George Pieczenik

Algorithms for Loop Matchings

A simplified (two-base) version of the problem of planar folding of long chains (e.g., RNA and DNA biomolecules) is formulated as a matching problem. The chain is prescribed as a loop or circular sequence of letters A and B, n units long. A matching here means a set of A-B base pairings or matches obeying a planarity condition: no two matches may cross each other if drawn on the interior of the loop. Also, no two adjacent letters may be matched. We present a dynamic programming algorithm requiring

Development of a novel synthetic oligopeptide for the detection of DNA damage in human spermatozoa

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Structural analysis of glycopeptides by polyacrylamide gel electrophoresis.

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Multimers of a suppressor transfer RNA: Supporting evidence for alternate conformations of the anticodon loop region☆

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Folding of two large nucleotide chains

storage which computes the size of the maximum for the given A-B base sequence and which also allows reconstructing a particular folded form of the original string which realizes the maximum matching size. The algorithm can be adapted to deal with sequences with larger alphabets and with weighted matchings.An algorithm is also presented for a modified problem closer to the biochemical problem of interest: We demand that every match must be adjacent to another match, forcing ...

Structural and combinatorial constraints on base pairing in large nucleotide sequences.

BACKGROUND The integrity of DNA in spermatozoa is considered an additional parameter of semen quality and a potential fertility predictor. Significant progress has been made in recent years towards the development of reliable tests for sperm chromatin integrity and DNA damage assessment. However, most of the techniques available are labor intensive, require expensive instrumentation or utilize enzymes whose activity could be compromised by the highly condensed nature of sperm chromatin. In addition, all the methods currently available involve the destruction of the sperm tested; none is able to select intact spermatozoa that could then be used for fertilization. The aim of the present study was to create a peptide ligand-based stain, capable of binding specific DNA structures, thereby revealing the presence of DNA damage, preferably in living cells. METHODS The peptide was bioinformatically modelled on the critical region of the p53 protein associated with DNA binding and fluorescently labeled with a terminal rhodamine B dye. The ability of this 21 amino acid synthetic peptide (DW1) to detect DNA damage in intact and fixed human spermatozoa was assessed in detail. Human sperm samples (n=20) were treated with reagents that induce single- and/or double-stranded DNA breaks. The effect of these treatments on peptide-labelling was measured and compared with results obtained using established tests for the evaluation of DNA damage, such as comet assay, terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL) and sperm chromatin dispersion test. RESULTS The peptide had a high affinity for single-stranded DNA, and DNA lesions such as double- and single-stranded breaks. The proportion of spermatozoa with intense staining was found to be closely associated with the percentage of cells possessing DNA damage. The analysis of 10 sperm samples using DW1 staining and TUNEL technique showed a significant correlation between the extent of DNA fragmentation for the two methods (r=0.892, Pearsons correlation, P<0.05). CONCLUSIONS We have produced a novel peptide-based stain capable of detecting DNA damage in individual sperm cells. Evaluation of sperm DNA fragmentation using this peptide may be an inexpensive and easier to use alternative to the tests in current use. Additionally, although DW1 currently requires removal of the membrane using a detergent, further research may allow this approach to be applied to the selection of viable spermatozoa with intact DNA for use in ICSI and/or intra-cytoplasmic morphologically selected sperm injection.

Inhibition of human spermatozoa–zona pellucida binding by a combinatorially derived peptide from a synthetic target

Abstract This work describes the use of polyacrylamide gel electrophoresis to resolve fluorescein-derivatized asialoglycopeptides. Specific exoglycosidase digestion of pronase glycopeptides of fetuin generates a series of degradation products that are resolved by polyacrylamide gel electrophoresis and are visualized by photography. The logarithm of the relative electrophoretic mobility of each degraded glycopeptide is linearly correlated to the number of monosaccharide residues sequentially removed by exoglycosidases. Such an approach allows the quantitative evaluation of the number of saccharide moieties removed by each enzyme at a detection sensitivity of less than 20 pmol of each compound. Use of specific endoglycosidases results in the direct sizing of oligosaccharide chains.

Combinatorial peptide library binding of mammalian spermatozoa identifies a ligand (HIPRT) in the axin protein: putative identification of a sperm surface axin binding protein and intriguing developmental implications

Abstract Multimeric aggregates of tyrosine suppressor tRNA have been identified. The formation of multimers requires a high concentration of tRNA, as is formed in an electrophoretic moving boundary, and a specific anticodon sequence. A simple model is presented where the anticodon loop, in an hf configuration (Crick et al. , 1976) interacts with the CCA stem of another tyrosine suppressor tRNA molecule.

Legal aspects of patenting time

We have already described the FOLD-A code designed for folding mRNAs and single stranded DNA molecules (Nussinov & Pieczenik, 1984). In this paper we describe its application to two long polynucleotide chains: the A protein gene of the MS2 RNA and the whole genome of the phi X 174 phage. The folded form of the single stranded DNA of the phi X 174 is a six armed star with the origin of replication in its center.

A positive-selection function for microRNA: an adaptor hypothesis revisited

In this paper we discuss the constraints and combinatorial problems of folding long RNA and single stranded DNA molecules into base paired structures. A computer code FOLD-A was designed to perform base pairing foldings of very long sequence chains and search for low energy configurations. The logic of the FOLD-A algorithm is described in some detail. The applications of FOLD-A to the A-protein gene of MS2 and the whole genome of the phi X 174 phage with over 5300 bases are discussed in the accompanying paper.