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

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, Pearson's 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.

The theory of genotypic selection: predicting the direction of evolution as a consequence of G:U base pairing and the existence of non-pathogenic strains of HIV-1.

One aspect of the Theory of Genotypic Selection states that G:U base pairs are selected for function and structure. RNA secondary structures stabilised by G:U base pairs are suggested to be involved in the evolution of attenuated strains of polio virus. Asymmetric mutations (C-->U and A-->G) and convergent evolutionary solutions are explained as a direct consequence of G:U base pairing. The possibility of a naturally occurring attenuated strain of HIV-1 is predicted.

Folding of two large nucleotide chains.

We have already described the FOLD-A code designed for folding mRNA's 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.

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

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.

Predicting coding function from nucleotide sequence or survival of "fitness" of tRNA.

The sequence of a nucleotide region of f1 bacteriophage was determined on a bonded ultrathin acrylamide gel with a discontinuous buffer system by using the dideoxy-DNA sequencing method. This sequence and one other were analyzed for maximal base pairing with tRNAs. The results allow a prediction of the direction and phase of possible coding functions. The implication of sequence constraints on mRNA codon frequency, tRNA structure, the origin of protein synthesis, and triplet reading are discussed in terms of neutral, Darwinian, and genotypic selectionist perspectives of evolution. The model of F. H. C. Crick, S. Brenner, A. Klug, and G. Pieczenik [(1976) Origins of Life 7, 389-397] for the origin of the genetic code is used to interpet contemporary adaptive and functional nucleic acid sequences.

A speculation on the origin of protein synthesis.

It is suggested that protein sythesis may have begun without even a primitive ribosome if the primitive tRNA could take up two configuration and could bind to the messenger RNA with five base-pairs instead of the present three. This idea would impose base sequence restriction on the early messages and on the early genetic code such that the first four amino acids coded were glycine, serine, aspartic acid and aspargine. A possible mechanism is suggested for the polymerization of the early message.