Base-pair exchange kinetics of the imino and amino protons of the 3′-phenazinium tethered DNA-RNA duplex,r(5′GAUUGAA3′):d(5′TCAATC3′-Pzn), and their comparison with those of B-DNA duplex

The dynamics of the opening-closing of the constituent base-pairs as well as of the exchange kinetics of the base-paired imino and amino protons with water in a DNA-RNA hybrid, [^5′r(G¹A²U³U⁴G⁵A⁶A⁷)^3′]:^5′p[d(T⁸C⁹A¹⁰A¹¹T¹²C¹³)]^3′-Pzn] duplex (I), are reported here in details for the first time. The exchange kinetics of amino and imino protons in the DNA-RNA hybrid (duplex I) have been compared with identical studies on the following B-DNA duplexes: d(C¹G²T³A⁴C⁵G⁶)₂ (II), d[p(^5′T¹G²T³T⁴T⁵G⁶ G⁷C⁸)^3′]:d[p(^5′C⁹C¹⁰A¹¹A¹²A¹³C¹⁴A¹⁵)^3′] (III), d(C⁵G⁶C⁷G⁸A⁹A¹⁰T¹¹T¹²C¹³G¹⁴C¹⁵G¹⁶)₂ (IV) and d(C¹G²C³G⁴C⁵G⁶C⁷G⁸A⁹A¹⁰T¹¹T¹²C¹³G¹⁴C¹⁵G¹⁶C¹⁷G¹⁸C¹⁹G²⁰)₂ (V). This comparative study shows that the life-times τ_o of various base-pairs in the DNA-RNA hybrid (I) varies in the range of ∼ 1 ms, and they are quite comparable to those of the shorter B-DNA duplexes (II) and (III), but very different from the τ_o of the larger duplexes (IV) and (V): the τ_o for the base pair of T¹¹ and T¹² residues in the 20-mer (duplex V) are 2.9 ± 2.3 ms and 23.2 ± 8.9 ms, respectively, while the corresponding τ_o in the 12-mer (duplex IV) are 2.8 ± 2.2 ms and 17.4 ± 5.4 ms. It has also been shown that the total energy of activation (E_a) assessed from the exchange rates of both imino and amino protons, representing energetic contributions from both base-pair and helix opening-closing as well as from the exchange process of the imino protons from the open state with the bound water, is close to the E_a of the short B-DNA duplex (E_a ≈ 28–47 kcal/mol).     

The First Example of a Hoogsteen Basepaired DNA Duplex in Dynamic Equilibrium with a Watson-Crick Basepaired Duplex—A Structural (NMR), Kinetic and Thermodynamic Study

Abstract

A single-point substitution of the O4′ oxygen by a CH₂ group at the sugar residue of A ⁶ (i.e. 2′-deoxyaristeromycin moiety) in a self-complementary DNA duplex, 5′- d(C¹G²C³G⁴A⁵A⁶T⁷T⁸C⁹G¹⁰C¹¹G¹²)₂ ^?3, has been shown to steer the fully Watson-Crick basepaired DNA duplex (1A), akin to the native counterpart, to a doubly A ⁶:T⁷ Hoogsteen basepaired (1B) B-type DNA duplex, resulting in a dynamic equilibrium of (1A)→←(1B): K_eq = k₁/k_-1 = 0.56±0.08. The dynamic conversion of the fully Watson-Crick basepaired (1A) to the partly Hoogsteen basepaired (1B) structure is marginally kinetically and thermodynamically disfavoured [k₁ (298K) = 3.9± 0.8 sec^?1; δH°? = 164±14 kJ/mol;-TδS°? (298K) = ?92 kJ/mol giving a δG₂₉₈°? of 72 kJ/mol. Ea (k1) = 167±14 kJ/mol] compared to the reverse conversion of the Hoogsteen (1B) to the Watson-Crick (1A) structure [k-1 (298K) = 7.0±0.6 sec-1, δH°? = 153±13 kJ/mol;-TδS°? (298K) = ?82 kJ/mol giving a δG₂₉₈°? of 71 kJ/mol. Ea (k-1) = 155±13 kJ/mol]. A comparison of δG₂₉₈°? of the forward (k1) and backward (k-1) conversions, (1A)→←(1B), shows that there is ca 1 kJ/mol preference for the Watson-Crick (1A) over the double Hoogsteen basepaired (1B) DNA duplex, thus giving an equilibrium ratio of almost 2:1 in favour of the fully Watson-Crick basepaired duplex. The chemical environments of the two interconverting DNA duplexes are very different as evident from their widely separated sets of chemical shifts connected by temperature-dependent exchange peaks in the NOESY and ROESY spectra. The fully Watson-Crick basepaired structure (1A) is based on a total of 127 intra, 97 inter and 17 cross-strand distance constraints per strand, whereas the double A ⁶:T⁷ Hoogsteen basepaired (1B) structure is based on 114 intra, 92 inter and 15 cross-strand distance constraints, giving an average of 22 and 20 NOE distance constraints per residue and strand, respectively. In addition, 55 NMR-derived backbone dihedral constraints per strand were used for both structures. The main effect of the Hoogsteen basepairs in (1B) on the overall structure is a narrowing of the minor groove and a corresponding widening of the major groove. The Hoogsteen basepairing at the central A ⁶:T⁷ basepairs in (1B) has enforced a syn conformation on the glycosyl torsion of the 2′- deoxyaristeromycin moiety, A ⁶, as a result of substitution of the endocyclic 4′-oxygen in the natural sugar with a methylene group in A ⁶. A comparison of the Watson-Crick basepaired duplex (1A) to the Hoogsteen basepaired duplex (1B) shows that only a few changes, mainly in α, σ and γ torsions, in the sugar-phosphate backbone seem to be necessary to accommodate the Hoogsteen basepair.     

The Residence Time of the Bound Water in the Hydrophobic Minor Groove of the Carbocyclic-Nucleoside Analogs of Dickerson-Drew Dodecamers

Summary

The residence time of the bound water molecules in the antisense oligodeoxyribonucleotides containing 7′-α-methyl (T_Me). carbocyclic thymidines in duplex (I), d⁵′(¹C²G³C⁴G⁵A⁶A⁷T_Mc ⁸T_Mc ⁹C¹⁰G¹¹C¹²G)₂ ³′, and 6′-a-hydroxy (T_OH) carbocyclic thymidines in duplex (II), d⁵′(¹C³G³C⁴G⁵A_OH ⁶ A_OH ⁷T_OH ⁸ T_OH ⁹C¹⁰G¹¹C¹²G)₂3, have been investigated using a combination of NOESY and ROESY experiments. Because of the presence of 7′-α-methyl groups of T_Me in the centre of the minor groove in duplex (I), the residence time of the bound water molecule is shorter than 0.3 ns. The dramatic reduction of the residence time of the water molecule in the minor groove in duplex (I) compared with the natural counterpart has been attributed to the replacement of second shell of hydration and disruption of hydrogen-bonding with 04′ in the minor groove by hydrophobic α-methyl groups, as originally observed in the X-ray study. This effect could not be attributed to the change of the width of the minor groove because a comparative NMR study of the duplex (I) and its natural counterpart showed that the widths of their minor grooves are more or less unchanged (r.m.s.d change in the core part is <0.63Å). For duplex (II) with polar 6′-α-hydroxyl groups pointed to the minor groove, the correlation time is much longer than 0.36ns as a result of the stabilising hydrogen-bonding interaction with N3 or 02 of the neighbouring nucleotides.     

Evidence for long-range interactions in DNA. Analysis of melting curves of block polymers d(C15A15)·d(T15G15), d(C20A15)·d(T15G20), and d(C20A10)·d(T10G20)

The influence of one DNA region on the stability of an adjoining region (telestability) was examined. Melting curves of three block DNA's, d(C₁₅A₁₅)·d(T₁₅G₁₅), d(C₂₀A₁₅)·d(T₁₅G₂₀), and d(C₂₀A₁₀)·d(T₁₀G₂₀) were analyzed in terms of the nearest neighbor Ising model. Comparisons of predicted and experimental curves were made in 0.01 M and 0.1 M sodium ion solutions. The nearest neighbor formalism was also employed to analyze block DNA transition in the presence of actinomycin, a G·C specific molecule. The results show that nearest neighbor base-pair interaction cannot predict the melting curves of the block DNA's. Adjustments in theoretical parameters to account for phosphate repulsion assuming a B conformation throughout the DNA's do not alter this conclusion. Changes in the theoretical parameters, which provide good overall agreement, are consistent with a substantial stabilization of the A·T region nearest the G·C block. The melting temperature T A·T for the average A·T pari in d(C₂₀A₁₀)·d(T₁₀G₂₀), with 10 A·T pairs, appears to be 4°C greater than T_A·T for d(C₁₅A₁₅)·d(T₁₅G₁₅) and d(C₂₀A₁₅)·d(T₁₅G₂₀), both with 15 A·T pairs. Actinomycin bound to the G·C end effectively stabilizes the A·T end by 9°C. These results indicate a long-range contribution to the interactions governing DNA stability. A possible mechanism for these interactions will be discussed.     

Molecular Dynamics Simulation of 7, 8-dihydro-8-Oxoguanine DNA

Abstract

To elucidate the effect of guanine lesion produced by the oxidative damage on DNA, 1 nanosecond molecular dynamics simulations of native and oxidized DNA were performed. The target DNA molecules are dodecamer duplex d(CGCGAATTCGCG)2 and its derivative duplex d(C₁G₂C₃(8-oxoG)₄A₅A₆T₇T₈C₉G₁₀C₁₁G₁₂)·d(C₁₃G₁₄C₁₅G₁₆A₁₇A₁₈T₁₉T₂₀C21_G22C₂₃G₂₄), which has one oxidized guanine, 7, 8-dihydro-8-oxoguanine (8-oxoG), at the fourth position. The local structural change due to the lesion of 8-oxoG and the global dynamic structure of the 8-oxoG DNA were studied. It was found that the 8-oxoG DNA remained structurally stable during the simulation due to newly produced hydrogen bonds around the (8-oxoG)₄ residue. However, there were distinguishable differences in structural parameters and dynamic property in the 8-oxoG DNA. The conformation around the (8- oxoG)₄ residue departed from the usual conformation of native DNA and took an unique conformation of ?-ζ in B_II conformation and χ in high anti orientation at the (8-oxoG)₄ residue, and adopted a very low helical twist angle at the C₃:G₂₂—(8-oxoG)₄:C₂₁ step. Further analysis by principal component analysis indicated that the formation of the hydrogen bonds around the (8-oxoG)₄ residue plays a role as a trigger for the conformational transition of the 8-oxoG DNA in the conformational space.     

Studies on formation and stability of the d[G(AG)5]* d[G(AG)5]·d[C(TC)5] and d[G(TG)5]* d[G(AG)5]· d[C(TC)5] triple helices

We have targeted the d[G(AG)₅] · d[C(TC)₅] duplex for triplex formation at neutral pH with either d[G(AG)₅] or d[G(TG)₅]. Using a combination of gel electrophoresis, uv and CD spectra, mixing and melting curves, along with DNase I digestion studies, we have investigated the stability of the 2:1 pur*pur · pyr triplex, d[G(AG)₅] * d[G(AG)₅] · d[C(TC)₅], in the presence of MgCl₂. This triplex melts in a monophasic fashion at the same temperature as the underlying duplex. Although the uv spectrum changes little upon binding of the second purine strand, the CD spectrum shows significant changes in the wavelength range 200–230 nm and about a 7 nm shift in the positive band near 270 nm. In contrast, the 1:1:1 pur/pyr*pur · pyr triplex, d[G(TG)₅] * d[G(AG)₅] · d[C(TC)₅], is considerably less stable thermally, melting at a much lower temperature than the underlying duplex, and possesses a CD spectrum that is entirely negative from 200 to 300 nm. Ethidium bromide undergoes a strong fluorescence enhancement upon binding to each of these triplexes, and significantly stabilizes the pur/pyr*pur · pyr triplex. The uv melting and differential scanning calorimetry analysis of the alternating sequence duplex and pur*pur · pyr triplex shows that they are lower in thermodynamic stability than the corresponding 10-mer d(G₃A₄G₃) · d(C₃T₄C₃) duplex and its pur*pur · pyr triplex under identical solution conditions. © 1997 John Wiley & Sons, Inc.     

Structure-specific binding of [Co(phen)2(HPIP)] to a DNA duplex containing sheared G:A mismatch base pairs

The binding of a Co(III) complex to the decanucleotide d(CCGAATGAGG)₂ containing two pairs of G:A mismatches was studied by 2D-NMR, UV absorption, and molecular modeling. NMR investigations indicate that racemic [Co(phen)₂(HPIP)]Cl₃ [HPIP = 2-(2-hydroxyphenyl) imidazo [4,5-f][1,10] phenanthroline] binds the decanucleotide by intercalation: the HPIP ligand selectively inserts between the stacked bases from the minor groove at the terminal regions and from the major groove at the sheared region. Further, molecular modeling revealed that the recognition shows strong enantioselectivity: the Λ-isomer preferentially intercalates into the T₆G₇:A₅A₄ region from the DNA major groove, while Δ-isomer favors the terminal C₁C₂:G₁₀G₉ region and intercalates from the minor groove. Detailed energy analysis suggests that the steric interaction, especially the electrostatic effect, is the primary determinants of the recognition event. Melting experiments indicate that binding stabilizes the DNA duplex and increases the melting temperature by 9.5 °C. The intrinsic binding constant of the complex to the mismatched duplex was determined to be 3.5 × 105 M⁻¹.     

Affinity and kinetic modulation of polyamide–DNA interactions by N‐modification of the heterocycles

Synthetic N‐methyl imidazole and N‐pyrrole containing polyamides (PAs) that can form “stacked” dimers can be programmed to target and bind to specific DNA sequences and control gene expression. To accomplish this goal, the development of PAs with lower molecular mass which allows for the molecules to rapidly penetrate cells and localize in the nucleus, along with increased water solubility, while maintaining DNA binding sequence specificity and high binding affinity is key. To meet these challenges, six novel f‐ImPy*Im PA derivatives that contain different orthogonally positioned moieties were designed to target 5′‐ACGCGT‐3′. The synthesis and biophysical characterization of six f‐ImPy*Im were determined by CD, ΔT_M, DNase I footprinting, SPR, and ITC studies, and were compared with those of their parent compound, f‐ImPyIm. The results gave evidence for the minor groove binding and selectivity of PAs 1 and 6 for the cognate sequence 5′‐ACGCGT‐3′, and with strong affinity, K_eq = 2.8 × 10⁸ M^?1 and K_eq = 6.2 × 10⁷ M^?1, respectively. The six novel PAs presented in this study demonstrated increased water solubility, while maintaining low molecular mass, sequence specificity, and binding affinity, addressing key issues in therapeutic development. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 497–507, 2013.     

INTERACTION OF PORPHYRIN WITH G-QUADRUPLEX STRUCTURES

Isothermal titration calorimetry (ITC) is a sensitive technique for probing bimolecular processes and can provide direct information about the binding affinity and stoichiometry and the key thermodynamic parameters involved. ITC has been used to investigate the interaction of the ligand H₂TMPyP to the two DNA quadruplexes, [d(AGGGT)]₄ and [d(TGGGGT)]₄. Analysis of the ITC data reveals that porphyrin/quadruplex binding stoichiometry under saturating conditions is 1:2 for [d(AGGGT)]₄ and 2:1 for [d(TGGGGT)]₄, respectively.     

A Single Carbocyclic Nucleotide Substitution in a 12mer DNA Gives a Hoogsteen Basepaired Duplex (Till 38°C) and a Hairpin (Till 65°C). A 600 MHz NMR Spectroscopic Study

Abstract

The impact of intramolecular stereoelectronic effects has been examined by comparison of the solution structures of natural oligo-DNA duplex, 5′(¹C²G³C⁴G⁵A⁶A⁷T⁸T⁹C¹⁰G¹¹C¹²G)₂ ³′, and its carbocyclic-nucleotide analogues in which the pentose sugar in 2′-dA residue is replaced with its carbocyclic counterpart (i.e. 2′-deoxyaristeromycin). Based on the NMR evidences, it has been shown, that 2′-deoxyaristeromycin analog exists in a dynamic equilibrium between the two forms of duplexes, one with W-C bp and the second with Hoogsteen bp in ca 1:1 ratio at lower temperature (below 35°C) and as hairpin at higher temperature (from ～40° – 60°C).     

CD studies of double-stranded polydeoxynucleotides composed of repeating units of contiguous homopurine residues

Double-stranded synthetic polydeoxynucleotides of the general form poly[d(G_nC_n)] · poly[d(G_nC_n)], poly[d(G_nC)] · poly[d(GC_n)], and poly[d(A_nT_n)] · poly[d(A_nT_n)] have been synthesized. When n = 4 or larger, the CD spectra of polymers of the form poly[d(G_nC_n)] · poly[d(G_nC_n)] or poly[d(G_nC)] · poly[d(GC_n)] closely resemble the spectrum of poly[dG] · poly[dC], suggesting that a string of four continguous guanosine residues is sufficient to induce a conformation resembling that of the polypurine · polypyrimidine. With polymers of the form poly[d(A_nT_n)] · poly[d(A_nT_n)], however, the CD spectrum only gradually approaches that of poly[dA] · poly[dT].     

Lack of association between human longevity and genetic polymorphisms in drug-metabolizing enzymes at the NAT2, GSTM1 and CYP2D6 loci

In the present study, the possible role of genetic polymorphism of three drug-metabolizing enzymes, debrisoquine/sparteine hydroxylase (CYP2D6), glutathione S-transferase μ (GSTM1), and N-acetyltransferase (NAT2), as a putative genetic component of human longevity, was explored. A total of 817 DNA samples from a centenarian and a control (20–70 years) population was subjected to PCR-coupled RFLP methods. Subjects were genotyped for the CYP2D6*3 (A₂₆₃₇ deletion) and CYP2D6*4 (G₁₉₃₄A transition) alleles, for four mutations of NAT2 [namely, NAT2*5A (C₄₈₁T), NAT2*6A (G₅₉₀A), NAT2*7A (G₈₅₇A), and NAT2*14A (G₁₉₁A)], and for the presence or absence of GSTM1 gene deletion. No significant difference was found at these three loci between centenarian and control subjects with respect to allelic variant frequencies, genotype distributions or predicted phenotypes deduced from genotype combinations. By comparing the distribution of combined genotypes for the polymorphisms tested at the CYP2D6, NAT2, and GSTM1 loci, none of the predicted phenotypes concerning debrisoquine hydroxylase extensive-metabolizer or poor-metabolizer phenotypes, slow or fast N-acetylation capacities, and active or defective glutathione S-transferase, could be correlated with human longevity, alone or in combination. Received: 4 September 1997/Accepted: 13 December 1997     

Recognition of O6-benzyl-2′-deoxyguanosine by a perimidinone-derived synthetic nucleoside: a DNA interstrand stacking interaction

The 2′-deoxynucleoside containing the synthetic base 1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)-tetrahydrofuran-2-yl)-1H-perimidin-2(3H)-one] (dPer) recognizes in DNA the O⁶-benzyl-2′-deoxyguanosine nucleoside (O⁶-Bn-dG), formed by exposure to N-benzylmethylnitrosamine. Herein, we show how dPer distinguishes between O⁶-Bn-dG and dG in DNA. The structure of the modified Dickerson–Drew dodecamer (DDD) in which guanine at position G⁴ has been replaced by O⁶-Bn-dG and cytosine C⁹ has been replaced with dPer to form the modified O⁶-Bn-dG:dPer (DDD-XY) duplex [5′-d(C¹G²C³X⁴A⁵A⁶T⁷T⁸Y⁹G¹⁰C¹¹G¹²)-3′]₂ (X = O⁶-Bn-dG, Y = dPer) reveals that dPer intercalates into the duplex and adopts the syn conformation about the glycosyl bond. This provides a binding pocket that allows the benzyl group of O⁶-Bn-dG to intercalate between Per and thymine of the 3′-neighbor A:T base pair. Nuclear magnetic resonance data suggest that a similar intercalative recognition mechanism applies in this sequence in solution. However, in solution, the benzyl ring of O⁶-Bn-dG undergoes rotation on the nuclear magnetic resonance time scale. In contrast, the structure of the modified DDD in which cytosine at position C⁹ is replaced with dPer to form the dG:dPer (DDD-GY) [5′-d(C¹G²C³G⁴A⁵A⁶T⁷T⁸Y⁹G¹⁰C¹¹G¹²)-3′]₂ duplex (Y = dPer) reveals that dPer adopts the anti conformation about the glycosyl bond and forms a less stable wobble pairing interaction with guanine.     

The Mycoplasma genitalium MG352‐encoded protein is a Holliday junction resolvase that has a non‐functional orthologue in Mycoplasma pneumoniae

Recombination between repeated DNA elements in the genomes of Mycoplasma species appears to lie at the basis of antigenic variation of several essential surface proteins. It is therefore imperative that the DNA recombinatorial pathways in mycoplasmas be unravelled. Here, we describe the proteins encoded by the Mycoplasma genitalium MG352 and Mycoplasma pneumoniae MPN528a genes (RecU_Mge and RecU_Mpn respectively), which share sequence similarity with RecU Holliday junction (HJ) resolvases. RecU_Mge was found to: (i) bind HJ substrates and large double‐stranded DNA molecules and (ii) cleave HJ substrates at the sequence 5′‐^G/_TC↓^C/_TT^A/_GG‐3′ in the presence of Mn²⁺. Interestingly, RecU_Mpn(from M. pneumoniae subtype 2 strains) did not possess obvious DNA binding or cleavage activities, which was found to be caused by the presence of a glutamic acid residue at position 67 of the protein, which is not conserved in RecU_Mge. Additionally, RecU_Mpn appears not to be expressed by subtype 1 M. pneumoniae strains, as these possess a TAA translation termination codon at position 181–183 of MPN528a. We conclude that RecU_Mge is a HJ resolvase that may play a central role in recombination in M. genitalium.     

Folding thermodynamics of the hybrid‐1 type intramolecular human telomeric G‐quadruplex

Guanine‐rich DNA sequences that may form G‐quadruplexes are located in strategic DNA loci with the ability to regulate biological events. G‐quadruplexes have been under intensive scrutiny owing to their potential to serve as novel drug targets in emerging anticancer strategies. Thermodynamic characterization of G‐quadruplexes is an important and necessary step in developing predictive algorithms for evaluating the conformational preferences of G‐rich sequences in the presence or the absence of their complementary C‐rich strands. We use a combination of spectroscopic, calorimetric, and volumetric techniques to characterize the folding/unfolding transitions of the 26‐meric human telomeric sequence d[A₃G₃(T₂AG₃)₃A₂]. In the presence of K⁺ ions, the latter adopts the hybrid‐1 G‐quadruplex conformation, a tightly packed structure with an unusually small number of solvent‐exposed atomic groups. The K⁺‐induced folding of the G‐quadruplex at room temperature is a slow process that involves significant accumulation of an intermediate at the early stages of the transition. The G‐quadruplex state of the oligomeric sequence is characterized by a larger volume and compressibility and a smaller expansibility than the coil state. These results are in qualitative agreement with each other all suggesting significant dehydration to accompany the G‐quadruplex formation. Based on our volume data, 432 ± 19 water molecules become released to the bulk upon the G‐quadruplex formation. This large number is consistent with a picture in which DNA dehydration is not limited to water molecules in direct contact with the regions that become buried but involves a general decrease in solute–solvent interactions all over the surface of the folded structure. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 216–227, 2014.     

Diverse modes of 5′‐[4‐(aminoiminomethyl)phenyl]‐[2,2′‐bifuran]‐5‐carboximidamide (DB832) interaction with multi‐stranded DNA structures

The modes of binding of 5′‐[4‐(aminoiminomethyl)phenyl]‐[2,2′‐Bifuran]‐5‐carboximidamide (DB832) to multi‐stranded DNAs: human telomere quadruplex, monomolecular R‐triplex, pyr/pur/pyr triplex consisting of 12 T*(T·A) triplets, and DNA double helical hairpin were studied. The optical adsorption of the ligand was used for monitoring the binding and for determination of the association constants and the numbers of binding sites. CD spectra of DB832 complexes with the oligonucleotides and the data on the energy transfer from DNA bases to the bound DB832 assisted in elucidating the binding modes. The affinity of DB832 to the studied multi‐stranded DNAs was found to be greater (K_ass ≈ 10⁷M^?1) than to the duplex DNA (K_ass ≈ 2 × 10⁵M^?1). A considerable stabilizing effect of DB832 binding on R‐triplex conformation was detected. The nature of the ligand tight binding differed for the studied multi‐stranded DNA depending on their specific conformational features: recombination‐type R‐triplex demonstrated the highest affinity for DB832 groove binding, while pyr/pur/pyr TTA triplex favored DB832 intercalation at the end stacking contacts and the human telomere quadruplex d[AG₃(T₂AG₃)₃] accommodated the ligand in a capping mode. Additionally, the pyr/pur/pyr TTA triplex and d[AG₃(T₂AG₃)₃] quadruplex bound DB832 into their grooves, though with a markedly lesser affinity. DB832 may be useful for discrimination of the multi‐sranded DNA conformations and for R‐triplex stabilization. © 2009 Wiley Periodicals, Inc. Biopolymers 93: 8–20, 2010. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Molecular mechanical calculations on the interaction of ethidium cation with double-helical DNA

Molecular mechanical calculations were done on complexes of ethidium cation with various base-paired deoxydinucleoside monophosphates [(ApT)₂, (TpA)₂, (A₂ · T₂), (GpC)₂, (CpG)₂, and (G₂ · C₂)] and deoxyhexanucleoside pentaphosphates [(ATATAT)₂, (TATATA)₂, (A₆ · T₆), (GCGCGC)₂, (CGCGCG)₂, and G₆ · C₆]. Relative binding energies, sequence preferences, and conformational aspects of the intercalation complexes were studied. The most detailed models used (an all-atom force field) gave results in good agreement with previous calculations and experimental work. Less-sophisticated models did not perform as well.     

Tetraplex Formation of d(GGGGGTTTTT): 1H NMR Study in Solution

Abstract

The oligonucleotide d(G₅T₅) can in principle form a fully matched duplex with G · T pairing and/or a tetraplex. Non-denaturing gel electrophoresis, circular dichroism and NMR experiments show that the tetraplex is exclusively formed by this oligomer in solution. In the presence of its complementary strand d(A₅C₅) at low temperature, d(G₅T₅) forms the tetraplex over the normally expected Watson-Crick duplex. However, when d(G₅T₅) and d(A₅C₅) are mixed together in equimolar amounts and heated for several minutes at 85°C, and then allowed to cool, the product was essentially the Watson-Crick duplex. The lack of resolution in the 500 MHz ¹H NMR spectra and the presence of extensive spin diffusion do not allow us to derive a quantitative structure for the tetraplex from the NMR data. However, we find good qualitative agreement between the NOESY and MINSY data and a theoretically derived stereochemically sound structure in which the G's and T's are part of a parallel tetraplex.     

Growth energetics of juvenile herring,Clupea harengus L.: food conversion efficiency and temperature dependency of metabolic rate

The relationship between rates of food consumption (C) and somatic growth (G) and the effect of temperature (T) on rates of mass lost during food deprivation were examined in 9–10 cm total length (TL) [1.0–1.5 g dry mass (DM)] juvenile Atlantic herring (Clupea harengus L.) in the laboratory. One feeding‐growth trial was conducted at 16°C using groups of herring feeding on known rations of brine shrimp (Artemia spp.) nauplii to quantify gross and net growth efficiency. Rates of mass lost by groups of herring (a proxy for metabolic rate, M) were measured in trials conducted at 9.7, 14.2 and 17.9°C. Gross growth efficiency (GGE = 100*G*C^?1) at 16°C was 25% at the highest rations (5.8–6.6% DM). The maintenance ration (C_main = C at zero G) was equal to 432 J*fish^?1*d^?1 or 2.0% DM*d^?1. At 16°C, net growth efficiency (100*G*(C?C_main)^?1) was 42%. The nucleic acid content (RNA‐DNA ratio, RD) in herring muscle tissue was strongly related to somatic growth (G, % DM*d^?1 = ?0.36*RD² + 3.21*RD ?3.92, r² = 0.90, P < 0.05, n = 8 groups). The effect of T (9.7–17.9°C) on M was described by a second order polynomial equation M = ?1.24*T + 38.2*T ? 218 (J*g DM^?1*d^?1) and M = ?10*T + 310*T ? 1815 (J*fish^?1*d^?1). This was the first study to investigate the influence of temperature on the metabolic rate of juvenile Atlantic herring under stress‐free conditions in the laboratory and provides the first estimates of gross and net growth efficiency for this species feeding on live prey.