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INTRODUCTION: Digital tools are widely used and effective in weight management interventions; however, usage declines over time. Strategies to promote continued engagement should be explored. We examined the effects of offering additional modes of weight reporting as well as periodic online campaigns to promote engagement, assessed by frequency of weight reporting, in a weight gain prevention study for young adults. METHODS: Using an observational design, self-reported weights obtained through digital tools were pooled across participants assigned to two interventions (n = 312). Analysis examined the effects before during and after introduction of an additional reporting modality (email) and for three time-limited refresher campaigns over 2 years. RESULTS: Adding a new modality to the three existing modes (SMS, web, and mobile web) increased weight reporting as well as the number of modalities participants used to report weights. The use of several modes of reporting was associated with more weights submitted (p < 0.01). Refresher campaigns did not increase the proportion of participants reporting; however, the number of weights submitted during the 4-week campaigns increased compared with the 4 weeks before the campaign (p's ≥ 0.45, <0.001, respectively). CONCLUSION: Using multiple digital modalities and periodic campaigns shows promise for sustaining engagement with weight reporting in a young adult population, and incorporating such strategies may mitigate typical declines in eHealth and mHealth interventions.
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BACKGROUND: Obesity is a major and worldwide health problem in children. OBJECTIVES: The Early Childhood Obesity Prevention Program is a multi-component, randomized, controlled trial of a pilot community-focused obesity prevention program for mother/newborn dyads. METHODS: Underserved, mother/newborn dyads were recruited to receive a standard home visitation program (Nurturing Families Network, NFN) or an enhanced program (NFN+) that incorporated behavioural change strategies (e.g., goal-setting, problem-solving) and focused on six obesity-associated behaviours (breastfeeding, juice/sugar-sweetened beverages, solids, infant sleep, TV/screen time and soothability) with linkages to community resources. Weight-for-length (WFL) z-score and maternal diet were secondary outcomes. RESULTS: Fifty-seven dyads were recruited and 47 fully eligible dyads were enrolled (NFN = 21, NFN+ = 26). Forty-one (87.2%) were assessed at 6 months and 34 (72.3%) at 12 months. Retention at 12 months was higher for NFN+ dyads (84.6% vs. 56.1%, p = 0.04). NFN+ mothers were more likely to continue breastfeeding at 6 and 12 months vs. NFN mothers (p = 0.03 and 0.003, respectively), and at 12 months, NFN+ infants had fewer nocturnal awakenings (p = 0.04). There were no differences in other primary outcome measures or in WFL z-score at 6 or 12 months. CONCLUSIONS: A multi-component behavioural intervention increased breastfeeding duration and decreased nocturnal awakenings in infants of low-income families.
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Terapia Conductista/métodos , Conductas Relacionadas con la Salud , Obesidad Infantil/prevención & control , Adulto , Lactancia Materna/estadística & datos numéricos , Niño , Preescolar , Dieta , Femenino , Estudios de Seguimiento , Estilo de Vida Saludable , Humanos , Lactante , Recién Nacido , Masculino , Madres , Proyectos Piloto , Pobreza , Evaluación de Programas y Proyectos de Salud/métodos , Encuestas y CuestionariosRESUMEN
OBJECTIVE: Pervasive weight stigma and discrimination have led to ongoing calls for efforts to reduce this bias. Despite increasing research on stigma-reduction strategies, perspectives of individuals who have experienced weight stigma have rarely been included to inform this research. The present study conducted a systematic examination of women with high body weight to assess their perspectives about a broad range of strategies to reduce weight-based stigma. METHODS: Women with overweight or obesity (N = 461) completed an online survey in which they evaluated the importance, feasibility and potential impact of 35 stigma-reduction strategies in diverse settings. Participants (91.5% who reported experiencing weight stigma) also completed self-report measures assessing experienced and internalized weight stigma. RESULTS: Most participants assigned high importance to all stigma-reduction strategies, with school-based and healthcare approaches accruing the highest ratings. Adding weight stigma to existing anti-harassment workplace training was rated as the most impactful and feasible strategy. The family environment was viewed as an important intervention target, regardless of participants' experienced or internalized stigma. CONCLUSION: These findings underscore the importance of including people with stigmatized identities in stigma-reduction research; their insights provide a necessary and valuable contribution that can inform ways to reduce weight-based inequities and prioritize such efforts.
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OBJECTIVE: Maintaining weight loss is a major challenge in obesity treatment. Individuals often indicate that waning motivation prompts cessation of effective weight management behaviors. Therefore, a novel weight loss maintenance program that specifically targets motivational factors was evaluated. DESIGN: Overweight women (N=338; 19% African American) with urinary incontinence were randomized to lifestyle obesity treatment or control and followed for 18 months. All participants in lifestyle (N=226) received the same initial 6-month group behavioral obesity treatment and were then randomized to (1) a novel motivation-focused maintenance program (N=113) or (2) a standard skill-based maintenance approach (N=113). MAIN OUTCOME MEASURE: Weight assessed at baseline, 6 and 18 months. RESULTS: Both treatment groups (motivation-focused and skill-based) achieved comparable 18-month weight losses (-5.48% for motivation-focused vs -5.55% in skill-based, P=0.98), and both groups lost significantly more than controls (-1.51%; P=0.0012 in motivation-focused and P=0.0021 in skill-based). CONCLUSIONS: A motivation-focused maintenance program offers an alternative, effective approach to weight maintenance expanding available evidence-based interventions beyond traditional skill-based programs.
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Terapia Conductista/métodos , Dieta Reductora/psicología , Motivación , Obesidad/psicología , Incontinencia Urinaria/psicología , Pérdida de Peso , Dieta Reductora/métodos , Femenino , Humanos , Persona de Mediana Edad , Obesidad/complicaciones , Obesidad/terapia , Cooperación del Paciente , Conducta de Reducción del Riesgo , Autoimagen , Resultado del Tratamiento , Incontinencia Urinaria/complicaciones , Incontinencia Urinaria/terapiaRESUMEN
OBJECTIVE: To compare the enrollment, attendance, retention and weight losses of young adults in behavioral weight loss (BWL) programs with older participants in the same trials. METHODS: Data were pooled from three NIH-funded adult BWL trials from two clinical centers in different regions of the country (total N=298); young adults were defined as those aged 18-35 years. Both young adults and adults were compared on session attendance, retention at the 6-month assessment, weight loss and physical activity at 6 months. RESULTS: Young adults represented 7% of the sample, attended significantly fewer sessions than did adults (52 vs 74%, respectively; P<0.001) and were less likely to be retained for the 6-month assessment (67 vs 95%, respectively; P<0.05). Controlling for demographic variables, study and baseline weight, the mean weight losses achieved were significantly less for young adults compared with adults (-4.3 kg (6.3) vs -7.7 kg (7.0), respectively; P<0.05); fewer young adults achieved > or =5% weight loss at 6 months compared with older participants (8/21 (38%) vs 171/277 (62%); P<0.05). After controlling for session attendance, differences in the mean weight loss were not significant (P=0.81). Controlling for baseline values, study and demographics, changes in total physical activity over the initial 6 months of treatment were less for young adults compared with adults, but these differences only approached statistical significance (P=0.07). CONCLUSION: These data indicate that standard programs do not meet the weight control needs of young adults. Research is urgently required to improve recruitment and retention efforts with this high-risk group.
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Terapia por Ejercicio/métodos , Obesidad/psicología , Cooperación del Paciente/psicología , Caminata/psicología , Pérdida de Peso , Adolescente , Adulto , Factores de Edad , Femenino , Grupos Focales , Conductas Relacionadas con la Salud , Humanos , Masculino , Minnesota/epidemiología , Actividad Motora , Obesidad/epidemiología , Obesidad/terapia , Evaluación de Programas y Proyectos de Salud , Rhode Island/epidemiología , Caminata/fisiología , Adulto JovenRESUMEN
OBJECTIVES: To examine whether a weight loss program delivered to one spouse has beneficial effects on the untreated spouse and the home environment. METHODS: We assessed untreated spouses of participants in three sites of Look AHEAD, a multicenter randomized controlled trial evaluating the impact of intentional weight loss on cardiovascular outcomes in overweight individuals with type 2 diabetes. Participants and spouses (n=357 pairs) were weighed and completed measures of diet and physical activity at 0 and 12 months. Spouses completed household food and exercise environment inventories. We examined differences between spouses of participants assigned to the intensive lifestyle intervention (ILI) or to the enhanced usual care (DSE; diabetes support and education). RESULTS: Spouses of ILI participants lost -2.2+/-4.5 kg vs -0.2+/-3.3 kg in spouses of DSE participants (P<0.001). In addition, more ILI spouses lost > or =5% of their body weight than DSE spouses (26 vs 9%, P<0.001). Spouses of ILI participants also had greater reductions in reported energy intake (P=0.007) and percent of energy from fat (P=0.012) than DSE spouses. Spouse weight loss was associated with participant weight loss (P<0.001) and decreases in high-fat foods in the home (P=0.05). CONCLUSION: The reach of behavioral weight loss treatment can extend to a spouse, suggesting that social networks can be utilized to promote the spread of weight loss, thus creating a ripple effect.
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Diabetes Mellitus Tipo 2/terapia , Angiopatías Diabéticas/terapia , Obesidad/terapia , Esposos/psicología , Índice de Masa Corporal , Pesos y Medidas Corporales , Diabetes Mellitus Tipo 2/psicología , Angiopatías Diabéticas/psicología , Ejercicio Físico , Femenino , Conductas Relacionadas con la Salud , Humanos , Masculino , Persona de Mediana Edad , Motivación , Conducta de Reducción del Riesgo , Pérdida de PesoRESUMEN
OBJECTIVE: The present study examined whether long-term weight loss maintenance is enhanced by maintaining the same diet regimen across the week and year or by dieting more strictly on weekdays and nonholiday periods than at other times. METHOD: National Weight Control Registry participants (N=1429) indicated on an eight-point scale whether they dieted more strictly on weekends than weekdays, adhered to the same diet regimen throughout the week, or dieted more strictly on weekdays. Participants responded to a similar question about holiday and vacation eating. Participants were then followed prospectively to determine whether scores on these questions were related to self-reported weight regain over the subsequent 12 months. RESULTS: There was a linear relationship between scores on the dieting consistency questions and weight change over the 1-y period (P's <0.01), with smaller weight gains in those who reported more consistency. Participants who reported a consistent diet across the week were 1.5 times more likely to maintain their weight within 5 pounds over the subsequent year (OR=1.58, 95% CI: 1.2-2.2) than participants who dieted more strictly on weekdays. A similar relationship emerged between dieting consistency across the year and subsequent weight regain. CONCLUSION: Dieting consistency appears to be a behavioral strategy that predicts subsequent long-term weight loss maintenance.
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Dieta Reductora/psicología , Conducta Alimentaria , Obesidad/dietoterapia , Adulto , Femenino , Estudios de Seguimiento , Vacaciones y Feriados , Humanos , Masculino , Persona de Mediana Edad , Obesidad/psicología , Periodicidad , Estudios Prospectivos , Recurrencia , Sistema de Registros , Aumento de PesoRESUMEN
While the majority of rheumatoid arthritis (RA) patients report that their pain is influenced by the weather, studies examining the impact of weather on RA pain have yielded equivocal results. It is not clear from the existing studies if the mixed results are due to limited statistical power (e.g. small sample sizes and restricted variability in weather indices) or the failure to consider individual differences. The current study addressed these weaknesses by having 75 RA patients (mean age = 52.7; 71% female) record their daily pain severity for 75 consecutive days. Objective weather indices including temperature, barometric pressure, relative humidity, and percentage of sunlight were obtained for the same dates from a local weather service. The results indicate that for the entire sample, pain levels were highest on cold, overcast days and following days with high barometric pressure. Pain levels also increased as a function of change in relative humidity from one day to the next. Individual difference analyses revealed significant variability between patients in their weather sensitivity patterns. In general, patients with higher levels of self-reported pain demonstrated more weather sensitivity. When considering the magnitude of these effects, however, weather variables accounted for only a small amount of change in pain scores. This pattern was true even for patients with the most pronounced pain-weather relationships. Thus, although weather sensitivity was found, the effect sizes were not clinically meaningful.
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Artritis Reumatoide/fisiopatología , Ritmo Circadiano/fisiología , Dolor/fisiopatología , Tiempo (Meteorología) , Adulto , Presión Atmosférica , Femenino , Humanos , Humedad , Masculino , Persona de Mediana Edad , Luz Solar , TemperaturaRESUMEN
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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Simulación por Computador , ADN/química , Proteínas de Unión al ADN/metabolismo , Modelos Moleculares , Conformación de Ácido Nucleico , Polidesoxirribonucleótidos/química , Rec A Recombinasas , Electricidad Estática , Proteína de Unión a TATA-Box , Factores de Transcripción/metabolismoRESUMEN
The deformability of double helical DNA is critical for its packaging in the cell, recognition by other molecules, and transient opening during biochemically important processes. Here, a complete set of sequence-dependent empirical energy functions suitable for describing such behavior is extracted from the fluctuations and correlations of structural parameters in DNA-protein crystal complexes. These elastic functions provide useful stereochemical measures of the local base step movements operative in sequence-specific recognition and protein-induced deformations. In particular, the pyrimidine-purine dimers stand out as the most variable steps in the DNA-protein complexes, apparently acting as flexible "hinges" fitting the duplex to the protein surface. In addition to the angular parameters widely used to describe DNA deformations (i.e., the bend and twist angles), the translational parameters describing the displacements of base pairs along and across the helical axis are analyzed. The observed correlations of base pair bending and shearing motions are important for nonplanar folding of DNA in nucleosomes and other nucleoprotein complexes. The knowledge-based energies also offer realistic three-dimensional models for the study of long DNA polymers at the global level, incorporating structural features beyond the scope of conventional elastic rod treatments and adding a new dimension to literal analyses of genomic sequences.
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ADN/química , Conformación de Ácido Nucleico , Proteínas/química , Dimerización , Modelos Moleculares , Unión Proteica , Purinas/química , Pirimidinas/químicaRESUMEN
Earlier a three-dimensional model for a new unusual DNA conformation referred to as Slipped Loop Structure (SLS) has been suggested by us (1). The same type of folding could occur with RNA as well which means that one must use the A-form of the double helix rather than the B-one. The present paper discusses the creation of an all-atom stereochemically sound model for SLS-RNA. This calculated model, while possessing the same folding topology as the SLS-DNA, differs dramatically from the SLS-DNA by an overall folding geometry. It also differs radically from the RNA-pseudoknot and can thus be regarded as a new type of an RNA folding.
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ARN/química , Secuencia de Bases , Estudios de Factibilidad , Modelos Moleculares , Datos de Secuencia Molecular , Conformación de Ácido NucleicoRESUMEN
High resolution chemical footprinting and cross-linking experiments have provided a basis for elucidating the overall architecture of the complex between the core DNA binding domain of p53 (p53DBD, amino acids 98-309) and the p21/waf1/cip1 DNA response element implicated in the G1/S phase cell cycle checkpoint. These studies complement both a crystal structure and earlier biophysical studies and provide the first direct experimental evidence that four subunits of p53DBD bind to the response element in a regular staggered array having pseudodyad symmetry. The invariant guanosines in the highly conserved C(A/T)|(T/A)G parts of the consensus half-sites are critical to the p53DBD-DNA binding. Molecular modeling of the complex using the observed peptide-DNA contacts shows that when four subunits of p53DBD bind the response element, the DNA has to bend approximately 50 degrees to relieve steric clashes among different subunits, consistent with recent DNA cyclization studies. The overall lateral arrangement of the four p53 subunits with respect to the DNA loop comprises a novel nucleoprotein assembly that has not been reported previously in other complexes. We suggest that this kind of nucleoprotein superstructure may be important for p53 binding to response elements packed in chromatin and for subsequent transactivation of p53-mediated genes.
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Ciclinas/química , Proteínas de Unión al ADN/química , ADN/química , Conformación de Ácido Nucleico , Estructura Secundaria de Proteína , Proteína p53 Supresora de Tumor/química , Secuencia de Bases , Sitios de Unión , Simulación por Computador , Inhibidor p21 de las Quinasas Dependientes de la Ciclina , Ciclinas/metabolismo , ADN/metabolismo , Metilación de ADN , Cartilla de ADN , Proteínas de Unión al ADN/metabolismo , Sustancias Macromoleculares , Modelos Moleculares , Datos de Secuencia Molecular , Oligodesoxirribonucleótidos/síntesis química , Oligodesoxirribonucleótidos/química , Reacción en Cadena de la Polimerasa , Programas Informáticos , Proteína p53 Supresora de Tumor/biosíntesis , Proteína p53 Supresora de Tumor/metabolismoRESUMEN
This study investigated individual differences in the diurnal cycle of cortisol and explored their relation to several psychosocial variables and to upper-respiratory symptoms. Cortisol and daily experience were assessed for 2 days in 109 healthy employed and unemployed community residents (mean age = 36.4 +/- 12.1, 69% female); self-report upper respiratory illness (URI) symptoms were assessed for an additional 10 days. Fifty-six (51%) participants showed typical declines in cortisol during both days, 19 (17%) showed no significant diurnal pattern on both days, and 34 (31%) showed different diurnal patterns on the 2 days. Individuals with no cycles did not differ from those with normal or inconsistent cycles on demographic factors, baseline psychological measures, health behaviors, or daily experiences over the two assessment days. Individuals without cortisol cycles, however, reported fewer URI symptoms than the remaining subjects. That 17% of our sample did not exhibit diurnal cycles of cortisol was surprising, given established views of normal endocrine function. Although average daily level of cortisol is related to a number of psychosocial and psychiatric factors (e.g. stress and depression), pattern of diurnal cycle was not related to any demographic or psychosocial measures in this study. The finding that flat cycles were related to fewer reports of URI symptoms suggests that perturbations in cycle may be related to processes associated with symptom susceptibility or symptom expression.
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Ritmo Circadiano/fisiología , Hidrocortisona/sangre , Individualidad , Adulto , Nivel de Alerta/fisiología , Depresión/sangre , Depresión/psicología , Susceptibilidad a Enfermedades/sangre , Susceptibilidad a Enfermedades/psicología , Femenino , Humanos , Masculino , Persona de Mediana Edad , Trastornos Psicofisiológicos/sangre , Trastornos Psicofisiológicos/psicología , Infecciones del Sistema Respiratorio/sangre , Infecciones del Sistema Respiratorio/psicología , Factores de Riesgo , Estrés Psicológico/complicaciones , Desempleo/psicologíaRESUMEN
The observed sequence dependence of the mean twist angles in 38 B-DNA crystal structures can be understood in terms of simple geometrical features of the constituent base-pairs. Structures with low twist appear to unwind in response to severe steric clashes of large exocyclic groups (such as NH2-NH2) in the major and minor grooves, while those with high twist are subjected to lesser contacts (H-O and H-H). We offer a simple clash function that depends on base-pair morphology (i.e. the chemical constitution of base-pairs) and satisfactorily accounts for the twist angles of the ten common Watson-Crick dimer steps both in the solid state and in solution. The twist-clash correlation that we find here still holds when extended to modified bases. In addition to Calladine's purine-purine clashes, we add other close contacts between bases in the grooves, and consider the conformational restrictions on the geometry of the sugar-phosphate backbone (namely, we emphasize the tendency of DNA to conserve virtual backbone length). The significance of this finding is threefold: (1) sequence-dependent DNA twisting is directly involved in protein-DNA interactions; (2) strong correlation between Twist and Roll helps to elucidate the bending of the double helix as a function of base sequence; (3) it is possible to anticipate the effects of chemical modifications on twisting and bending. The mutual correlations of other structural parameters with the twist make this angle a primary determinant of DNA conformational heterogeneity.
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ADN/ultraestructura , Conformación de Ácido Nucleico , Secuencia de Bases , ADN/química , Enlace de Hidrógeno , Modelos Estructurales , Datos de Secuencia Molecular , SolucionesRESUMEN
Description of open CAN format (Compressed Amino acids and Nucleotides) is presented for storing genetic information in compressed form in data banks (DB). Data compression principles are demonstrated in detail on examples of EMBL DB (sequences of nucleotides), SWISSPROT DB (sequences of amino acids) and PDB DB (3D structures). A unified compressed data format provides a possibility to integrate EMBL, SWISSPROT, and PDB DB in one data bank. We are going to use this approach for integration of GENBANK and other similar DBs. One of the outcomes of the research is a library of data retrieval procedures for access to DB, providing developers of the application software packages with a uniform interface to DBs with biologically related data. The proposed scheme for data representation was recommended by the Expert Commission of the Informatics Section of the RSSIP "Human Genome" as a standard for distribution of data banks in Russia.
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Bases de Datos Factuales , Programas Informáticos , Secuencia de Aminoácidos , Secuencia de Bases , Genoma Humano , Humanos , Conformación ProteicaRESUMEN
Short tandem repeats (5-8 base pairs) are not uncommon in the prokaryotic and eukaryotic DNA. Regions with such sequence motifs, when under superhelical stress, manifest unusual sensitivity to single-strand specific nuclease. To explain this, it has been suggested that one DNA thread should be shifted relatively to another, so that they could form two single-stranded loops protruding from the opposite chains and separated on the DNA helix by the length of a direct repeat. The structure was proposed to play a role in the regulation of transcription, organization of chromatin and in the recombination. Such type of folding could have been extra-stabilized by base pairing between the loops. This attractive possibility of the interloop minihelix formation requires a delicate stereochemical analysis and direct experimental support. Formation of the interloop minihelix in the Slipped Loop Structure (SLS) was tested by a chemical modification method at one nucleotide level resolution. The results show that bases located within the proposed interloop helix are well protected from the probes used. This fact encourages us to publish a 3-D model for the SLS-form DNA (and RNA). The SLS is characterized by a remarkable symmetry having three mutually perpendicular dyad axes. Scanning the bank of nucleotide sequences has revealed more than 500 sites, the transcripts of which are capable of folding into the SLS form, which allow us to regard the SLS form as a novel universal structural form. Remarkably, the abundance of SLS in intrones three times exceeds that of the coding sequences. This may reflect a functional role (or roles) of the SLS conformation.
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ADN/química , Conformación de Ácido Nucleico , Animales , Secuencia de Bases , Dicroismo Circular , Electroforesis , Humanos , Ratones , Datos de Secuencia Molecular , ARN Ribosómico 28S/química , ARN Ribosómico 28S/genética , ARN Nuclear Pequeño/química , ARN Nuclear Pequeño/genética , Receptores de Interleucina-1/química , Receptores de Interleucina-1/genéticaRESUMEN
We have performed a conformational analysis of DNA double helices with parallel directed backbone strands. The calculations were made for homopolymers poly(dG).poly(dC). All possible models of base binding were checked. By the potential energy optimization the dihedral angles and helices parameters of stable conformations of parallel double polynucleotides were calculated. The dependences of conformational energy on the base pair structure were studied. Possible structure of parallel helices with various nucleotide composition are discussed.
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ADN/química , Polidesoxirribonucleótidos/química , Conformación de Ácido NucleicoRESUMEN
A method has been developed to solve structures of DNA oligomers in solution from the experimental NOE data. The method is a combination of two approaches: (1) full matrix NOESY simulations and (2) conformational calculations of DNA double helix based on generalized helical parameters. The process of the refinement of a solution structure does not involve NMR-derived interproton distance constraints; rather it consists of a direct fitting of a structure to the experimental NOE data, a weighted sum of energy, and R factor being under minimization. A helical parameters-based generation of DNA forms makes it possible to organize the search for the optimal structure more effectively, systematically varying starting conformations. The method has been used to calculate a structure for the self-complementary DNA hexamer GGATCC, which is consistent with the available experimental data. The structure belongs to the B family of forms, although the local structural heterogeneity is very strong. Sugar puckers vary from O4'-exo to C3'-exo; helical steps are open with different magnitudes toward the minor groove. Next, we have addressed the question of how uniquely the structure is defined by the existing NMR data. Different structural parameters have been systematically varied, and their effect on individual NOE's and the R factor has been studied. Two energetically conjugated parameters, sugar puckers and glycosidic angles, can be determined very reliably, because of the strong dependences of the intraresidue H6/H8 to H2'/H2''/H3' NOE's. In contrast, the local helical conformation of DNA and the geometry of base pairs proved to be underdetermined by the existing NOE information, because the effect of any helical parameter on interproton distances can be compensated by the concerted changes in other parameters.
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Espectroscopía de Resonancia Magnética , Conformación de Ácido Nucleico , Oligodesoxirribonucleótidos/química , Composición de Base , Secuencia de Bases , Carbohidratos/química , Fenómenos Químicos , Química Física , Desoxirribonucleasa BamHI , Glicósidos/química , Datos de Secuencia Molecular , Estructura Molecular , SolucionesRESUMEN
The ability of oligonucleotides 3'-d(GT)5pO(CH2)5Opd(GT)5-5' (anti[d(GT)]) and 3'-d(GT)5pO(CH2)6Opd(GT)5-3' (par[d(GT)]) to form hairpins and higher associates is studied. Optical methods of thermal denaturation and circular dichroism as well as the fluorescence of ethidium bromide and acridine orange bound to oligonucleotides were used. At room temperatures the formation of hairpin structure with parallel and antiparallel strands is possible. Thermodynamic parameters of par[d(GT)] and anti[d(GT)] are similar and equal to delta H = -15 kcal/mol, delta S = -50 cal/mol. deg. In the temperature range 3-10 degrees C par[d(GT)] and anti[d(GT)] form four-stranded structures with parallel chains, in which layers of four G-residues alternate with unpaired T-residues being bulged out easily. On comparison of occurrence of alternating (GT)n, (GC)n and (G)n sequences in genome it can be stated that (GT)n biological functions could be connected with conformational possibilities of the four-stranded parallel structures with unpaired T-residues.
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Polidesoxirribonucleótidos/química , Secuencias Repetitivas de Ácidos Nucleicos , Dicroismo Circular , Etidio/química , Conformación de Ácido Nucleico , Desnaturalización de Ácido Nucleico , Espectrometría de FluorescenciaRESUMEN
To investigate the influence of thermal fluctuations on DNA curvature the Metropolis procedure at 300 K was applied to B-DNA decamers containing A5.T5 and A4.T4 blocks. Monte Carlo simulations have confirmed the DNA bending anisotropy: B-DNA bends most easily in a groove direction (roll). The A5.T5 block is more rigid than the other sequences; the pyrimidine-purine dimers are found to be the most flexible. For A5TCTCT, A5CTCTC, and A5GAGAG, the average bend angle per decamer is 20-25 degrees in a direction toward the minor groove in the center of the A5.T5 tract, which is consistent with both the "junction" and "wedge AA" models. However, in A5T5, A4T4CG, and T4A4GC, bending is directed into the grooves at the 5' and 3' ends of purine tracts. Thus, directionality of bending caused by An.Tn blocks strongly depends on their neighboring sequences. These calculations demonstrate that the sequence-dependent variation of the minor-groove width mimics the observed hydroxyl radical cleavage pattern. To estimate the effect of fluctuations on the overall shape of curved DNA fragments, longer pieces of DNA (up to 200 base pairs) were generated. For sequences with strong curvature (A5X5 and A4T4CG), the static model and Monte Carlo ensemble give similar results but, for moderately and slightly curved sequences (A5T5 or T4A4GC), the static model predicts a much smaller degree of bending than does the statistical representation. Considering fluctuations is important for quantitative interpretation of the gel electrophoresis measurements of DNA curvature, where both the static and statistical bends are operative.