Reverse Complement Calculator

Base pairing is governed by hydrogen bonding geometry and size complementarity. Purines (A, G) are two-ring structures that pair with pyrimidines (T/U, C) which are one-ring structures, maintaining a constant helix diameter. A-T pairs form two hydrogen bonds, while G-C pairs form three. Any other pairing would create geometric distortions incompatible with the regular DNA helix structure.

Chargaff's first rule states that in any double-stranded DNA, %A = %T and %G = %C (the base pair rule). Chargaff's second rule states that this approximate equality also holds for single-stranded DNA (within a single strand), which is a statistical tendency rather than a strict chemical requirement. These rules were key evidence leading to the Watson-Crick model of DNA structure.

The human genome has approximately 3.2 billion base pairs with ~41% GC content. This gives roughly 1.89 billion A-T pairs (× 2 H-bonds) + 1.31 billion G-C pairs (× 3 H-bonds) = approximately 7.71 billion hydrogen bonds per haploid genome. Each diploid cell has about 15.4 billion hydrogen bonds across all chromosomes.

Hydrogen bond count is correlated with Tm but does not predict it accurately alone. Base stacking interactions (van der Waals forces between adjacent base pairs) actually contribute more to duplex stability than hydrogen bonds. Nearest-neighbor models that account for both stacking and base pairing provide much more accurate Tm predictions than simple hydrogen bond counting.

In single-stranded nucleic acids (ssDNA, mRNA, viral RNA genomes), Chargaff's rules don't strictly apply. However, Chargaff's second rule notes that even in single strands, %A ≈ %T and %G ≈ %C approximately hold, possibly due to inversions and palindromic sequences in genomes. Significant deviations in dsDNA suggest the data is unreliable or the molecule has unusual modifications.

Non-canonical base pairs include Hoogsteen pairs (using the major groove face of purines), wobble pairs (G-U/T, common in RNA), and mismatches. These occur in RNA secondary structures, G-quadruplexes, triple-stranded DNA, and during replication errors. Over 28 types of non-Watson-Crick base pairs have been characterized, particularly important in RNA structure and function.

5-methylcytosine (5mC) still pairs normally with G via three hydrogen bonds. The methyl group protrudes into the major groove without disrupting Watson-Crick geometry. However, methylation affects protein-DNA interactions (methyl-CpG binding proteins) and can promote C→T mutations through spontaneous deamination of 5mC to thymine, contributing to mutational hotspots at CpG sites.

The value of 649 Da/bp represents the average molecular weight of a base pair including both nucleotides of the two complementary strands minus one water molecule (lost during phosphodiester bond formation). Specifically: average nucleotide ≈ 330 Da × 2 strands = 660 Da, minus water and phosphodiester bond corrections gives approximately 649 Da/bp.

For RNA, replace T with U in the input. The complement of A is U (in RNA) rather than T. GC base pairing remains the same. For RNA:DNA hybrids, the RNA strand follows RNA rules (A, U, G, C) and the DNA strand follows DNA rules (A, T, G, C). The hydrogen bond counts remain the same: A-U has 2 H-bonds, G-C has 3 H-bonds.