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PubMed1981

Sequence and properties of the human KB cell and mouse L cell D-loop regions of mitochondrial DNA.

The sequences of the displacement-loop (D-loop) regions of mitochondrial DNA (mtDNA) from mouse L cells and human KB cells have been determined and provide physical maps to aid in the identification of sequences involved in the regulation of replication and expression of mammalian mtDNA. Both D-loop regions are bounded by the genes for tRNAPhe and tRNAPro. This region contains the most highly divergent sequences in mtDNA with the exceptions of three small conserved sequence blocks near the 5' ends of D-loop strands, a 225 nucleotide conserved sequence block in the center of the D-loop strand template region, and a short sequence associated with the 3' ends of D-loop strands. A sequence similar to that associated with the 3' termini of D-loop strands overlaps one of the conserved sequence blocks near the 5' ends of D-loop strands. The large, central conserved sequence probably does not code for a protein since no open reading frames are discretely conserved. Numerous symmetric sequences and potential secondary structures exist in these sequences, but none appear to be clearly conserved between species.

Animals↗
PubMed2003

Molecular dynamics reveals the stabilizing role of loop closing residues in kissing interactions: comparison between TAR-TAR* and TAR-aptamer.

A RNA aptamer (R06) raised against the trans- activation responsive (TAR) element of HIV-1 was previously shown to generate a loop-loop complex whose stability is strongly dependent on the selected G and A residues closing the aptamer loop. The rationally designed TAR* RNA hairpin with a loop sequence fully complementary to the TAR element, closed by U,A residues, also engages in a loop-loop association with TAR, but with a lower stability compared with the TAR-R06 complex. UV absorption monitored thermal denaturation showed that TAR-TAR*(GA), in which the U,A kissing residues were exchanged for G,A, is as stable as the selected TAR-R06 complex. Consequently, we used the TAR-TAR* structure deduced from NMR studies to model the TAR-R06 complex with either GA, CA or UA loop closing residues. The results of the molecular dynamics trajectories correlate well with the thermal denaturation experiments and show that the increased stability of the GA variant results from an optimized stacking of the bases at the stem-loop junction and from stable interbackbone hydrogen bonds.

Base Pairing↗
PubMed2005

Solution structure of psi32-modified anticodon stem-loop of Escherichia coli tRNAPhe.

Nucleoside base modifications can alter the structures and dynamics of RNA molecules and are important in tRNAs for maintaining translational fidelity and efficiency. The unmodified anticodon stem-loop from Escherichia coli tRNA(Phe) forms a trinucleotide loop in solution, but Mg2+ and dimethylallyl modification of A37 N6 destabilize the loop-proximal base pairs and increase the mobility of the loop nucleotides. The anticodon arm has three additional modifications, psi32, psi39, and A37 C2-thiomethyl. We have used NMR spectroscopy to investigate the structural and dynamical effects of psi32 on the anticodon stem-loop from E.coli tRNA(Phe). The psi32 modification does not significantly alter the structure of the anticodon stem-loop relative to the unmodified parent molecule. The stem of the RNA molecule includes base pairs psi32-A38 and U33-A37 and the base of psi32 stacks between U33 and A31. The glycosidic bond of psi32 is in the anti configuration and is paired with A38 in a Watson-Crick geometry, unlike residue 32 in most crystal structures of tRNA. The psi32 modification increases the melting temperature of the stem by approximately 3.5 degrees C, although the psi32 and U33 imino resonances are exchange broadened. The results suggest that psi32 functions to preserve the stem integrity in the presence of additional loop modifications or after reorganization of the loop into a translationally functional conformation.

Anticodon↗
PubMed2006

A supersecondary structure library and search algorithm for modeling loops in protein structures.

We present a fragment-search based method for predicting loop conformations in protein models. A hierarchical and multidimensional database has been set up that currently classifies 105,950 loop fragments and loop flanking secondary structures. Besides the length of the loops and types of bracing secondary structures the database is organized along four internal coordinates, a distance and three types of angles characterizing the geometry of stem regions. Candidate fragments are selected from this library by matching the length, the types of bracing secondary structures of the query and satisfying the geometrical restraints of the stems and subsequently inserted in the query protein framework where their fit is assessed by the root mean square deviation (r.m.s.d.) of stem regions and by the number of rigid body clashes with the environment. In the final step remaining candidate loops are ranked by a Z-score that combines information on sequence similarity and fit of predicted and observed phi/psi main chain dihedral angle propensities. Confidence Z-score cut-offs were determined for each loop length that identify those predicted fragments that outperform a competitive ab initio method. A web server implements the method, regularly updates the fragment library and performs prediction. Predicted segments are returned, or optionally, these can be completed with side chain reconstruction and subsequently annealed in the environment of the query protein by conjugate gradient minimization. The prediction method was tested on artificially prepared search datasets where all trivial sequence similarities on the SCOP superfamily level were removed. Under these conditions it is possible to predict loops of length 4, 8 and 12 with coverage of 98, 78 and 28% with at least of 0.22, 1.38 and 2.47 A of r.m.s.d. accuracy, respectively. In a head-to-head comparison on loops extracted from freshly deposited new protein folds the current method outperformed in a approximately 5:1 ratio an earlier developed database search method.

Algorithms↗
PubMed2001

Loop fold nature of globular proteins.

Protein chains make numerous returns in globules, thus forming loops, closed by tight residue-to-residue contacts-closed loops. Previous statistical analysis of the sizes and locations of the closed loops in all major protein folds revealed that the loops have an almost standard contour length of 25-30 amino acid residues and follow one after another along the chain. In this work the closed loops of the major folds are presented in three dimensions. A special image filtering procedure is introduced that allows one to visualize the standard size closed loops for the first time. The loop positions along the sequences are verified by detection of loop-end clusters.

Data Interpretation, Statistical↗
PubMed2003

Dissection of the structural determinants involved in formation of the dimeric form of D-amino acid oxidase from Rhodotorula gracilis: role of the size of the betaF5-betaF6 loop.

The role of the long loop connecting beta-strands F5 and F6 (21 amino acids, Pro302-Leu-Asp-Arg-Thr-Lys-Ser-Pro-Leu-Ser-Leu-Gly-Arg-Gly-Ser-Ala-Arg-Ala-Ala-Lys-Glu322) present in Rhodotorula gracilis d-amino acid oxidase (RgDAAO) was investigated by site-directed mutagenesis. This loop was proposed to play an important role in the 'head-to-tail' monomer-monomer interaction of this dimeric flavoenzyme: in particular, by means of electrostatic interactions between positively charged residues of the betaF5-betaF6 loop of one monomer and negatively charged residues belonging to the alpha-helices I3' and I3" of the other monomer. We produced a mutant of RgDAAO (namely, DAAO-DeltaLOOP2), in which only minor structural perturbations were introduced (only five amino acids were deleted; new sequence of the betaF5-betaF6 loop is Pro302-Leu-Asp-Arg-Thr-Leu-Gly-Arg-Gly-Ser-Ala-Arg-Ala-Ala-Lys-Glu317), and the charge of the betaF5-betaF6 loop not modified. The DeltaLOOP2 mutant is monomeric, has a weaker binding with the FAD cofactor, a decrease of the kinetic efficiency, and slight modifications in its spectral properties. The short version of the loop does not allow a correct monomer-monomer interaction, and its presence in the monomeric DAAO is a destabilizing structural element since the DeltaLOOP2 mutant is highly susceptible to proteolysis. These results, confirming the role of this loop in the subunits interaction and thus in stabilization of the sole dimeric form of RgDAAO, put forward the evidence that even a short deletion of the loop generates a consistent variation of the enzyme structure-function properties.

D-Amino-Acid Oxidase↗
PubMed1996

Identification of G-protein binding sites of the human interleukin-8 receptors by functional mapping of the intracellular loops.

Interleukin 8 (IL-8) is considered to be a major mediator of the inflammatory response. Recent evidence indicates that a direct physical association occurs between IL-8 receptors and the alpha subunit of guanine nucleotide regulatory protein (Gi(alpha)2) upon stimulation of human neutrophils by IL-8. In the present study, we identified by site-directed mutagenesis key residues within the three intracellular loops of the IL-8RA receptor involved in the interaction with Gi(alpha)2. We first systematically mutated, in groups of two to four, all the residues in the three intracellular loops of the IL-8 type A receptor to alanine and analyzed the mutant receptors transiently expressed in 293 cells. Four residues in the second intracellular loop (Y136, L137, I139, V140) and one residue in the third intracellular loop (M241) were shown to be crucial for mediating calcium signaling in response to IL-8. Other residues in the second and third intracellular loops were also found to affect IL-8RA-mediated signaling, but to a lesser extent. These effects were not due to lower expression or low IL-8 binding affinities to the mutated receptors. Mutagenesis of the residues in the first intracellular loop had only weak effects on the mobilization of calcium induced by IL-8. We then used a coimmunoprecipitation protocol with anti-Gi(alpha)2 antibodies to determine the involvement of the two regions defined above in Gi(alpha)2 coupling to IL-8 type A receptors. Whereas the anti-Gi(alpha)2 antibodies coimmunoprecipitated IL-8 receptors in the wild-type cells, this interaction was lost in cells expressing mutated receptors that affected intracellular calcium mobilization. The peptides corresponding to the regions of the type A receptor found to be critical for Gi(alpha)2 coupling and induction of intracellular calcium mobilization were next introduced into cells expressing wild-type IL-8RA or IL-8RB to assess their role in coupling Gi(alpha)2 to both IL-8 receptors. The results obtained in the latter experiments suggest that the same regions of the second intracellular loop (Y136, L137, I139, V140) and of the third intracellular loop (M241) are critically involved in the coupling of both IL-8RA and IL-8 RB to Gi(alpha)2 as well as to a downstream effector (or effectors) involved in calcium mobilization.

Adult↗
PubMed1995

A model for technology assessment as applied to closed loop infusion systems. Technology Assessment Task Force of the Society of Critical Care Medicine.

OBJECTIVES: To test a model for the assessment of critical care technology on closed loop infusion control, a technology that is in its early stages of development and testing on human subjects. DATA SOURCES: A computer-assisted search of the English language literature and reviews of the gathered data by experts in the field of closed loop infusion control systems. STUDY SELECTION: Studies relating to closed loop infusion control that addressed one or more of the questions contained in our technology assessment template were analyzed. Study design was not a factor in article selection. However, the lack of well-designed clinical outcome studies was an important factor in determining our conclusions. DATA EXTRACTION: A focus person summarized the data from the selected studies that related to each of the assessment questions. The preliminary data summary developed by the focus person was further analyzed and refined by the task force. Experts in closed loop systems were then added to the group to review the summary provided by the task force. These experts' comments were considered by the task force and this final consensus report was developed. DATA SYNTHESIS: Closed loop system control is a technological concept that may be applicable to several aspects of critical care practice. This is a technology in the early stages of evolution and much more research and data are needed before its introduction into usual clinical practice. Furthermore, each specific application and each device for each application (e.g., nitroprusside infusion, ventilator adjustment), although based on the same technological concept, are sufficiently different in terms of hardware and computer algorithms to require independent validation studies. CONCLUSIONS: Closed loop infusion systems may have a role in critical care practice. However, for most applications, further development is required to move this technology from the innovation phase to the point where it can be evaluated so that its role in critical car practice can be defined. Each application of closed loop infusion systems must be independently validated by appropriately designed research studies. Users should be provided with the clinical parameters driving each closed loop system so that they can ensure that it agrees with their opinion of acceptable medical practice. Clinical researchers and leaders in industry should collaborate to perform the scientifically valid, outcome-based research that is necessary to evaluate the effect of this new technology. The original model we developed for technology assessment required the addition of several more questions to produce a complete analysis of an emerging technology. An emerging technology should be systematically assessed (using a model such as the model developed by the Society of Critical Care Medicine), before its introduction into clinical practice in order to provide a focus for human outcome validation trials and to minimize the possibility of widespread use of an unproven technology.

Algorithms↗
PubMed2000

Anterior loop of the mental canal: an anatomical-radiologic study.

This study sought to characterize the anatomical dimensions of the anterior mental loop and to determine the accuracy of conventional radiographs in identifying its presence and dimensions. The study group consisted of 46 hemimandibles fixed in formalin. Radiographs of the area between the mental foramen and the midline were obtained and evaluated for each hemimandible, followed by dissection and physical examination of the same area. Anatomically, an anterior loop of the mental nerve was observed in only 13 hemimandibles (28%). The anterior extension of the loop ranged from 0.4 to 2.19 mm. No correlation was found between the radiographic image and the anatomical shape of the loop. Of the radiographically diagnosed loops, 40% were not seen in anatomical examination. In cases with a false radiologic loop, a correlation was found between the diameter of the origin of the incisive canal and the radiologic interpretation of the loop. The radiologic appearance or diagnosis of the anterior mental loop in cadaver mandibles does not disclose the true ramification of the inferior alveolar nerve to the mental and incisive nerve.

Cadaver↗
PubMedDate not supplied

Closed-loop resuscitation of burn shock.

Fluid therapy for burn shock is adjusted to establish a target level of urinary output. However, the means for adjusting infusion rate are not defined. Our objective was to compare the performance of automated computer-controlled resuscitation with manual control for burn resuscitation. Sheep with a 40% TBSA full-thickness burn, administered under halothane anesthesia, were resuscitated to restore and maintain normal sheep urinary outputs in a target range of 1 to 2 ml/kg per hour over the course of 48 hours using closed-loop resuscitation (n = 10) or manual hourly adjustment of infusion rate (n = 11). The automated closed-loop resuscitation system is based on a proportional-integral-derivative algorithm, which adjusted infusion rate based on continuous monitoring and changes in urinary output. Mean urinary outputs over the course of 48 hours were in target range and were virtually identical at 1.9 +/- 0.5 ml/kg per hour for the closed-loop group and 2.0 +/- 0.7 ml/kg per hour for the technician group. Mean infusion rates and infused volumes also were similar. The closed-loop group exhibited significantly lower hourly variation for both urinary output and infusion rate compared hourly control. Hourly targets were achieved in 41% of the measurements in technician group compared with 48% for the closed-loop group (P = .23). Hourly urinary output in the technician group was undertarget by 25% as opposed to 16% with the closed-loop group (P = .02). Automated closed-loop control of infusion rates after burn injury produced urinary outputs in target ranges with less variation and less under target values than manual hourly adjustments. Closed-loop resuscitation may provide an improvement over current resuscitation regimens.

Algorithms↗
PubMed1987

The effects of Clostridium difficile crude toxins and toxin A on ileal and colonic loops in immune and non-immune rabbits.

Rabbits were solidly immunised by parenteral injection of purified Clostridium difficile toxin A such that they resisted an intravenous challenge with a normally lethal dose of toxin A. Ileal and colonic loops constructed in non-immune and immune animals received challenge injections of crude culture filtrate or purified toxin A of C. difficile. Protection of ileum was manifest after sufficient initial mucosal damage resulted in release of high levels of antitoxin A into the loop lumen of immune animals. There was less fluid accumulation in ligated ileal loops of immune than of non-immune rabbits. Less protection was observed when loops were challenged with crude culture filtrate containing toxins A and B than when challenged with purified toxin A. In-vitro studies with Ussing chambers yielded no evidence for tissue-localised immunity as judged by electrical responses and histology of toxin-treated tissue from non-immune and immune animals. No differences were found in the degree of epithelial damage, or volume or composition of fluid accumulating in colonic loops of non-immune and immune rabbits challenged with toxin A or crude culture filtrate. However, in colonic loops of immune rabbits there was no overt tissue-localised haemorrhage, whereas in those of non-immune rabbits tissue-localised haemorrhage was marked. In contrast to our findings with ileal loops, fluid accumulating in colonic loops was watery and contained substantially less total protein and (in immune animals) antitoxin A.

Animals↗
PubMed2024

PRC1 and CTCF-Mediated Transition from Poised to Active Chromatin Loops Drives Bivalent Gene Activation.

Polycomb Repressive Complex 1 (PRC1) and CCCTC-binding factor (CTCF) are critical regulators of 3D chromatin architecture that influence cellular transcriptional programs. Spatial chromatin structures comprise conserved compartments, topologically associating domains (TADs), and dynamic, cell-type-specific chromatin loops. Although the role of CTCF in chromatin organization is well-known, the involvement of PRC1 is less understood. In this study, we identified an unexpected, essential role for the canonical Pcgf2-containing PRC1 complex (cPRC1.2), a known transcriptional repressor, in activating bivalent genes during differentiation. Our Hi-C analysis revealed that cPRC1.2 forms chromatin loops at bivalent promoters, rendering them silent yet poised for activation. Using mouse embryonic stem cells (ESCs) with CRISPR/Cas9-mediated gene editing, we found that the loss of Pcgf2, though not affecting the global level of H2AK119ub1, disrupts these cPRC1.2 loops in ESCs and impairs the transcriptional induction of crucial target genes necessary for neuronal differentiation. Furthermore, we identified CTCF enrichment at cPRC1.2 loop anchors and at Polycomb group (PcG) bodies, nuclear foci with concentrated PRC1 and its tethered chromatin domains, suggesting that PRC1 and CTCF cooperatively shape chromatin loop structures. Through virtual 4C and other genomic analyses, we discovered that establishing neuronal progenitor cell (NPC) identity involves a switch from cPRC1.2-mediated chromatin loops to CTCF-mediated active loops, enabling the expression of critical lineage-specific factors. This study uncovers a novel mechanism by which pre-formed PRC1 and CTCF loops at lineage-specific genes maintain a poised state for subsequent gene activation, advancing our understanding of the role of chromatin architecture in controlling cell fate transitions.

Journal Article↗
PubMed2005

Generalized directed loop method for quantum Monte Carlo simulations.

Efficient quantum Monte Carlo update schemes called directed loops have recently been proposed, which improve the efficiency of simulations of quantum lattice models. We propose to generalize the detailed balance equations at the local level during the loop construction by accounting for the matrix elements of the operators associated with open world-line segments. Using linear programming techniques to solve the generalized equations, we look for optimal construction schemes for directed loops. This also allows for an extension of the directed loop scheme to general lattice models, such as high-spin or bosonic models. The resulting algorithms are bounce free in larger regions of parameter space than the original directed loop algorithm. The generalized directed loop method is applied to the magnetization process of spin chains in order to compare its efficiency to that of previous directed loop schemes. In contrast to general expectations, we find that minimizing bounces alone does not always lead to more efficient algorithms in terms of autocorrelations of physical observables, because of the nonuniqueness of the bounce-free solutions. We therefore propose different general strategies to further minimize autocorrelations, which can be used as supplementary requirements in any directed loop scheme. We show by calculating autocorrelation times for different observables that such strategies indeed lead to improved efficiency; however, we find that the optimal strategy depends not only on the model parameters but also on the observable of interest.

Journal Article↗
PubMed2002

Structures of Plasmodium falciparum triosephosphate isomerase complexed to substrate analogues: observation of the catalytic loop in the open conformation in the ligand-bound state.

The glycolytic enzymes of Plasmodium falciparum (Pf) are attractive drug targets as the parasites lack a functional tricarboxylic cycle and hence depend heavily on glycolysis for their energy requirements. Structural comparisons between Pf triosephosphate isomerase (PfTIM) and its human homologue have highlighted the important differences between the host and parasite enzymes [Velanker et al. (1997), Structure, 5, 751-761]. Structures of various PfTIM-ligand complexes have been determined in order to gain further insight into the mode of inhibitor binding to the parasite enzyme. Structures of two PfTIM-substrate analogue complexes, those of 3-phosphoglycerate (3PG) and glycerol-3-phosphate (G3P), have been determined and refined at 2.4 A resolution. Both complexes crystallized in the monoclinic space group P2(1), with a molecular dimer in the asymmetric unit. The novel aspect of these structures is the adoption of the 'loop-open' conformation, with the catalytic loop (loop 6, residues 166-176) positioned away from the active site; this loop is known to move by about 7 A towards the active site upon inhibitor binding in other TIMs. The loop-open form in the PfTIM complexes appears to be a consequence of the S96F mutation, which is specific to the enzymes from malarial parasites. Structural comparison with the corresponding complexes of Trypanosoma brucei TIM (TrypTIM) shows that extensive steric clashes may be anticipated between Phe96 and Ile172 in the 'closed' conformation of the catalytic loop, preventing loop closure in PfTIM. Ser73 in PfTIM (Ala in all other known TIMs) appears to provide an anchoring water-mediated hydrogen bond to the ligand, compensating for the loss of a stabilizing hydrogen bond from Gly171 NH in the closed-loop liganded TIM structures.

Animals↗
PubMed2003

Low free energy cost of very long loop insertions in proteins.

Long insertions into a loop of a folded host protein are expected to have destabilizing effects because of the entropic cost associated with loop closure unless the inserted sequence adopts a folded structure with amino- and carboxy-termini in close proximity. A loop entropy reduction screen based on this concept was used in an attempt to retrieve folded sequences from random sequence libraries. A library of long random sequences was inserted into a loop of the SH2 domain, displayed on the surface of M13 phage, and the inserted sequences that did not disrupt SH2 function were retrieved by panning using beads coated with a phosphotyrosine containing SH2 peptide ligand. Two sequences of a library of 2 x 10(8) sequences were isolated after multiple rounds of panning, and were found to have recovery levels similar to the wild-type SH2 domain and to be relatively intolerant to further mutation in PCR mutagenesis experiments. Surprisingly, although these inserted sequences exhibited little nonrandom structure, they do not significantly destabilize the host SH2 domain. Additional insertion variants recovered at lower levels in the panning experiments were also found to have a minimal effect on the stability and peptide-binding function of the SH2 domain. The additional level of selection present in the panning experiments is likely to involve in vivo folding and assembly, as there was a rough correlation between recovery levels in the phage-panning experiments and protein solubility. The finding that loop insertions of 60-80 amino acids have minimal effects on SH2 domain stability suggests that the free energy cost of inserting long loops may be considerably less than polymer theory estimates based on the entropic cost of loop closure, and, hence, that loop insertion may have provided an evolutionary route to multidomain protein structures.

Amino Acid Sequence↗
PubMed2006

Active TEM-1 beta-lactamase mutants with random peptides inserted in three contiguous surface loops.

Engineering of alternative binding sites on the surface of an enzyme while preserving the enzymatic activity would offer new opportunities for controlling the activity by binding of non-natural ligands. Loops and turns are the natural substructures in which binding sites might be engineered with this purpose. We have genetically inserted random peptide sequences into three relatively rigid and contiguous loops of the TEM-1 beta-lactamase and assessed the tolerance to insertion by the percentage of active mutants. Our results indicate that tolerance to insertion could not be correlated to tolerance to mutagenesis. A turn between two beta-strands bordering the active site was observed to be tolerant to random mutagenesis but not to insertions. Two rigid loops comprising rather well-conserved amino acid residues tolerated insertions, although with some constraints. Insertions between the N-terminal helix and the first beta-strand generated active libraries if cysteine residues were included at both ends of the insert, suggesting the requirement for a stabilizing disulfide bridge. Random sequences were relatively well accommodated within the loop connecting the final beta-strand to the C-terminal helix, particularly if the wild-type residue was retained at one of the loops' end. This suggests two strategies for increasing the percentage of active mutants in insertion libraries. The amino acid distribution in the engineered loops was analyzed and found to be less biased against hydrophobic residues than in natural medium-sized loops. The combination of these activity-selected libraries generated a huge library containing active hybrid enzymes with all three loops modified.

Amino Acid Sequence↗
PubMed1977

Ultrastructure of the human dermal microcirculation. II. The capillary loops of the dermal papillae.

Electron microscopy was used to define the ultrastructure of the capillary loops in the dermal papillae of normal, eczematous, and psoriatic skin. Capillary loops were reconstructed from 1-mum plastic-embedded sections. Ultrathin sections were taken at 4- to 6-mum intervals for correlation with the thick sections. The capillary loops of normal forearm and elbow skin could be divided into two segments: an intrapapillary and extrapapillary portion. The intrapapillary portion had the ultrastructural characteristics of an arterial capillary--homogeneous-appearing basement membrane without bridged fenestrations. The ascending limb in the extrapapillary portion was also an arterial capillary and the descending limb in the same portion had venous characteristics--multilayered basement membrane. The intrapapillary arterial loop developed venous characteristics abruptly after the vessel left the dermal papilla proper. The capillary loops in acute nummular eczema were identical in ultrastructure to those of normal skin. Bridged fenestrations were found in one capillary loop in eczema but not in normal skin. By contrast, the intrapapillary capillary loops in psoriasis were venous capillaries which were characterized by bridge fenestrations and multilayered basement membrane. The ultrastructural features of the capillary loops and those of the microcirculatory segments in the horizontal dermal plexus should provide sufficient criteria for one to evaluate the nature of vascular abnormalities that occur in the upper dermis.

Adult↗
PubMed1994

Polymorphic sequence in the D-loop region of equine mitochondrial DNA.

The D-loop regions in equine mitochondrial DNA were cloned from three thoroughbred horses by polymerase chain reaction (PCR). The total number of bases in the D-loop region were 1114 bp, 1115 bp and 1146 bp. The equine D-loop region is A/T rich like many other mammalian D-loops. The large central conserved sequence block and small conserved sequence blocks 1, 2 and 3, that are common to other mammals, were observed. Between conserved sequence blocks 1 and 2 there were tandem repeats of an 8 bp equine-specific sequence TGTGCACC, and the number of tandem repeats differed among individual horses. The base composition in the unit of these repeats is G/C rich as are the short repeats in the D-loops of rabbit and pig. Comparing DNA sequences between horse and other mammals, the difference in the D-loop region length is mostly due to the difference in the number of DNA sequences at both extremities. The similarities of the DNA sequences are in the middle part of the D-loop. In comparison of the sequences among three thoroughbred horses, it was determined that the region between tRNA(Pro) and the large central conserved sequence block was the richest in variation. PCR primers in the D-loop region were designed and the expected maternal inheritance was confirmed by PCR-RFLP (restriction fragment length polymorphism).

Animals↗