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Virus Packing

This script calculates the approximate packing efficiency of a virus: the percentage of capsid volume that is taken up by DNA. It makes several assumptions:

• The capsid is spherical.
• dsDNA is a 2 nm diameter cylinder of length 340 nm * N, where N is the number of kilo- base pairs (kbp) in the genome.
• dsRNA is a 2 nm diameter cylinder of length 270 nm * N, where N is the number of kilo- base pairs.
• ssDNA is a 1.4 nm diameter cylinder of length 340 nm * N, where N is the number of kilo-bases (very inaccurate!)
• ssRNA is a 1.4 nm diameter cylinder of length 270 nm * N, where N is the number of kilo-bases (very inaccurate!)
• For the interstrand spacing, the strands are hexagonally packed.
• I calculated radius of gyration as sqrt(Lp), with p taken as 50, 60, 1.5, and 1.5, repsectively.

See this page for some discussion of DNA and RNA structure. This long list of viruses is a good source of information on the sizes of different types. Clicking the names of the viruses will give you more information and references for the parameters I used.

Virus	Type	Diameter (nm)	Genome (kbp)	Efficiency (%)	Spacing (nm)	Rgyr (um)	Confinement factor
lambda wt	dsDNA	55	48.5	59.5	2.47	0.91	35999
lambda b221 cI26	dsDNA	55	37.4	45.9	2.81	0.80	24377
T7	dsDNA	55	40	49.0	2.72	0.82	26963
phi29	dsDNA	44.1	19.3	45.9	2.81	0.57	17530
T4	dsDNA	92	169	44.3	2.86	1.69	50030
N4	dsDNA	66	72	51.1	2.66	1.11	37682
PRD1	dsDNA	42	15	41.3	2.96	0.50	13904
MS2	ssRNA	23	3.569	23.3	2.76	0.04	36
HSV-1	dsDNA	125	152	15.9	4.78	1.61	17014
smallpox virus	dsDNA	220	186	3.6	10.04	1.78	4224
mimivirus	dsDNA	400	800	2.6	11.81	3.69	6269
poliovirus	ssRNA	27	7.4	29.8	2.44	0.05	67
west nile	ssRNA	34	11	22.2	2.83	0.07	61
CCMV	ssRNA	20.8	3.2	28.2	2.51	0.04	41
SARS	ssRNA	100	29.8	2.4	8.61	0.11	11
HIV	ssRNA	70	18.4	4.3	6.43	0.09	15
Custom:	dsDNA ssDNA dsRNA ssRNA

Notice the huge range of packing efficiencies! High packing efficiency may imply a highly pressurized capsid. Many of the numbers I used are rough outer diameters - an inner diameter, when available, will give you a better estimate of the pressure.

For information on our experiments to measure the pressure in viruses, contact Paul, grayson@caltech.edu, or see our group webpage: http://www.rpgroup.caltech.edu/.

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