Destabilizing effect of a fluorouracil extra base in a hybrid RNA duplex compared with bromo and chloro analogues.

In the presence of cobalt, rhodium or iridium hexammine salts, the RNA/DNA hybrid r-GCUUCGGC-d(X)U (with X = F, Cl or Br) crystallizes as a double-stranded helix with four consecutive G-U and C-U mismatches. The deoxy chloro- and bromouracil derivatives are isomorphous, space group C2, unit-cell parameters a = 53.80, b = 19.40, c = 50.31 A, beta = 109.9 degrees, with the same infinite helix arrangement in the packing along the c axis with one extra DNA halogenouracil base included in the stacking. However, the fluorouracil derivative, with unit-cell parameters a = 53.75, b = 19.40, c = 45.84 A, beta = 105.7 degrees, is not isomorphous. The corresponding extra DNA base d(F)U of the second strand is ejected out of the helical stack, leading to a shortening of the c axis. The specific destabilization of the fluorouracil for the duplex building is analyzed in terms of the polarization effect of the halogen atom attached to the 3'-terminal base that modulates its interactions.

A zipper-like duplex in DNA: the crystal structure of d(GCGAAAGCT) at 2.1 A resolution.

BACKGROUND: The replication origin of the single-stranded (ss)DNA bacteriophage G4 has been proposed to fold into a hairpin loop containing the sequence GCGAAAGC. This sequence comprises a purine-rich motif (GAAA), which also occurs in conserved repetitive sequences of centromeric DNA. ssDNA analogues of these sequences often show exceptional stability which is associated with hairpin loops or unusual duplexes, and may be important in DNA replication and centromere function. Nuclear magnetic resonance (NMR) studies indicate that the GCGAAAGC sequence forms a hairpin loop in solution, while centromere-like repeats dimerise into unusual duplexes. The factors stabilising these unusual secondary structure elements in ssDNA, however, are poorly understood. RESULTS: The nonamer d(GCGAAAGCT) was crystallised as a bromocytosine derivative in the presence of cobalt hexammine. The crystal structure, solved by the multiple wavelength anomalous dispersion (MAD) method at the bromine K-edge, reveals an unexpected zipper-like motif in the middle of a standard B-DNA duplex. Four central adenines, flanked by two sheared G.A mismatches, are intercalated and stacked on top of each other without any interstrand Watson-Crick base pairing. The cobalt hexammine cation appears to participate only in crystal cohesion. CONCLUSIONS: The GAAA consensus sequence can dimerise into a stable zipper-like duplex as well as forming a hairpin loop. The arrangement closes the minor groove and exposes the intercalated, unpaired, adenines to the solvent and DNA-binding proteins. Such a motif, which can transform into a hairpin, should be considered as a structural option in modelling DNA and as a potential binding site, where it could have a role in DNA replication, nuclease resistance, ssDNA genome packaging and centromere function.

The use of intraoperative radiolymphoscintigraphy for sentinel node biopsy in patients with malignant melanoma.

BACKGROUND: Selective lymphadenectomy or "sentinel node" biopsy has been introduced recently by Morton and colleagues (Arch Surg 1992;127:392-9) to stage patients with intermediate and thick malignant melanomas. It has proven to be an effective way to identify nodal basins at risk for metastasis without the morbidity of a complete lymph node dissection. The majority of biopsies can be performed under local anesthesia with small incisions, but technical difficulties occasionally result in unsuccessful explorations. Identification of the sentinel node can be enhanced by a intraoperative radiolymphoscintigraphy, a technique introduced Alex and Krag (Surg Oncol 1993;137-43) that uses radiolabeled sulfur colloid and a hand-held gamma probe. OBJECTIVE: We used intraoperative radiolymphoscintigraphy in conjunction with 1% lymphazurin blue dye to define the sentinel node(s) in 148 patients with greater than 0.76 mm in thickness or Clark level IV melanomas. Sentinel lymph nodes were isolated, harvested, and examined using conventional histopathology, and immunohistochemistry for S-100 and HMB-45 antibodies. RESULTS: The overall success rate of sentinel lymph node localization was 97% using a combination of the two techniques. Twenty-one (14%) patients had micrometastasis, and 17 of these subsequently underwent complete lymph node dissection. A total of 220 of 275 (80%) sentinel nodes harvested were radioactive or "hot" compared with 165 of 275 (60%) with the blue dye alone. Four of the patients with micrometastasis had sentinel nodes positive by gamma probe, but negative by blue dye mapping techniques. CONCLUSION: Our results suggest that intraoperative radiolymphoscintigraphy using a hand-held gamma detecting probe improves the identification of sentinel lymph nodes during selective lymphadenectomy. This may reduce the number of "unsuccessful explorations" using the vital blue dye technique for lymphatic mapping, and appeal to a greater variety of surgeons, including dermatologic surgeons.

A continuous transition from A-DNA to B-DNA in the 1:1 complex between nogalamycin and the hexamer dCCCGGG.

The antibiotic nogalamycin, a drug with high specificity for TG and CG steps in double-stranded DNA, has been crystallized as a 1:1 complex with the hexamer d(CCCGGG). The antibiotic is inserted at the central CG step of the duplex, with the two sugars oriented in the same direction and with strong interactions with the DNA within the grooves. The amino-glucose residue makes an integral part of a well defined major groove hydration network with van der Waals contacts and several strong hydrogen bonds to the duplex. The nogalose residue resides in the minor groove, making primarily van der Waals contacts. The single site allows an accurate molecular description of the intercalation, without perturbations from end effects observed previously. The local unwinding induced by nogalamycin is completely relaxed 2 base pairs away from the intercalation site. The two strands of the DNA show a continuous deformation from the A to the B form: 1) the cytosines toward the 5' end of the nogalomycin site in each strand have c3'-endo conformations while 5 guanosines toward the 3' ends have c2'-endo conformations; 2) within each strand, the phosphate-phosphate distances increase in a continuous manner from 5.7 A (A-form) to 7.1 A (B-form).

The tumor biology of melanoma nodal metastases.

Approximately 20 per cent of melanomas greater than 0.76 mm in thickness will metastasize to the regional lymph nodes if treated with wide local excision alone (WLE). Elective lymph node dissection (ELND) is associated with significant morbidity, which includes lymphedema, wound complications, and paresthesias of the extremity. An alternative operative approach uses selective lymphadenectomy with the identification of the sentinel node, defined as the first node in the lymphatic basin that drains the primary cutaneous site. This study consisted of 132 patients with melanomas greater than 0.76 mm. One hundred nine patients (83%) had histologic negative sentinel nodes, and 23 patients (17%) had one or more sentinel nodes positive for disease. In patients with metastatic disease, 30/35 (86%) sentinel nodes were positive, and 25/357 (7%) nonsentinel nodes were positive (P < 0.001). In 18 patients (78%) of the 23 patients with metastatic disease, the sentinel node was the only node positive, strongly suggesting that there is an orderly progression of metastases. Two patients developed metastatic nodal disease after removal of a negative sentinel node (false negative rate = 1.5). The mean follow-up was 1 year. Sentinel node histology reflects the histology of the remainder of the nodes in the lymphatic basin and "skip" metastases, defined as a negative sentinel node but positive nodes higher in the regional chain positive for metastases or an axillary recurrence after a negative sentinel node biopsy, are rare for malignant melanoma. Harvesting the sentinel node in patients with intermediate or greater thickness melanoma will, therefore, identify a subset of patients with metastatic disease who have the most to benefit from a complete node dissection. This surgical approach allows for complete pathological staging and therapeutic management of patients while significantly reducing expense and overall morbidity.

Self-association of a DNA loop creates a quadruplex: crystal structure of d(GCATGCT) at 1.8 A resolution.

BACKGROUND: The flexibility of DNA enables it to adopt three interconvertible types of duplex termed the A-, B- and Z-forms. It can also produce hairpin loops, triplex structures and guanine-rich quadruplex structures. Conformational flexibility assists in the tight packaging of DNA, for example in chromosomes. This is important given the large quantity of genetic information that must be packaged efficiently. Moreover, the ability of DNA to specifically self-associate or interact with complementary sequences is fundamental to many biological processes. Structural studies provide information about DNA conformation and DNA-DNA interactions and suggest features that might be relevant to how the molecule performs its biological role. RESULTS: We have characterized the structure of a synthetic heptanucleotide that folds into a novel loop structure. The loop is stabilized by association with a cation, by intra-strand hydrogen bonds between guanine and cytosine that are distinct from the normal Watson-Crick hydrogen bonds, and by van der Waals interactions. Two loops associate through the formation of four G.C pairs that exhibit pronounced base-stacking interactions. The formation of a symmetric A.A base pair further stabilizes loop dimerization. Stacking of the A.A pair on a symmetry-related A.A pairing assists the formation of a four-stranded assembly. A T.T pairing is also observed between symmetry-related loops. CONCLUSIONS: This analysis provides a rare example of an experimentally determined non-duplex DNA structure. It provides conformational detail relevant to the tight packaging or folding of a DNA strand and illustrates how a cation might modulate phosphate-phosphate repulsion in a tightly packed structure. The observation of base quartets involving G.C base pairs suggests a further structure to be considered in DNA-DNA interactions. The structure also provides detailed geometries for A.A and T.T base pairs.

Metabolic balance studies in premature infants.

Many investigators over the past three decades have successfully conducted traditional metabolic balance studies in efforts to determine the retention rates of key nutrients important to the optimal growth of preterm infants. Differences in methodologies discussed in this review may explain the inconsistent results of balance studies reported for some nutrients, particularly calcium. These methodologic differences include (1) variability in nutrient intake and nutritional course prior to the balance period, (2) differences in the method of stool collection (with and without markers), (3) use of single versus repeated balance periods, and (4) different durations of balance periods. The data presented here suggest that the variability of net fat absorptions among VLBW infants was decreased when an acclimation period of nutrient intake supportive of growth was provided prior to a metabolic balance study. In addition, the use of markers affected the estimates of net calcium absorption but not fat absorption. Additional factors that may influence net calcium absorption and methods for the estimation of calcium absorption in VLBW infants warrant further investigation. This review describes the methods of specimen collection for metabolic balance studies in VLBW preterm infants that demonstrated reproducible data. The recent application of stable isotope methodology to metabolic balance studies can be extremely advantageous in identifying the rates of nutrient absorption versus endogenous secretion in the GI tract.

Structure of a mispaired RNA double helix at 1.6-A resolution and implications for the prediction of RNA secondary structure.

The nonamer r(GCUUCGGC)dBrU, where dBrU is 5-bromo-2'-deoxyuridine, contains the tetraloop sequence UUCG. It crystallizes in the presence of Rh(NH3)6Cl3. In solution the oligomer is expected to form a hairpin loop but the x-ray structure analysis, to a resolution of 1.6 A, indicates an eight-base-pair A-RNA duplex containing a central block of two G.U and two C.U pairs. Self-pairs which approximate to Watson-Crick geometry are also formed in the extended crystal structure between symmetry-related BrU residues and are part of infinite double-helical stacks. The G.U pair is a wobble base pair analogous to the G.T pair found in DNA fragments. The C.U mismatch involves one hydrogen-bonded contact between the bases and a bridging water molecule which ensures a good fit of the base pair in the RNA helix. The BrU.BrU pair is held by two hydrogen bonds in an orientation which is compatible with duplex geometry. The structure observed within the crystal has some parallels with the structure of globular RNAs, and the presence of stable, noncanonical base pairs has implications for the prediction of RNA secondary structure.

Perineal reconstruction after surgical extirpation of pelvic malignancies using the transpelvic transverse rectus abdominal myocutaneous flap.

BACKGROUND: The nonhealing perineal wound is often a catastrophic complication after aggressive surgical extirpation of pelvic malignancies. METHODS: Eleven patients underwent perineal reconstruction using an inferiorly based transpelvic transverse rectus abdominal myocutaneous (TRAM) flap for large nonhealing postsurgical perineal wounds. After debridement of the perineum, the rectus muscles and their skin islands were mobilized, preserving their inferior epigastric blood supply. The flap was then taken through the midline abdominal incision transpelvically into the perineal defect. The study population was composed of three men and eight women ranging in age from 43 to 76 years (mean 59). The primary diagnosis was recurrent carcinoma of the rectum or anus (n = 5), recurrent squamous cell carcinoma of the vulva or cervix (n = 4), and recurrent sacral chordoma (n = 2). All patients had received adjuvant radiation therapy and all patients had undergone one to four previous attempts at perineal closure. The perineal defect ranged in size from 72 cm2 to 1,250 cm2 (mean 337). RESULTS: There were no perioperative deaths. Ten of the 11 patients (91%) had primary wound healing of the TRAM flap, perineal wound, and donor site. One patient with recurrent chordoma developed recurrent tumor at the suture line 4 months postoperatively. CONCLUSIONS: The inferiorly based transpelvic TRAM flap is a safe and effective reconstructive technique for recalcitrant nonhealing perineal wounds after extirpation of pelvic malignancies.

Identification of submicroscopic lymph node metastases in patients with malignant melanoma.

In order to detect micrometastatic disease, our laboratory has developed a method for evaluating lymph node sections from patients with stage 1 or 2 melanoma. Lymph nodes isolated from standard dissections are bivalved; one half is subjected to routine histopathological evaluation and the other half disrupted and placed into cell culture. The cultured cells are identified by cytologic examination, immunohistologic staining, and the presence of melanoma-associated antigens. Lymph nodes (448) from 62 patients with malignant melanoma were evaluated by tissue culture. Fifteen patients were upgraded from stage 1 or 2 to stage 3 disease after micrometastases were identified in lymph node cultures. Recurrence of disease in histologically node negative patients, during a mean 24-month follow-up, has only been observed thus far in patients with culture positive lymph nodes. In addition, these results add evidence to the belief that missed micrometastatic disease in regional nodes is a sign of occult systemic metastases that would account for the defined recurrence rate in histologically node negative patients.

Detection of submicroscopic lymph node metastases in patients with melanoma.

A cell culture technique was developed to investigate submicroscopic lymph node metastases in patients with stage 1 or 2 malignant melanoma. Lymph nodes were isolated from standard dissections and bivalved. Half of the node was evaluated by routine histopathologic examination, while the other half was processed and placed into tissue culture. Three hundred twenty-three lymph nodes were collected from 41 patients. The cell culture technique identified 155 of 323 lymph nodes containing micrometastases, while only 20 of 323 lymph nodes tested positive with routine histochemical processing. Nine patients were upgraded from stage 1 or 2 to stage 3 disease after micrometastases were identified in lymph node cultures. Identification of melanoma was confirmed by cytologic examination, immunohistologic staining, and the presence of GD3 ganglioside and 250-kd glycoprotein melanoma-associated antigens. This study provides evidence that the culture of lymph nodes is a sensitive method for the detection of micrometastases. In addition, this procedure may change prognosis and identify candidates for adjuvant therapies.

Localization of malignant melanoma using monoclonal antibodies.

Finding a screening test to evaluate patients with cancer for occult metastatic disease, as well as imaging all known disease, is a goal of research efforts. Twenty-nine evaluable patients with deeply invasive (stage I), regional nodal (stage II), or systemic (stage III) melanoma underwent imaging by administration of a preparation of the antimelanoma antibody labeled with technetium 99m. Scan results indicated that 28 of 32 confirmed metastatic sites were imaged with this technique (88% sensitivity). Analysis of the individual positive sites revealed that nodal basins and visceral metastases accounted for the highest percentage of metastatic sites imaged, with 14 (88%) of 16 nodal basin metastases and all four visceral metastases being detected through imaging. Occult nodal disease was detected in the iliac nodal chain in two of the 29 patients. The imaging of benign tumors and nodal basins not containing disease accounted for a confirmed false-positive rate of 21%. Three (10%) of the 29 scan results were confirmed to be false-negative. In vivo tumor localization with monoclonal antibodies showed a sensitivity similar to that of other roentgenographic procedures for identifying metastatic disease and was useful in two of three patients in identifying occult iliac nodal disease, a region that is difficult to evaluate with physical examination and other imaging modalities.

The expanding role of lymphoscintigraphy in the management of cutaneous melanoma. First Place Winner: Conrad Jobst award.

Accepted therapy for intermediate-thickness melanomas is wide local excision and regional lymphadenectomy for nodes known to be in the lymph drainage basin. Lymphoscintigraphy has been shown to be of great help in predicting the drainage pattern of truncal, shoulder, proximal extremity, and head and neck melanomas. Lymphoscintigraphy using Technetium-99 antimony sulfur colloid was performed on 17 patients with cutaneous melanomas at H. Lee Moffitt Cancer Center at the University of South Florida. Of 13 patients with primary truncal and shoulder lesions, drainage patterns were discordant 54 per cent of the time and resulted in dissection of nodal groups different than would otherwise have been planned. This resulted in several lymph nodes positive for metastatic disease removed from operative sites not expected to show metastatic spread by clinical experience alone. The discordant rate for head and neck drainage was also high with 2 of 3 forehead studies showing drainage to both anterior and posterior cervical chains when only anterior chain drainage was expected, while only one of these drained to the preauricular nodes. Again, this led to elective lymph-node dissections of nodal basins not anticipated on clinical grounds alone. After a mean follow-up of 2 years, in which 60 to 75 per cent of all recurrences from melanoma are expected to occur, there has been no lymph-node metastasis development in basins that were not predicted by the scan. It is clear from our data that well-known historical patterns of lymph drainage in addition to the clinical impression of experienced surgeons cannot reliably predict the lymphatic drainage of many truncal, shoulder, and head and neck melanomas.(ABSTRACT TRUNCATED AT 250 WORDS)

Results of a multicenter outpatient burn study on the safety and efficacy of Dimac-SSD, a new delivery system for silver sulfadiazine.

Dimac with silver sulfadiazine (Dimac-SSD), a new silver sulfadiazine delivery system, was evaluated prospectively in a multicenter study for the treatment of outpatient burn injuries. The goal of this study was to evaluate the effect of Dimac-SSD on the microbiology of the burn wounds and to quantitate its clinical safety and efficacy. A total of 197 patients were evaluated. Eight (4%) of these patients did not complete the study. Six patients withdrew because of local discomfort caused by the Dimac-SSD and two patients were terminated because of technical problems. The mean +/- SD duration of treatment with Dimac-SSD was 12 +/- 8.5 days, during which time the mean number of dressing changes was 2.9 per patient. During treatment with Dimac-SSD, the burn wound bacterial flora remained stable and overgrowth with Pseudomonas species or Gram-negative bacilli did not occur. Only four (2%) patients developed clinical infections; thus the Dimac-SSD appeared to have good antimicrobial effectiveness. This dressing was not associated with any organ system or metabolic side-effects and patient discomfort during application and removal was minimal. Thus this new delivery system for silver sulfadiazine was associated with excellent wound healing, a low incidence of wound infections, reduced frequency for dressing changes, and excellent patient compliance.

Refined crystal structure of an octanucleotide duplex with I.T. mismatched base pairs.

The structure of the synthetic deoxyoctamer d(GGIGCTCC) has been determined by single crystal X-ray diffraction techniques to a resolution of 1.7A. The sequence crystallises in space group P6(1), with unit cell dimensions a = b = 45.07, c = 45.49A. The refinement converged with a crystallographic residual R = 0.14 and the location of 81 solvent molecules. The octamer forms an A-DNA duplex with 6 Watson-Crick (G.C) base pairs and 2 inosine-thymine (I.T) pairs. Refinement of the structure shows it to be essentially isomorphous with that reported for d(GGGGCTCC) with the mispairs adopting a "wobble" conformation. Conformational parameters and base stacking interactions are compared to those for the native duplex d(GGGGCCCC) and other similar sequences. A rationale for the apparent increased crystal packing efficiency and lattice stability of the I.T octamer is given.

Coexistence of A- and B-form DNA in a single crystal lattice.

It is well known that DNA can exist in a variety of conformations which can be interconverted by relatively mild changes in conditions. The in vivo conformation of DNA is usually thought to be the B form, but there is recent evidence that other conformations may be important in DNA-protein recognition. Different fragments of DNA crystallized under virtually identical conditions can form A, B or Z helices. A fragment that adopted an A conformation in a crystal was found in the B conformation in solution, whereas NMR spectroscopy of A-DNA films revealed the presence of a substantial amount of disordered B-DNA. Until now, however, a DNA fragment of a given sequence has not been crystallized in more than one global conformation. We report here an X-ray diffraction study of crystals of the DNA octamer dGGBrUABrUACC. In addition to a 'framework' of A-DNA, which gives discrete X-ray reflections, there are partially disordered B-DNA helices, recognized by their diffuse scattering features.