We report the complete thermodynamic library of all 10 Watson-Crick DNA nearest-neighbor interactions. We obtained the relevant thermodynamic data from calorimetric studies on 19 DNA oligomers and 9 DNA polymers. We show how these thermodynamic data can be used to calculate the stability and predict the temperature-dependent behavior of any DNA duplex structure from knowledge of its base sequen...

The discovery of naturally occurring enzymes which cleave DNA at sites specific to particular nucleotide sequences has had a great impact on molecular biology. The function of these enzymes in uivo is to protect bacterial cells from viral invasion by degradation of foreign DNA. Several hundred of these “restriction” enzymes are known and they are a very common tool both for analysis and manipul...

We present a computer method utilizing published values for base pairing energies to compute the most energetically favorable secondary structure of an RNA from its primary nucleotide sequence. After listing all possible double-helical regions, every pair of mutally incompatible regions (whose nucleotides overlap) is examined to determine whether parts of those two regions can be combined by br...

Primitive platyhelminths, especially Acoel turbellarians, are thought to be key to understanding the origin and evolution of metazoa. In order to infer their phylogenetic position within the phylum Platyhelminths, we determined and compared the complete nucleotide sequence of a region of about 750 base pairs in the central part of an 18S rDNA for ten turbellarians, including two species of the ...

The DNA-binding region of Myb consists of three imperfect tandem repeats (R1, R2, and R3). We have determined the solution structure of a specific DNA complex of the minimum DNA-binding domain (R2R3) by heteronuclear multidimensional NMR. Both R2 and R3 contain three helices, and the third helix in each is found to be a recognition helix. R2 and R3 are closely packed in the major groove, so tha...

Ribosomal RNAs have secondary structures that are maintained by internal Watson-Crick pairing. Through analysis of chordate, arthropod, and plant 5S ribosomal RNA sequences, we show that Darwinian selection operates on these nucleotide sequences to maintain functionally important secondary structure. Insect phylogenies based on nucleotide positions involved in pairing and the production of seco...

GC content bias describes the dependence between fragment count (read coverage) and GC content found in Illumina sequencing data. This bias can dominate the signal of interest for analyses that focus on measuring fragment abundance within a genome, such as copy number estimation (DNA-seq). The bias is not consistent between samples; and there is no consensus as to the best methods to remove it ...

DNA sequences of 56 human genes for which information on both exons and introns was available were examined. The variance in G+C content among genes is estimated and shown to be substantial. There is a high correlation in G+C content between exons and introns within the same gene. The dinucleotide frequencies of introns are similar to those of intergenic spacer regions and are in reasonable agr...

The nucleotide sequence has been determined for a 664-base pair region of maize (Zea mays L.) mtDNA which contains the 3' end of the 18S rRNA gene, the 5S rRNA gene, and an intergenic region of 108 base pairs. Specific regions of the 18S rRNA gene show striking homology with the corresponding gene in Escherichia coli.

Mononucleotide conformations are important in understanding the structural aspects of nucleic acids and polynucleotides. In order to study the influence of stacking interactions between adjacent bases in a polynucleotide on the preferred conformations of mononucleotides, conformational energy calculations have been carried out on dinucleoside monophosphate fragments. Four base sequences-d(ApT),...