comparison with other experimental information not specifically used in deriving the model shows that it fits well with published data on RNA-protein binding sites, mutation sites on the RNA causing resistance to antibiotics, tertiary interactions in the RNA, and a potential secondary structural "switch". Of the sites on 16 S RNA that have been found to be accessible to chemical modification in the 30 S subunit, 87% are at obviously exposed positions in the model. In contrast, 70% of the sites corresponding to positions that have ribose 2'-O-methylations in the eukaryotic 18 S RNA from Xenopus laevis are at non-exposed (i.e. internal) positions in the model. All nine of the modified bases in the E. coli 16 S RNA itself show a remarkable distribution, in that they form a "necklace" in one plane around the "throat" of the subunit. Insertions in eukaryotic 18 S RNA, and corresponding deletions in chloroplast or mammalian mitochondrial ribosomal RNA relative to E. coli 16 S RNA represent distinct sub-domains in the structure.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- R Brimacombe
- Max-Planck-Institut für Molekulare Genetik, Abteilung Wittmann, Berlin-Dahlem, Germany
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Basu AK, Niedernhofer LJ, Essigmann JM. Deoxyhexanucleotide containing a vinyl chloride induced DNA lesion, 1,N6-ethenoadenine: synthesis, physical characterization, and incorporation into a duplex bacteriophage M13 genome as part of an amber codon. Biochemistry 1987; 26:5626-35. [PMID: 3314993 DOI: 10.1021/bi00392a007] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Organic synthesis and recombinant DNA techniques have been used to situate a single 1,N6-ethenoadenine (epsilon Ade) DNA adduct at an amber codon in the genome of an M13mp19 phage derivative. The deoxyhexanucleotide d[GCT(epsilon A)GC] was chemically synthesized by the phosphotriester method. Mild nonaqueous conditions were employed for deprotection because of the unstable nature of the epsilon Ade adduct in aqueous basic milieu. Physical studies involving fluorescence, circular dichroism, and 1H NMR indicated epsilon Ade to be very efficiently stacked in the hexamer, especially with the 5'-thymine. Melting profile and circular dichroism studies provided evidence of the loss of base-pairing capabilities attendant with formation of the etheno ring. The modified hexanucleotide was incorporated into a six-base gap formed in the genome of an M13mp19 insertion mutant; the latter was constructed by blunt-end ligation of d(GCTAGC) in the center of the unique SmaI site of M13mp19. Phage of the insertion mutant, M13mp19-NheI, produced light blue plaques on SupE strains because of the introduced amber codon. Formation of a hybrid between the single-strand DNA (plus strand) of M13mp19-NheI with SmaI-linearized M13mp19 replicative form produced a heteroduplex with a six-base gap in the minus strand. The modified hexamer [5'-32P]d-[GCT(epsilon A)GC], after 5'-phosphorylation, was ligated into this gap by using bacteriophage T4 DNA ligase to generate a singly adducted genome with epsilon Ade at minus strand position 6274. Introduction of the radiolabel provided a useful marker for characterization of the singly adducted genome, and indeed the label appeared in the anticipated fragments when digested by several restriction endonucleases. Evidence that ligation occurred on both 5' and 3' sides of the oligonucleotide also was obtained. The adduct was introduced into a unique NheI site, and it was observed that this restriction endonuclease was able to cleave the adducted genome, albeit at a lower rate compared to unmodified DNA. The M13mp19-NheI genome containing epsilon Ade will be used as a probe for studying mutagenesis and repair of this DNA adduct in Escherichia coli.
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Affiliation(s)
- A K Basu
- Department of Applied Biological Sciences, Massachusetts Institute of Technology, Cambridge 02139
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Lewis DF, Griffiths VS. Molecular electrostatic potential energies and methylation of DNA bases: a molecular orbital-generated quantitative structure-activity relationship. Xenobiotica 1987; 17:769-76. [PMID: 3630211 DOI: 10.3109/00498258709043984] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
1. The results of molecular orbital (MO) calculations, by the MINDO/3 method, on DNA bases, are reported; which point to a radical mechanism of alkylation. 2. Molecular electrostatic potential energy maps indicate propensity for alkylation by N-methyl-N-nitrosourea at key atoms on DNA bases. 3. A correlation between the MO-derived parameters net atomic charges on heteroatoms and superdelocalizability with percentage alkylation by N-methyl-N-nitrosourea is shown.
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Chuprina VP. Anomalous structure and properties of poly (dA).poly(dT). Computer simulation of the polynucleotide structure with the spine of hydration in the minor groove. Nucleic Acids Res 1987; 15:293-311. [PMID: 3822805 PMCID: PMC340411 DOI: 10.1093/nar/15.1.293] [Citation(s) in RCA: 100] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The results of the search for low-energy conformations of poly(dA).poly(dT) and of the poly(dA).poly(dT) "complex" with the spine of hydration similar to that found by Dickerson and co-workers (Kopka, M.L., Fratini, A.V., Drew, H.R. and Dickerson, R.E. (1983) J. Mol. Biol. 163, 129-146) in the minor groove of the CGCGAATTCGCG crystals are described. It is shown that the existence of such a spine in the minor groove of poly(dA).poly(dT) is energetically favourable. Moreover, the spine of hydration makes the polynucleotide conformation similar to the poly(dA).poly(dT) structure in fibers and to the conformation of the central part of CGCGAATTCGCG in crystals; it also acquires features characteristic of the structure of poly(dA).poly(dT) and DNA oligo(dA)-tracts in solution. It is shown that the existence of the TpA step in conformations characteristic of the poly(dA).poly(dT) complex with the spine of hydration is energetically unfavourable (in contrast to the ApT step) and therefore this step should result in destabilization of the spine of hydration in the DNA minor groove. Thus, it appears that the spine of hydration as described by Dickerson and co-workers is unlikely to exist in the poly d(A-T).poly d(A-T) structure. The data obtained permit us to interpret a large body of experimental facts concerning the unusual structure and properties of poly(dA).poly(dT) and oligo(dA)-tracts in DNA both in fibers and in solution. The results provide evidence of the existence of the minor groove spine of hydration both in fibers and in solution on A/T tracts of DNA which do not contain the TpA step. The spine plays an active role in the formation of the anomalous conformation of these tracts.
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Abstract
Can we make any generalizations from examination of the crystal structures in hand? The results of study of the very well-determined high-resolution structures indicate that the counterions have a very strong effect on organizing the water structure and that these counterions are bonded in a sequence-specific manner. Hence, the sodium ion bonds in the minor groove of ApU and only to the phosphate backbone in GpC. Not surprisingly then, the water network in ApU is predominantly in its minor groove. Similarly, the negative sulfate counterion in the major groove of the 3:2 complex between proflavine and CpG has a significant influence on the water structure in that crystal. The crystallization of two positive proflavine molecules with two negative nucleic acid chains obviates the need for inorganic ions and may provide additional insight about nucleic acid water structure. The presence of the charged aromatic hydrocarbon appears to provide the correct mixture of hydrophilicity and hydrophobicity that allows for both the gathering and ordering of water molecules around the nucleic acid molecule, not unlike what was previously observed in the semiclathrate structures. This same type of hydrophobic aggregation might pertain along the major groove side of structures containing the appropriate arrangement of methyl-containing thymine bases. Although it is very tempting at this point to make further rules and predictions, experience has shown that, especially in the case of nucleic acids, such prognostications would be premature. What is clearly needed are some more high-quality crystal structures of a variety of sequences under different and controlled conditions. Analyses of these may then put us in a position to successfully predict both the structure of water and its effects on nucleic acid conformation.
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Sklenar H, Lavery R, Pullman B. The flexibility of the nucleic acids: (I). "SIR", a novel approach to the variation of polymer geometry in constrained systems. J Biomol Struct Dyn 1986; 3:967-87. [PMID: 3271421 DOI: 10.1080/07391102.1986.10508477] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A novel and powerful methodology is developed which allows the alteration of molecular structures subjected to constraints and its application to polynucleotides with mononucleotide repeat symmetry, including the treatment of the flexible sugar rings is described. In contrast to procedures proposed by other authors, the constraints are formulated as differential equations which are linear with respect to the differentials of the geometrical variables. These equations can be solved easily by stepwise numerical integration involving sucessive infinitesimal rotations (SIR). Moreover, these equations define a set of independent curvilinear coordinates which can be used directly as the parameters of the energy functional in an energy minimisation procedure. This methodology allows the scanning of the full configurational space of a complex macromolecule, with direct access to the helicoidal variables in the case of periodic systems. Through this approach many problems involving biomacromolecular conformation, which would otherwise be intractable, may be studied with considerable ease.
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Affiliation(s)
- H Sklenar
- Central Institute of Molecular Biology, Academy of Sciences of the GDR, Berlin-Buch
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Anukanth A, Ponnuswamy PK. 2'5'-linked polynucleotides do form a double-stranded helical structure: a result from the energy minimization study of A2'p5'A. Biopolymers 1986; 25:729-52. [PMID: 3708111 DOI: 10.1002/bip.360250414] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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