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We investigate the projected impact of six climate mitigation scenarios on U.S. emissions of carbon dioxide (CO2), sulfur dioxide (SO2), and nitrogen oxides (NOx) associated with energy use in major sectors of the U.S. economy (commercial, residential, industrial, electricity generation, and transportation). We use the EPA U.S. 9-region national database with the MARKet Allocation energy system model to project emissions changes over the 2005 to 2050 time frame. The modeled scenarios are two carbon tax, two low carbon transportation, and two biomass fuel choice scenarios. In the lower carbon tax and both biomass fuel choice scenarios, SO2 and NOx achieve reductions largely through pre-existing rules and policies, with only relatively modest additional changes occurring from the climate mitigation measures. The higher carbon tax scenario projects greater declines in CO2 and SO2 relative to the 2050 reference case, but electricity sector NOx increases. This is a result of reduced investments in power plant NOx controls in earlier years in anticipation of accelerated coal power plant retirements, energy penalties associated with carbon capture systems, and shifting of NOx emissions in later years from power plants subject to a regional NOx cap to those in regions not subject to the cap. [ABSTRACT FROM AUTHOR]

The cancer chemotherapeutic agent cis-diamminedichloroplatinum(II) or cisplatin reacts primarily with guanines in DNA to form 1,2-Pt-GG and 1,3-Pt-GNG intrastrand cross-links and, to a lesser extent, G-G interstrand cross-links. Recent NMR evidence has suggested that cisplatin can also form a coordination complex with the phosphodiester intemucleotide linkage of DNA. We have examined the effects of the phosphodiester backbone on the reactions of cisplatin with oligodeoxyribonucleotides that lack or contain a GTG sequence. Cisplatin forms a stable adduct with TpT that can be isolated by reversed phase HPLC. The cis-Pt-TpT adduct contains a single Pt, as determined by atomic absorption spectroscopy (AAS) and by electrospray ionization mass spectrometry (ESI-MS), and is resistant to digestion by snake venom phosphodiesterase. Treatment of the adduct with sodium cyanide regenerates TpT. Similar adduct formation was observed when T(pT)s was treated with cisplatin, bitt not when the phosphodiester linkages of T(pT)[sub8] were replaced with methylphosphonate groups. These results suggest that the platinum may be coordinated with the oxygens of the thymine and possibly with those of the phosphodiester group. As expected, reaction of a 9-mer containing a GTG sequence with cisplatin yielded an adduct that contained a I ,3-Pt-GTG intrastrand cross-link. However, we found that the number and placement of phosphodiesters surrounding a GTG sequence significantly affected intrastrand cross-link formation. Increasing the number of negatively charged phosphodiesters in the oligonucleotide increased the amount of GTG platination. Surrounding the GTG sequence with nonionic methylphosphonate linkages inhibited or eliminated crosslink formation. These observations suggest that interactions between cisplatin and the negatively charged phosphodiester backbone may play an important role in facilitating platination of guanine nucleolides in DNA. [ABSTRACT FROM AUTHOR]

The dynamics of the furanose rings in the GCGC moiety of the DNA oligomer [d(G1A2T3A4G5C6G7C8T9A10T11C12)]2 are studied by using deuterium solid-state NMR (SSNMR). SSNMR spectra obtained from DNAs selectively deuterated on the furanose rings of nucleotides within the 5′-GCGC-3′ moiety indicated that all of these positions are structurally flexible. The furanose ring within the deoxycytidine that is the methylation target displays the largest-amplitude structural changes according to the observed deuterium NMR line shapes, whereas the furanose rings of nucleotides more remote from the methylation site have less-mobile furanose rings (i.e., with puckering amplitudes < 0.3 Å). Previous work has shown that methylation reduces the amplitude of motion in the phosphodiester backbone of the same DNA, and our observations indicate that methylation perturbs backbone dynamics through the furanose ring. These NMR data indicate that the 5′-GCGC-3′ is dynamic, with the largest-amplitude motions occurring nearest the methylation site. The inherent flexibility of this moiety in DNA makes the molecule more amenable to the large-amplitude structural rearrangements that must occur when the DNA binds to the Hhal methyltransferase. [ABSTRACT FROM AUTHOR]

Phenolic resins, phenol-formaldehyde polymers previously thought to be nonbiodegradable, are produced at an annual rate of 2.2 million metric tons in the United States for many industrial and commercial applications. Three independent lines of evidence established their biodegradability with the white-rot fungus Phanerochaete chrysosporium. Chromatic transformation of growth medium (yellow to pink) indicated initial biodegradation of the resin 3 days after inoculation. A degradation product, 13C -labeled phenol, was detected with gas chromatography—mass spectroscopy. Scanning electron micrographs revealed physical evidence of degradation. This is the first demonstrated biodegradation of these phenol—formaldehyde polymers and stands as a platform for investigation into bioremediation and biorecycling of phenolic resins. [ABSTRACT FROM AUTHOR]

Examines oligo-2'-O-methylribonucleoside methylphosphonates (mr-AOMP) syntheses and interaction with HIV TAR RNA. Resistance of mr-AOMP to hydrolysis; Sensitivity of interactions with methylphosphonate linkages in oligomers; High affinity of mr-AOMP for TAR RNA; Anti-TAR mr-AOMP as antisense compounds in cell culture.

Reports the examination of a series of psoralen-derivatized oligodeoxyribonucleoside methylphosphonates for their abilities to cross-link to DNA and RNA oligonucleoside targets. Description of experimental procedures; Results of experiment; Discussion of results; References.

The article discusses the study on a new and general strategy for the synthesis of a single nanocomposite material that yields pure and stable white photoluminescence and electroluminescense. The efficacy of the white-emitting nanocomposites in simple single-layer polymer light-emitting diodes was examined in a conventional device configuration. Key information on the study are further discussed.

Reports on triplex formation by an oligodeoxyribonucleotide containing N4-(6-aminopyridinyl)-2'-deoxycytidine. Ability of nucleoside analogs to support triplex formation; Absorbance versus temperature profiles of solutions; Biphasic curves indicative of triplex formation.

Platinum-derivatized homopyrimidine triplex-forming oligonucleotides (Pt-TFOs) consisting of 2'-0-methyl-5-methyluridine, 2'-0-methyl-5-methylcytidine, and a single 3'-N7-frcms-chlorodiam-mine platinum(ll)-2'-deoxyguanosine were designed to cross-link to the transcribed strand at four different sequences in the human androgen receptor (AR) gene. Fluorescence microscopy showed that a fluorescein-tagged Pt-TFO localizes in both the cytoplasm and nucleus when it is transfected into LAPC-4 cells, a human prostate cancer cell line, using Lipofectamine 2000. A capture assay employing streptavidin-coated magnetic beads followed by polymerase chain reaction (PCR) amplification was used to demonstrate that 5'-biotin-conjugated Pt-TFOs cross-link in vitro to their four designated AR gene targets in genomic DNA extracted from LAPC-4 cells. Similarly, the capture assay was used to examine cross-linking between the 5'-biotin-conjugated Pt-TFOs and the AR gene in LAPC-4 cells in culture. Three of the four Pt-TFOs cross-linked to their designated target, suggesting that different regions of the AR gene are not uniformly accessible to Pt-TFO cross-linking. LAPC-4 cells were transfected with fluorescein-tagged Pt-TFO or a control oligonucleotide that does not bind or cross-link to AR DNA The levels of AR mRNA in highly fluorescent cells isolated by fluorescence-activated cell sorting were determined by RT-qPCR, and the levels of AR protein were monitored by immunofluorescence microscopy. Decreases in mRNA and protein levels of 40 and 30%, respectively, were observed for fluorescein-tagged Pt-TFO versus control treated cells. Although the levels of knockdown of AR mRNA and protein were modest, the results suggest that Pt-TFOs hold potential as agents for controlling gene expression by cross-linking to DNA and disrupting transcription. [ABSTRACT FROM AUTHOR]

Bifunctional DNA alkylating agents form a diverse assortment of covalent DNA interstrand cross-linked (ICL) structures that are potent cytotoxins. Because it is implausible that cells could possess distinct DNA repair systems for each individual ICL, it is believed that common structural and dynamic features of ICL damage are recognized, rather than specific structural characteristics of each cross-linking agent. Investigation of the structural and dynamic properties of ICLs that might be important for recognition has been complicated by heterogeneous incorporation of these lesions into DNA. To address this problem, we have synthesized and characterized several homogeneous ICL DNAs containing site-specific staggered N4-cytosine-ethyl-N4-cytosine cross-links. Staggered cross-links were introduced in two ways, in a manner that preserves the overall structure of B-form duplex DNA and in a manner that highly distorts the DNA structure, with the goal of understanding how structural and dynamic properties of diverse ICL duplexes might flag these sites for repair. Measurements of base pair opening dynamics in the B-form ICL duplex by 1H NMR line width or imino proton solvent exchange showed that the guanine base opposite the cross-linked cytosine opened at least 1 order of magnitude more slowly than when in a control matched normal duplex. To a lesser degree, the B-form ICL also induced a decrease in base pair opening dynamics that extended from the site of the cross-link to adjacent base pairs. In contrast, the non-B-form ICL showed extensive conformational dynamics at the site of the cross-link, which extended over the entire DNA sequence. Because DNA duplexes containing the B-form and non-B-form ICL cross-links have both been shown to be incised when incubated in mammalian whole cell extracts, while a matched normal duplex is not, we conclude that intrinsic DNA dynamics is not a requirement for specific damage incision of these ICLs. Instead, we propose a general model in which destabilized ICL duplexes serve to energetically facilitate binding of DNA repair factors that must induce bubbles or other distortions in the duplex. However, the essential requirement for incision is an immobile Y-junction where the repair factors are stably bound at the site of the ICL, and the two DNA strands are unpaired. [ABSTRACT FROM AUTHOR]

Chemotherapeutic alkylating agents, such as bifunctional nitrogen mustards and cisplatins, generate interstrand DNA cross-links that inhibit cell proliferation by arresting DNA transcription and replication. A synthetic N4C-ethyl-N4C interstrand cross-link between opposing cytidines mimics the DNA damage produced by this class of clinically important compounds and can be synthesized in large quantities to study the repair, physical properties, and structures of these DNA adducts. The X-ray structure of a DNA duplex d(CCAAC*GTTGG)2 containing a synthetic N4C-ethyl-N4C interstrand cross-link between the cytosines of the central CpG step (*) has been determined at 1.65 Å resolution. This structure reveals that the ethyl cross-link in the CpG major groove does not significantly disrupt the B-form DNA helix. Comparison of the N4C-ethyl-N4C cross-linked structure with the structure of an uncross-linked oligonucleotide of the same sequence reveals that the cross-link selectively stabilizes a preexisting alternative conformation. The conformation preferred by the cross-linked DNA is constrained by the geometry of the ethyl group bridging the cytosine amines. Characteristics of the cross-linked CpG step include subtle differences in the roll of the base pairs, optimized Watson-Crick hydrogen bonds, and loss of a divalent cation binding site. Given that the N4C-ethyl-N4C cross-link stabilizes a preexisting conformation of the CpG step, this synthetically accessible substrate presents an ideal model system for studying the genomic effects of covalently coupling the DNA strands, independent of gross alterations in DNA structure. [ABSTRACT FROM AUTHOR]

The article discusses the mechanism for the formation and repair of highly toxic DNA interstrand cross-links. At the genetic level, protein members of several repair pathways play a role in the repair of damaged DNA. The repair of DNA interstrand cross-links in eukaryotes involves factors from the nucleotide excision repair and homologous recombination pathways.

Analyzes the bending deformations in DNA complexes. Transition temperature of ethyl cross-linked duplex; Evidence of an anomalous mobilities in native polyacrylamide gels of multimers; Physical properties of the duplex.

Describes the synthesis and characterization of DNA duplexes containing an N[sup 4]C-ethyl-N[sup 4]C interstrand cross-link. Synthesis of duplexes with a defined interstrand cross-link; Incorporation of the duplexes into longer pieces of DNA; DNA repair; Bifunctional alkylating agents.

Impacts of emissions changes from four potential U.S. CO2 emission reduction policies on 2050 air quality are analyzed using the community multiscale air quality model (CMAQ). Future meteorology was downscaled from the Goddard Institute for Space Studies (GISS) ModelE General Circulation Model (GCM) to the regional scale using the Weather Research Forecasting (WRF) model. We use emissions growth factors from the EPAUS9r MARKAL model to project emissions inventories for two climate tax scenarios, a combined transportation and energy scenario, a biomass energy scenario and a reference case. Implementation of a relatively aggressive carbon tax leads to improved PM2.5 air quality compared to the reference case as incentives increase for facilities to install flue-gas desulfurization (FGD) and carbon capture and sequestration (CCS) technologies. However, less capital is available to install NOX reduction technologies, resulting in an O3 increase. A policy aimed at reducing CO2 from the transportation sector and electricity production sectors leads to reduced emissions of mobile source NOX, thus reducing O3. Over most of the U.S., this scenario leads to reduced PM2.5 concentrations. However, increased primary PM2.5 emissions associated with fuel switching in the residential and industrial sectors leads to increased organic matter (OM) and PM2.5 in some cities. [ABSTRACT FROM AUTHOR]

We have previously reported on a liquid chromatography-mass spectrometry method to determine the disposition of [13C18]-oleic acid following intravenous and oral administration in vivo. This approach has enabled us to study a variety of aspects of lipid metabolism including a quantitative assessment of triglyceride synthesis. Here we present a more rigorous evaluation of the constraints imposed upon the analytical method in order to generate accurate data using this stable-isotope tracer approach along with more detail on relevant analytical figures of merit including limits of quantitation, precision, and accuracy. The use of mass isotopomer distribution analysis (MIDA) to quantify plasma triglyceride synthesis is specifically highlighted, and a re-evaluation of the underlying mathematics has enabled us to present a simplified series of equations. The derivation of this MIDA model and the significance of all underlying assumptions are explored in detail, and examples are given of how it can successfully be applied to detect differences in plasma triglyceride synthesis in lean and high-fat diet fed mouse models. More work is necessary to evaluate the applicability of this approach to triglyceride stores with slower rates of turnover such as in adipose or muscle tissue; however, the present report provides investigators with the tools necessary to conduct such studies. [ABSTRACT FROM AUTHOR]

DNA nterstrand cross-links (ICLs) are cytotoxic products of common anticancer drugs and cellular metabolic processes, whose mechanism(s) of repair remains poorly understood. In this study, we show that cross-link structure affects ICL repair in nonreplicating reporter plasmids that contain a mispaired N4C-ethyl-N4C (C-C),. N3T-ethyl-N3T (T.-T), or. Nll-ethyl-N3T (l-T) ICL. The T-T and l-T cross-links obstruct the hydrogen bond face of the base and mimic the NIG-ethyl-N3C ICL created by bis-chloroethylnitrosourea, whereas the C-C cross-link does not interfere with base pair formation. Host-cell reactivation (HCR) assays in human and hamster cells showed that repair of these ICLs primarily involves the transcription-coupled nucleotide excision repair (TC-NER) pathway. Repair of the C-C ICL was 5-fold more efficient than repair of the T-T or I-T ICLs, suggesting the latter cross-links hinder lesion bypass following initial ICL unhooking. The level of luciferase expression from plasmids containing a C-C cross-link remnant on either the transcribed or nontranscribed strand increased in NER-deficient cells, indicating NER involvement occurs at a step prior to remnant removal, whereas expression from similar T-T remnant plasmids was inhibited in NER-deficient cells, demonstrating NER is required for remnant removal. Sequence analysis of repaired plasmids showed a high proportion of C residues inserted at the site of the T-T and l-T cross-links, and HCR assays showed that RevI was likely responsible for these insertions. In Contrast, both C and G residues were inserted at the C-C cross-link site, and Revl was not required for repair, suggesting replicative or other translesion polymerases can bypass the C-C remnant. [ABSTRACT FROM AUTHOR]

ABSTRACT: Interstrand cross-links (ICLs) are formed by many chemotherapeutic agents and may also arise endogenously. The mechanisms used to repair these lesions remain unclear in mammalian cells. Repair in Escherichia coli and Saccharomyces cerevisiae requires an initial unhooking step to release the tethered DNA strands. We used a panel of linear substrates containing different site-specific ICLs to characterize how structure affects ICL processing in mammalian cell extracts. We demonstrate that ICLinduced distortions affect NER-dependent and -independent processing events. The NER-dependent pathway produces dual incisions 5' to the site of the ICL as described previously [Bessho, T., et al. (1997) Mol. Cell. Biol. 17 (12), 6822-6830] but does not release the cross-link. Surprisingly, we also found that the interstrand cross-linked duplexes were unhooked in mammalian cell extracts in a manner independent of the NER pathway. Unhooking occurred identically in extracts prepared from human and rodent cells and is dependent on ATP hydrolysis and metal ions. The structure of the unhooked product was characterized and was found to contain the remnant of the cross-link. Both the NER-mediated dual 5' incisions and unhooking reactions were greatly stimulated by ICL-induced distortions, including increased local flexibility and disruption of base pairs surrounding the site of the ICL. These results suggest that in DNA not undergoing transcription or replication, distortions induced by the presence of an ICL could contribute significantly to initial cross-link recognition and processing. [ABSTRACT FROM AUTHOR]

The dynamics of the phosphodiester backbone in the [5'-GCGC-3'][sub2] moiety of the DNA oligomer [d(G[sub1]A[sub2]T[sub3]A[sub4]G̱[sub5]C̱[sub6]G̱[sub7]C̱[sub8]T[sub9]A[sub10]T[sub11]C[sub12])][sub2] are studied using deuterium solid-state NMR (SSNMR). SSNMR spectra obtained from DNAs nonstereospecifically deuterated on the 5' methylene group of nudleotides within the [5'-GCGC-3'][sub2] moiety indicated that all of these positions are structurally flexible. Previous work has shown that methylation reduces the amplitude of motion in the phosphodiester backbone and furanose ring of the same DNA, and our observations indicate that methylation perturbs backbone dynamics through not only a loss of mobility but also a change of direction of motion. These NMR data indicate that the [5'-GCGC-3'][sub2] moiety is dynamic, with the largest amplitude motions occurring nearest the methylation site. The change of orientation of this moiety in DNA upon methylation may make the molecule less amenable to binding to the Hhal endonuclease. [ABSTRACT FROM AUTHOR]

We are developing triple helix forming oligonucleotides (TFOs) for gene targeting. Previously, we synthesized bioactive TFOs containing 2′-O-methylribose (2′-OMe) and 2′-O-aminoethylribose (2′-AE) residues. Active TFOs contained four contiguous 2′-AE residues and formed triplexes with high thermal stability and rapid association kinetics. In an effort to further improve bioactivity, we synthesized three series of TFOs containing the 2′-AE patch and additional ribose modifications distributed throughout the remainder of the oligonucleotide. These were either additional 2′-AE residues, the conformationally locked BNA/LNA ribose with a 2′-O,4′-C-methylene bridge, or the 2′-O,4′-C-ethylene analogue (ENA). The additionally modified TFOs formed triplexes with greater thermal stability than the reference TFO, and some had improved association kinetics. However, the most active TFOs in the biochemical and biophysical assays were the least active in the bioassay. We measured the thermal stability of triplexes formed by the TFOs in each series on duplex targets containing a change in sequence at a single position. The Tm value of the variant sequence triplexes increased as the number of all additional modifications increased. A simple explanation for the failure of the improved TFOs in the bioassay was that the increased affinity for nonspecific targets lowered the effective nuclear concentration. Enhancement of TFO bioactivity will require chemical modifications that improve interaction with the specific targets while retaining selectivity against mismatched sequences. [ABSTRACT FROM AUTHOR]

Triple helix forming oligonucleotides (TFOs) may have utility as gene targeting reagents for ‘in situ’ gene therapy of genetic disorders. Triplex formation is challenged by negative charge repulsion between third strand and duplex phosphates, and destabilizing positive charge repulsion between adjacent protonated cytosines within pyrimidine motif third strands. Here we describe the synthesis of TFOs designed to target a site in the human β-globin gene, which is the locus for mutations that underlie the β-globinopathies, including sickle cell anemia. The target is an uninterrupted polypurine:polypyrimidine sequence, containing four adjacent cytosines, next to a psoralen cross-link site. Pyrimidine motif TFOs that contained four adjacent cytosines or 5-methylcytosines did not form stable triplexes at physiological pH, despite the introduction of otherwise stabilizing base and sugar analogues. We synthesized a series of pso-TFOs containing 2′-O-methyl (OMe) and 2′-O-aminoethoxy substitutions (AE), as well as 8-oxo-adenine (A8) and 2′-O-methylpseudoisocytidine (P) as neutral cytosine replacements. Thermal stability measurements indicated that TFOs with A8 did not meet criteria established in previous work. However, TFOs with P did form triplexes with appropriate Tm and kON values. A pso-TFO with AE and P residues was sufficiently active to permit the determination of targeting in living cells by direct measurement of cross-link formation at the target site. Our results validate the modification format described in our previous studies and indicate that P substitutions are an effective solution to the problem of targeting genomic sequences containing adjacent cytosines. [ABSTRACT FROM AUTHOR]

Interstrand DNA cross-links are the principal cytotoxic lesions produced by chemotherapeutic bifunctional alkylating agents. Using an N4C-ethyl-N4C inter strand DNA cross-link to mimic this class of clinically important cancer chemotherapeutic agents, we have characterized the repair, structure, and flexibility of DNA that contains this cross-link in two different orientations. Plasmid DNAs in which the cytosines of single CpU or UpC steps are covalently linked were efficiently processed by repair proficient and homologous recombination deficient strains of Escherichia coli. Repair in a nucleotide excision repair (NER) deficient strain was less efficient overall and displayed a 4-fold difference between the two cross- link orientations. Both the structure and flexibility of DNA containing these cross-links were examined using a combination of 1H NMR, restrained molecular dynamics simulations, and atomic force microscopy (AFM). The NMR structure of a defamer containing a CpG interstrand cross-link shows the cross-link easily accommodated within the duplex with no disruption of hydrogen bonding and only minor perturbations of helical parameters. In contrast, disruptions caused by the GpC cross-link produced considerable conformational flexibility that precluded structure determination by NMR. AFM imaging of cross-link-containing plasmid DNA showed that the increased flexibility observed in the UpC cross-link persists when it is embedded into much larger DNA fragments. These differences may account for the different repair efficiencies seen in NER deficient cells. [ABSTRACT FROM AUTHOR]

The solution structure of the undecamer d(CGAAAT*TTTCG)2, where T* represents a N³T-ethyl-N³T interstrand cross link, was elucidated using molecular dynamics calculations restrained by NOE and dihedral data obtained from NMR spectroscopy. The ethyl moiety is particularly well-accommodated between the minor and major grooves. This is an exceptional example of the plasticity along the axis defined by the stem and a unique finding of an interstrand cross link occupying the area associating minor and major grooves. The mismatch-aligned tethered bases preserve good intrastrand stacking with flanking bases. Base-pair steps adjacent to the lesion site are overwound. Accommodation of the lesion also results in an increase in mispair staggering alignment modulated by flexibility because of the tetrahedral geometry of the exocyclic ethyl carbon atoms. This is mechanically coupled with a small measure of concomitant propeller twisting without an increase in intrastrand base-step distance. Both x displacementand sugar puckering are indicative of canonical B DNA throughout the stem. We have thus established that the lesion defined by mismatch-aligned minor groove N³T-ethyl-N³T cross-linked thymine bases produces very localized distortions in a DNA stem that may be difficult to recognize by repair mechanisms that are not transcription- or replication-coupled. Thus, this synthetic DNA is a valuable structural probe to study mechanisms of repair. [ABSTRACT FROM AUTHOR]

We are developing triple helix-forming oligonucleotides (TFOs) as gene targeting reagents in living mammalian cells. We have described psoralen-linked TFOs with 2'-0-methyl and 2'-0-(2-aminoethyl) (2'-AE) substitutions that are active in a gene knockout assay in cultured cells. The assay is based on mutagenesis by psoralen, a photoactive DNA cross-linker. Previous work showed that TFOs with three or four 2'-AE residues were disproportionately more active than those with one or two substitutions. Here we demonstrate that for optimal bioactivity the 2'-AE residues must be clustered rather than dispersed. We have further characterized bioactive and inactive TFOs in an effort to identify biochemical and biophysical correlates of biological activity. While thermal stability is a standard monitor of TFO biophysical activity, we find that T[Subm] values do not distinguish bioactive and inactive TFOs. In contrast, measurements of TFO association rates appear to correlate well with bioactivity, in that triplex formation occurs disproportionately faster with the TFOs containing three or four 2'-AE residues. We asked if extending the incubation time prior to photoactivation would enhance the bioactivity of a TFO with a slow on rate relative to the TFO with a faster association rate. However, there was no change in bioactivity differential. These results are compatible with a model in which TFO binding in vivo is followed by relatively rapid elution by cellular functions, similar to that described for transcription factors. Under these circumstances, TFOs with faster on rates would be favored because they would be more likely to be in triplexes at the time of photoactivation. [ABSTRACT FROM AUTHOR]

The solution structure of an interstrand cross-linked self-complementary oligodeoxynucleotide containing directly opposed alkylated N[sup 4]C-ethyl-N[sup 4]C cytosine bases was determined by molecular dynamics calculations guided by NMR-derived restraints. The undecamer d(CGAAAC[sup *]TTTCG)[sub 2], where C[sup *] represents directly opposed alkylated N[sup 4]C-ethyl-N[sup 4]C cytosine bases, serves as model for the cytotoxic cross-links formed by bifunctional alkylating agents used in cancer therapy. The structure of the duplex shows the cross-link protruding into the major groove. An increase in the diameter of the DNA at the pseudoplatform formed by the cross-linked residues creates an A-DNA characteristic hole in the central portion of the DNA. This results in a centrally underwound base step and a number of subsequent overwinding steps leading to an overall axis bend toward the major groove. The structure shows narrowing of both minor and major grooves in the proximity of the cross-link. The perturbation leads to preferential intrastrand base stacking, disruption of adjacent canonical (A·T) base pairing, and buckling of base pairs, the extent of which diminishes with progression away from the lesion site. Overall, the distortion induced by the cross-link spreads over three base pairs on the 5'- and 3'-sides of the cross-link. [ABSTRACT FROM AUTHOR]

Investigates the bioactivity of the aminoethyl residues by triple helix forming oligonucleotide (TFO). Synthesis of TFO; Sensitivity of the pyrimidine motif triplexes to hydrogen-ion concentration; Formation of the triplexes by the TFO.

Examines the synthesis and characterization of duplexes with interstrand cross-links of different orientations. Formation of thermal transition temperatures; Stabilization of circular dichroism spectrum and molecular models; Migration of ligated oligomers by polyacrylamide gel.