Sequence Length Calculator

Sequence length is the starting point for three separate physical quantities. Molecular weight is computed by summing residue masses and subtracting the water lost at each bond, since polymerisation is a condensation reaction releasing 18.02 g/mol per linkage. The deoxynucleoside monophosphates average roughly 331 for dAMP, 307 for dCMP, 347 for dGMP and 322 for dTMP, which is why the familiar shortcuts hold: about 330 Da per single-stranded base, about 650 Da per base pair of duplex DNA, and about 110 Da per amino acid residue. Physical extension follows from helical geometry. B-form DNA rises 0.34 nm per base pair with roughly 10.5 base pairs per turn and a diameter near 2 nm; A-form RNA duplex is more compressed at about 0.28 nm per base; an extended polypeptide contributes roughly 0.35 nm per residue. The scale of the results is often the useful output. Lambda phage DNA at 48,502 bp is about 16.5 micrometres long, the E. coli genome at 4.6 Mb approaches 1.6 mm, and a diploid human genome of roughly 6.4 Gb amounts to close to two metres of DNA inside one nucleus. Coding arithmetic is equally direct: three nucleotides per codon means an open reading frame of n bases encodes about n/3 minus one residues once the stop codon is removed. Several caveats apply. Circular molecules have n phosphodiester bonds rather than n-1, so the water correction changes. The average isotopic masses used here differ from the monoisotopic masses reported by mass spectrometry, and a terminal 5-prime phosphate adds roughly 79 Da. Contour length is also not end-to-end distance: double-stranded DNA has a persistence length near 50 nm, so anything longer than a few hundred base pairs behaves as a flexible coil rather than a rigid rod.

The dimensional constants used here come from fibre diffraction. Rosalind Franklin and Raymond Gosling's B-form images at King's College London showed a helical repeat of 3.4 nm with ten residues per turn, and Watson and Crick's 1953 model converted that into the 0.34 nm rise per base pair still quoted today. The solution value was later refined to about 10.5 base pairs per turn through work in the late 1970s and early 1980s by James Wang and by Daniel Rhodes and Aaron Klug, who measured the periodicity of nuclease cutting on surface-bound DNA. Maurice Wilkins, Franklin and colleagues had meanwhile established the A-form geometry that RNA duplexes adopt, with its shorter axial rise. Measuring length itself moved through several technologies. Before sequencing, sizes were inferred from sedimentation coefficients, viscometry and electron microscopy contour tracing. Agarose gel electrophoresis, standardised in the 1970s with markers such as the lambda HindIII digest, made size estimation routine to within a few percent. Frederick Sanger's dideoxy method, published in 1977 and applied to the 5,386-nucleotide bacteriophage phi X174 genome, replaced estimation with exact counts, and length became a property read directly from a file rather than measured on a bench. Residue mass tables of the kind used in this calculation were assembled from the amino acid and nucleotide chemistry literature and are maintained today by resources such as ExPASy and the EMBOSS suite.